[med-svn] [pycorrfit] 01/05: Imported Upstream version 0.8.2
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Wed Mar 19 14:43:13 UTC 2014
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository pycorrfit.
commit e694669c67f0e5c556c5b54e416df611c70a85fc
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Tue Feb 18 16:08:08 2014 +0100
Imported Upstream version 0.8.2
---
ChangeLog.txt | 8 +
MANIFEST.in | 2 +-
PyCorrFit_doc.pdf | Bin 444211 -> 568711 bytes
Readme.txt | 18 +
bin/pycorrfit | 9 +-
doc-src/Bibliography.bib | 3445 ++++++++++----------
doc-src/Images/PyCorrFit_Screenshot_CSFCS.png | Bin 0 -> 123086 bytes
doc-src/Images/PyCorrFit_Screenshot_Main.png | Bin 81892 -> 89638 bytes
doc-src/PyCorrFit_doc.tex | 4 +-
doc-src/PyCorrFit_doc_content.tex | 787 +++--
doc-src/PyCorrFit_doc_models.tex | 123 +-
.../CSFCS_DiO-in-DOPC.fcsfit-session.zip | Bin 0 -> 387189 bytes
.../ConfocalFCS_Alexa488_xcorr.fcsfit-session.zip | Bin 0 -> 71711 bytes
setup.py | 5 +-
src/frontend.py | 40 +
src/page.py | 5 +-
src/plotting.py | 10 +-
src/tools/statistics.py | 144 +-
18 files changed, 2362 insertions(+), 2238 deletions(-)
diff --git a/ChangeLog.txt b/ChangeLog.txt
index 8a206eb..abdd46d 100644
--- a/ChangeLog.txt
+++ b/ChangeLog.txt
@@ -1,3 +1,11 @@
+0.8.2
+- The documentation has been thoroughly reworked
+- The user is now warned if he does not have a TeX distribution installed
+- Improvements:
+ - Complete support for installing PyCorrFit with virtualenv and pip
+ (This is documented in the wiki)
+ - Statistics tool now displays average and SD (#43)
+- Bugfix: TeX did not work on Ubuntu due to missing imports
0.8.1
- Thanks to Alex Mestiashvili for providing initial setup.py files
and for debianizing PyCorrFit (@mestia)
diff --git a/MANIFEST.in b/MANIFEST.in
index 1d5a49f..924013e 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -2,6 +2,6 @@ include doc-src/*.tex
include doc-src/*.bib
include doc-src/Images/*
include external_model_functions/*
-include README.md
+include Readme.txt
include ChangeLog.txt
include PyCorrFit_doc.pdf
diff --git a/PyCorrFit_doc.pdf b/PyCorrFit_doc.pdf
index ad0d65a..194e7d3 100644
Binary files a/PyCorrFit_doc.pdf and b/PyCorrFit_doc.pdf differ
diff --git a/Readme.txt b/Readme.txt
new file mode 100644
index 0000000..81624f6
--- /dev/null
+++ b/Readme.txt
@@ -0,0 +1,18 @@
+Scientific tool for fitting correlation curves on a logarithmic plot.
+
+In current biomedical research, fluorescence correlation spectroscopy (FCS) is applied
+to characterize molecular dynamic processes in vitro and in living cells. Commercial
+FCS setups only permit data analysis that is limited to a specific instrument by
+the use of in-house file formats or a finite number of implemented correlation
+model functions. PyCorrFit is a general-purpose FCS evaluation software that,
+amongst other formats, supports the established Zeiss ConfoCor3 ~.fcs file format.
+PyCorrFit comes with several built-in model functions, covering a wide range of
+applications in standard confocal FCS. In addition, it contains equations dealing
+with different excitation geometries like total internal reflection (TIR). For more
+information, visit the official homepage at http://pycorrfit.craban.de.
+
+
+- Latest downloads: https://github.com/paulmueller/PyCorrFit/releases
+- Documentation: https://github.com/paulmueller/PyCorrFit/raw/master/PyCorrFit_doc.pdf
+- Write model functions: https://github.com/paulmueller/PyCorrFit/wiki/Writing-model-functions
+- Need help? https://github.com/paulmueller/PyCorrFit/wiki/Creating-a-new-issue
diff --git a/bin/pycorrfit b/bin/pycorrfit
index 07a5d62..0ee17a9 100644
--- a/bin/pycorrfit
+++ b/bin/pycorrfit
@@ -1,11 +1,16 @@
#!/bin/sh
-
+# debian
if [ -f "/usr/share/pyshared/pycorrfit/PyCorrFit.py" ]
then
python /usr/share/pyshared/pycorrfit/PyCorrFit.py
-elif [ -f /usr/local/lib/python2.7/dist-packages/pycorrfit/PyCorrFit.py ]
+elif [ -f "/usr/local/lib/python2.7/dist-packages/pycorrfit/PyCorrFit.py" ]
+# pip
then
python /usr/local/lib/python2.7/dist-packages/pycorrfit/PyCorrFit.py
+# pip and virtualenv
+elif [ -f "../lib/python2.7/site-packages/pycorrfit/PyCorrFit.py" ]
+then
+ python ../lib/python2.7/site-packages/pycorrfit/PyCorrFit.py
else
echo "Could not find PyCorrFit.py. Please notify the author."
fi
diff --git a/doc-src/Bibliography.bib b/doc-src/Bibliography.bib
index d812036..7da50fa 100755
--- a/doc-src/Bibliography.bib
+++ b/doc-src/Bibliography.bib
@@ -1,1744 +1,1709 @@
-% This file was created with JabRef 2.7b.
+% This file was created with JabRef 2.10b2.
% Encoding: UTF-8
- at ARTICLE{Aragon1976,
- author = {S. R. Aragon and R. Pecora},
- title = {Fluorescence correlation spectroscopy as a probe of molecular dynamics},
- journal = {The Journal of Chemical Physics},
- year = {1976},
- volume = {64},
- pages = {1791-1803},
- number = {4},
- doi = {10.1063/1.432357},
- owner = {paul},
- publisher = {AIP},
- timestamp = {2012.11.02}
-}
-
- at ARTICLE{Ashkin1970,
- author = {Ashkin, A.},
- title = {Acceleration and Trapping of Particles by Radiation Pressure},
- journal = {Physical Review Letters},
- year = {1970},
- volume = {24},
- pages = {156--159},
- month = {Jan},
- doi = {10.1103/PhysRevLett.24.156},
- issue = {4},
- owner = {paul},
- publisher = {American Physical Society},
- timestamp = {2012.11.13}
-}
-
- at ARTICLE{Axelrod1984,
- author = {Axelrod, D and Burghardt, T P and Thompson, N L},
- title = {Total Internal Reflection Fluorescence},
- journal = {Annual Review of Biophysics and Biomolecular Structure},
- year = {1984},
- volume = {13},
- pages = {247--268},
- number = {1},
- month = jun,
- booktitle = {Annual Review of Biophysics and Bioengineering},
- comment = {doi: 10.1146/annurev.bb.13.060184.001335},
- doi = {10.1146/annurev.bb.13.060184.001335},
- issn = {0084-6589},
- owner = {paul},
- publisher = {Annual Reviews},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Bag2012,
- author = {Bag, Nirmalya and Sankaran, Jagadish and Paul, Alexandra and Kraut,
- Rachel S. and Wohland, Thorsten},
- title = {Calibration and Limits of Camera-Based Fluorescence Correlation Spectroscopy:
- A Supported Lipid Bilayer Study},
- journal = {ChemPhysChem},
- year = {2012},
- volume = {13},
- pages = {2784--2794},
- number = {11},
- doi = {10.1002/cphc.201200032},
- issn = {1439-7641},
- keywords = {fluorescence spectroscopy, membrane, multiplexing, point spread function,
- total internal reflection},
- owner = {paul},
- publisher = {WILEY-VCH Verlag},
- timestamp = {2012.09.20}
-}
-
- at ARTICLE{Bestvater2010,
- author = {Felix Bestvater and Zahir Seghiri and Moon Sik Kang and Nadine Gr\"{o}ner
- and Ji Young Lee and Kang-Bin Im and Malte Wachsmuth},
- title = {EMCCD-based spectrally resolved fluorescence correlation spectroscopy},
- journal = {Optics Express},
- year = {2010},
- volume = {18},
- pages = {23818--23828},
- number = {23},
- month = {Nov},
- abstract = {We present an implementation of fluorescence correlation spectroscopy
- with spectrally resolved detection based on a combined commercial
- confocal laser scanning/fluorescence correlation spectroscopy microscope.
- We have replaced the conventional detection scheme by a prism-based
- spectrometer and an electron-multiplying charge-coupled device camera
- used to record the photons. This allows us to read out more than
- 80,000 full spectra per second with a signal-to-noise ratio and a
- quantum efficiency high enough to allow single photon counting. We
- can identify up to four spectrally different quantum dots in vitro
- and demonstrate that spectrally resolved detection can be used to
- characterize photophysical properties of fluorophores by measuring
- the spectral dependence of quantum dot fluorescence emission intermittence.
- Moreover, we can confirm intracellular cross-correlation results
- as acquired with a conventional setup and show that spectral flexibility
- can help to optimize the choice of the detection windows.},
- doi = {10.1364/OE.18.023818},
- keywords = {CCD, charge-coupled device; Confocal microscopy; Spectroscopy, fluorescence
- and luminescence},
- owner = {paul},
- publisher = {OSA},
- timestamp = {2012.11.07}
-}
-
- at ARTICLE{Blom2009,
- author = {Blom, Hans and Chmyrov, Andriy and Hassler, Kai and Davis, Lloyd
- M. and Widengren, Jerker},
- title = {Triplet-State Investigations of Fluorescent Dyes at Dielectric Interfaces
- Using Total Internal Reflection Fluorescence Correlation Spectroscopy},
- journal = {The Journal of Physical Chemistry A},
- year = {2009},
- volume = {113},
- pages = {5554-5566},
- number = {19},
- doi = {10.1021/jp8110088},
- owner = {paul},
- timestamp = {2012.11.02}
-}
-
- at ARTICLE{Blom2002,
- author = {Hans Blom and Mathias Johansson and Anna-Sara Hedman and Liselotte
- Lundberg and Anders Hanning and Sverker H{\aa}rd and Rudolf Rigler},
- title = {Parallel Fluorescence Detection of Single Biomolecules in Microarrays
- by a Diffractive-Optical-Designed 2 x 2 Fan-Out Element},
- journal = {Applied Optics},
- year = {2002},
- volume = {41},
- pages = {3336--3342},
- number = {16},
- month = {Jun},
- abstract = {We have developed a multifocal diffractive-optical fluorescence correlation
- spectroscopy system for parallel excitation and detection of single
- tetramethylrhodamine biomolecules in microarrays. Multifocal excitation
- was made possible through the use of a 2 {\texttimes} 2 fan-out diffractive-optical
- element with uniform intensity in all foci. Characterization of the
- 2 {\texttimes} 2 fan-out diffractive-optical element shows formation
- of almost perfect Gaussian foci of submicrometer lateral diameter,
- as analyzed by thermal motion of tetramethylrhodamine dye molecules
- in solution. Results of parallel excitation and detection in a high-density
- microarray of circular wells show single-biomolecule sensitivity
- in all four foci simultaneously.},
- doi = {10.1364/AO.41.003336},
- keywords = {Diffractive optics; Confocal microscopy; Fluorescence microscopy;
- Fluorescence, laser-induced},
- owner = {paul},
- publisher = {OSA},
- timestamp = {2012.11.07}
-}
-
- at ARTICLE{Brinkmeier1999,
- author = {M. Brinkmeier and K. Dörre and J. Stephan and M. Eigen},
- title = {Two-beam cross-correlation: a method to characterize transport phenomena
- in micrometer-sized structures.},
- journal = {Analytical Chemistry},
- year = {1999},
- volume = {71},
- pages = {609--616},
- number = {3},
- month = {Feb},
- abstract = {To determine flow properties, namely, the velocity and angle of the
- flow in microstructured channels, an experimental realization based
- on fluorescence correlation spectroscopy is described. For this purpose,
- two micrometer-sized spatially separated volume elements have been
- created. The cross-correlation signal from these has been recorded
- and evaluated mathematically. In addition to previous results, two-beam
- cross-correlation allows for fast and easy determination of even
- small (down to 200 μm/s) flow velocities, as well as simultaneous
- measurement of diffusion properties of single dye molecules within
- a rather short detection time of 5-100 s and an error rate of less
- than 20\%. The spatial flow resolution is around 1-2 μm, limited
- by the diameter of the volume element. Furthermore, vectorial flow
- data can be obtained and evaluated. A discussion of the theoretical
- background and an experimental verification of the theoretical results
- is performed. The feasibility of fast and easy data processing is
- shown if the flow time is the only desired information. Possible
- applications of this precise and simple method are the determination
- of transportation effects within artificial microstructures for CE
- and HPLC, fast chemical kinetics, and high-throughput screening.},
- doi = {10.1021/ac980820i},
- institution = {Max-Planck-Institut für biophysikalische Chemie, Am Fassberg, D-37077
- Göttingen, Germany.},
- language = {eng},
- medline-pst = {ppublish},
- owner = {paul},
- pmid = {21662718},
- timestamp = {2012.11.07}
-}
-
- at ARTICLE{Brutzer2012,
- author = {Brutzer, Hergen and Schwarz, Friedrich W. and Seidel, Ralf},
- title = {Scanning Evanescent Fields Using a pointlike Light Source and a Nanomechanical
- DNA Gear},
- journal = {Nano Letters},
- year = {2012},
- volume = {12},
- pages = {473-478},
- number = {1},
- doi = {10.1021/nl203876w},
- owner = {paul},
- timestamp = {2012.08.09}
-}
-
- at ARTICLE{Buchholz2012,
- author = {Jan Buchholz and Jan Wolfgang Krieger and G\'{a}bor Mocs\'{a}r and
- Bal\'{a}zs Kreith and Edoardo Charbon and Gy\"{o}rgy V\'{a}mosi and
- Udo Kebschull and J\"{o}rg Langowski},
- title = {FPGA implementation of a 32x32 autocorrelator array for analysis
- of fast image series},
- journal = {Optics Express},
- year = {2012},
- volume = {20},
- pages = {17767--17782},
- number = {16},
- month = {Jul},
- abstract = {With the evolving technology in CMOS integration, new classes of 2D-imaging
- detectors have recently become available. In particular, single photon
- avalanche diode (SPAD) arrays allow detection of single photons at
- high acquisition rates (\&\#x02265; 100kfps), which is about two
- orders of magnitude higher than with currently available cameras.
- Here we demonstrate the use of a SPAD array for imaging fluorescence
- correlation spectroscopy (imFCS), a tool to create 2D maps of the
- dynamics of fluorescent molecules inside living cells. Time-dependent
- fluorescence fluctuations, due to fluorophores entering and leaving
- the observed pixels, are evaluated by means of autocorrelation analysis.
- The multi-\&\#x003C4; correlation algorithm is an appropriate choice,
- as it does not rely on the full data set to be held in memory. Thus,
- this algorithm can be efficiently implemented in custom logic. We
- describe a new implementation for massively parallel multi-\&\#x003C4;
- correlation hardware. Our current implementation can calculate 1024
- correlation functions at a resolution of 10\&\#x003BC;s in real-time
- and therefore correlate real-time image streams from high speed single
- photon cameras with thousands of pixels.},
- doi = {10.1364/OE.20.017767},
- keywords = {Detectors; Arrays; Cameras; Correlators ; Fluorescence microscopy;
- Three-dimensional microscopy; Spectroscopy, fluorescence and luminescence;
- Avalanche photodiodes (APDs)},
- owner = {paul},
- publisher = {OSA},
- timestamp = {2012.10.24}
-}
-
- at PHDTHESIS{Burkhardt2010,
- author = {Burkhardt, Markus},
- title = {Electron multiplying CCD – based detection in Fluorescence Correlation
- Spectroscopy and measurements in living zebrafish embryos},
- school = {Biophysics, BIOTEC, Technische Universität Dresden, Tatzberg 47–51,
- 01307 Dresden, Germany},
- year = {2010},
- note = {\url{http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-61021}},
- owner = {paul},
- timestamp = {2012.10.24}
-}
-
- at ARTICLE{Burkhardt:06,
- author = {Markus Burkhardt and Petra Schwille},
- title = {Electron multiplying CCD based detection for spatially resolved fluorescence
- correlation spectroscopy},
- journal = {Optics Express},
- year = {2006},
- volume = {14},
- pages = {5013--5020},
- number = {12},
- month = {Jun},
- abstract = {Fluorescence correlation spectroscopy (FCS) is carried out with an
- electron multiplying CCD (EMCCD). This new strategy is compared to
- standard detection by an avalanche photo diode showing good agreement
- with respect to the resulting autocorrelation curves. Applying different
- readout modes, a time resolution of 20 {\textmu}s can be achieved,
- which is sufficient to resolve the diffusion of free dye in solution.
- The advantages of implementing EMCCD cameras in wide-field ultra
- low light imaging, as well as in multi-spot confocal laser scanning
- microscopy, can consequently also be exploited for spatially resolved
- FCS. First proof-of-principle FCS measurements with two excitation
- volumes demonstrate the advantage of the flexible CCD area detection.},
- doi = {10.1364/OE.14.005013},
- keywords = {CCD, charge-coupled device; Medical optics and biotechnology; Fluorescence,
- laser-induced},
- publisher = {OSA}
-}
-
- at ARTICLE{Chiantia2006,
- author = {Chiantia , Salvatore and Ries , Jonas and Kahya, Nicoletta and Schwille,
- Petra},
- title = {Combined AFM and Two-Focus SFCS Study of Raft-Exhibiting Model Membranes},
- journal = {ChemPhysChem},
- year = {2006},
- volume = {7},
- pages = {2409--2418},
- number = {11},
- doi = {10.1002/cphc.200600464},
- issn = {1439-7641},
- keywords = {fluorescent probes, force measurements, membranes, sphingolipids},
- owner = {paul},
- publisher = {WILEY-VCH Verlag},
- timestamp = {2012.10.24}
-}
-
- at ARTICLE{Dertinger2007,
- author = {Dertinger, Thomas and Pacheco, Victor and von der Hocht, Iris and
- Hartmann, Rudolf and Gregor, Ingo and Enderlein, Jörg},
- title = {Two-Focus Fluorescence Correlation Spectroscopy: A New Tool for Accurate
- and Absolute Diffusion Measurements},
- journal = {ChemPhysChem},
- year = {2007},
- volume = {8},
- pages = {433--443},
- number = {3},
- doi = {10.1002/cphc.200600638},
- issn = {1439-7641},
- keywords = {diffusion coefficients, fluorescence spectroscopy, fluorescent dyes,
- time-resolved spectroscopy},
- owner = {paul},
- publisher = {WILEY-VCH Verlag},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Einstein1905,
- author = {Einstein, A.},
- title = {Über die von der molekularkinetischen Theorie der Wärme geforderte
- Bewegung von in ruhenden Flüssigkeiten suspendierten Teilchen},
- journal = {Annalen der Physik},
- year = {1905},
- volume = {322},
- pages = {549--560},
- number = {8},
- doi = {10.1002/andp.19053220806},
- issn = {1521-3889},
- owner = {paul},
- publisher = {WILEY-VCH Verlag},
- timestamp = {2012.11.02}
-}
-
- at ARTICLE{Elson1974,
- author = {Elson, Elliot L. and Magde, Douglas},
- title = {Fluorescence correlation spectroscopy. I. Conceptual basis and theory},
- journal = {Biopolymers},
- year = {1974},
- volume = {13},
- pages = {1--27},
- number = {1},
- doi = {10.1002/bip.1974.360130102},
- issn = {1097-0282},
- owner = {paul},
- publisher = {Wiley Subscription Services, Inc., A Wiley Company},
- timestamp = {2012.09.24}
-}
-
- at ARTICLE{Enderlein1999,
- author = {J\"{o}rg Enderlein and Thomas Ruckstuhl and Stefan Seeger},
- title = {Highly Efficient Optical Detection of Surface-Generated Fluorescence},
- journal = {Applied Optics},
- year = {1999},
- volume = {38},
- pages = {724--732},
- number = {4},
- month = {Feb},
- abstract = {We present a theoretical study of a new highly efficient system for
- optical light collection, designed for ultrasensitive fluorescence
- detection of surface-bound molecules. The main core of the system
- is a paraboloid glass segment acting as a mirror for collecting the
- fluorescence. A special feature of the system is its ability to sample
- not only fluorescence that is emitted below the angle of total internal
- reflection (the critical angle) but also particularly the light above
- the critical angle. As shown, this is especially advantageous for
- collecting the fluorescence of surface-bound molecules. A comparison
- is made with conventional high-aperture microscope objectives. Furthermore,
- it is shown that the system allows not only for highly efficient
- light collection but also for confocal imaging of the detection region,
- which is of great importance for rejecting scattered light in potential
- applications such as the detection of only a few molecules.},
- doi = {10.1364/AO.38.000724},
- keywords = {Geometric optical design; Microscopy; Detection; Fluorescence microscopy},
- owner = {paul},
- publisher = {OSA},
- timestamp = {2012.11.02}
-}
-
- at ARTICLE{Hansen1998,
- author = {Hansen, Richard L and Harris, Joel M},
- title = {Measuring Reversible Adsorption Kinetics of Small Molecules at Solid/Liquid
- Interfaces by Total Internal Reflection Fluorescence Correlation
- Spectroscopy},
- journal = {Analytical Chemistry},
- year = {1998},
- volume = {70},
- pages = {4247--4256},
- number = {20},
- doi = {10.1021/ac980925l},
- owner = {paul},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Hashmi2007,
- author = {Sara M. Hashmi and Michael Loewenberg and Eric R. Dufresne},
- title = {Spatially extended FCS for visualizing and quantifying high-speed
- multiphase flows in microchannels},
- journal = {Optics Express},
- year = {2007},
- volume = {15},
- pages = {6528--6533},
- number = {10},
- month = {May},
- abstract = {We report the development of spatially extended fluorescence correlation
- spectroscopy for visualizing and quantifying multiphase flows in
- microchannels. We employ simultaneous detection with a high-speed
- camera across the width of the channel, enabling investigation of
- the dynamics of the flow at short time scales. We take advantage
- of the flow to scan the sample past the fixed illumination, capturing
- frames up to 100 KHz. At these rates, we can resolve the motion of
- sub-micron particles at velocities up to the order of 1 cm/s. We
- visualize flows with kymographs and quantify velocity profiles by
- cross-correlations within the focal volume. We demonstrate the efficacy
- of our approach by measuring the depth-resolved velocity profile
- of suspensions of sub-micron diameter silica particles flowing up
- to 1.5 mm/s.},
- doi = {10.1364/OE.15.006528},
- keywords = {Velocimetry; Flow diagnostics; Fluorescence, laser-induced},
- owner = {paul},
- publisher = {OSA},
- timestamp = {2012.11.07}
-}
-
- at ARTICLE{Hassler2005,
- author = {Hassler, Kai and Anhut, Tiemo and Rigler, Rudolf and G\"{o}sch, Michael
- and Lasser, Theo},
- title = {High Count Rates with Total Internal Reflection Fluorescence Correlation
- Spectroscopy},
- journal = {Biophysical Journal},
- year = {2005},
- volume = {88},
- pages = {L01--L03},
- number = {1},
- month = jan,
- doi = {10.1529/biophysj.104.053884},
- issn = {0006-3495},
- owner = {paul},
- publisher = {Cell Press},
- refid = {S0006-3495(05)73079-4 DOI - 10.1529/biophysj.104.053884},
- timestamp = {2012.05.02}
-}
-
- at ARTICLE{Hassler2005a,
- author = {Kai Hassler and Marcel Leutenegger and Per Rigler and Ramachandra
- Rao and Rudolf Rigler and Michael G\"{o}sch and Theo Lasser},
- title = {Total internal reflection fluorescence correlation spectroscopy (TIR-FCS)
- with low background and high count-rate per molecule},
- journal = {Optics Express},
- year = {2005},
- volume = {13},
- pages = {7415--7423},
- number = {19},
- month = {Sep},
- abstract = {We designed a fluorescence correlation spectroscopy (FCS) system for
- measurements on surfaces. The system consists of an objective-type
- total internal reflection fluorescence (TIRF) microscopy setup, adapted
- to measure FCS. Here, the fluorescence exciting evanescent wave is
- generated by epi-illumination through the periphery of a high NA
- oil-immersion objective. The main advantages with respect to conventional
- FCS systems are an improvement in terms of counts per molecule (cpm)
- and a high signal to background ratio. This is demonstrated by investigating
- diffusion as well as binding and release of single molecules on a
- glass surface. Furthermore, the size and shape of the molecule detection
- efficiency (MDE) function was calculated, using a wave-vectorial
- approach and taking into account the influence of the dielectric
- interface on the emission properties of fluorophores.},
- doi = {10.1364/OPEX.13.007415},
- keywords = {Spectroscopy, fluorescence and luminescence; Spectroscopy, surface;
- Fluorescence, laser-induced},
- owner = {paul},
- publisher = {OSA},
- timestamp = {2012.09.21}
-}
-
- at OTHER{HaunertG,
- author = {Gerhard Haunert},
- howpublished = {Personal communication},
- note = {Acal BFi Germany GmbH},
- owner = {paul},
- timestamp = {2012.10.11},
- year = {2012}
-}
-
- at ARTICLE{Haupts1998,
- author = {Haupts, Ulrich and Maiti, Sudipta and Schwille, Petra and Webb, Watt
- W.},
- title = {Dynamics of fluorescence fluctuations in green fluorescent protein
- observed by fluorescence correlation spectroscopy},
- journal = {Proceedings of the National Academy of Sciences},
- year = {1998},
- volume = {95},
- pages = {13573-13578},
- number = {23},
- abstract = {We have investigated the pH dependence of the dynamics of conformational
- fluctuations of green fluorescent protein mutants EGFP (F64L/S65T)
- and GFP-S65T in small ensembles of molecules in solution by using
- fluorescence correlation spectroscopy (FCS). FCS utilizes time-resolved
- measurements of fluctuations in the molecular fluorescence emission
- for determination of the intrinsic dynamics and thermodynamics of
- all processes that affect the fluorescence. Fluorescence excitation
- of a bulk solution of EGFP decreases to zero at low pH (pKa = 5.8)
- paralleled by a decrease of the absorption at 488 nm and an increase
- at 400 nm. Protonation of the hydroxyl group of Tyr-66, which is
- part of the chromophore, induces these changes. When FCS is used
- the fluctuations in the protonation state of the chromophore are
- time resolved. The autocorrelation function of fluorescence emission
- shows contributions from two chemical relaxation processes as well
- as diffusional concentration fluctuations. The time constant of the
- fast, pH-dependent chemical process decreases with pH from 300 μs
- at pH 7 to 45 μs at pH 5, while the time-average fraction of molecules
- in a nonfluorescent state increases to 80% in the same range. A second,
- pH-independent, process with a time constant of 340 μs and an associated
- fraction of 13% nonfluorescent molecules is observed between pH 8
- and 11, possibly representing an internal proton transfer process
- and associated conformational rearrangements. The FCS data provide
- direct measures of the dynamics and the equilibrium properties of
- the protonation processes. Thus FCS is a convenient, intrinsically
- calibrated method for pH measurements in subfemtoliter volumes with
- nanomolar concentrations of EGFP.},
- doi = {10.1073/pnas.95.23.13573},
- owner = {paul},
- timestamp = {2012.11.01}
-}
-
- at ARTICLE{Haustein2007,
- author = {Haustein, Elke and Schwille, Petra},
- title = {Fluorescence Correlation Spectroscopy: Novel Variations of an Established
- Technique},
- journal = {Annual Review of Biophysics and Biomolecular Structure},
- year = {2007},
- volume = {36},
- pages = {151-169},
- number = {1},
- doi = {10.1146/annurev.biophys.36.040306.132612},
- owner = {paul},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Helmers2003,
- author = {Heinz Helmers and Markus Schellenberg},
- title = {CMOS vs. CCD sensors in speckle interferometry},
- journal = {Optics \& Laser Technology},
- year = {2003},
- volume = {35},
- pages = {587 - 595},
- number = {8},
- doi = {10.1016/S0030-3992(03)00078-1},
- issn = {0030-3992},
- keywords = {CCD sensors},
- owner = {paul},
- timestamp = {2012.10.06}
-}
-
- at ARTICLE{Holekamp2008,
- author = {Terrence F. Holekamp and Diwakar Turaga and Timothy E. Holy},
- title = {Fast Three-Dimensional Fluorescence Imaging of Activity in Neural
- Populations by Objective-Coupled Planar Illumination Microscopy},
- journal = {Neuron},
- year = {2008},
- volume = {57},
- pages = {661 - 672},
- number = {5},
- doi = {10.1016/j.neuron.2008.01.011},
- issn = {0896-6273},
- keywords = {SYSBIO},
- owner = {paul},
- timestamp = {2012.11.13}
-}
-
- at ARTICLE{Humpolickova2006,
- author = {Jana Humpol\'{i}\v{c}kov\'{a} and Ellen Gielen and Ale\v{s} Benda
- and Veronika Fagulova and Jo Vercammen and Martin vandeVen and Martin
- Hof and Marcel Ameloot and Yves Engelborghs},
- title = {Probing Diffusion Laws within Cellular Membranes by Z-Scan Fluorescence
- Correlation Spectroscopy},
- journal = {Biophysical Journal},
- year = {2006},
- volume = {91},
- pages = {L23 - L25},
- number = {3},
- doi = {10.1529/biophysj.106.089474},
- issn = {0006-3495},
- owner = {paul},
- timestamp = {2012.10.25}
-}
-
- at ARTICLE{Jin2004,
- author = {Jin, S. and Huang, P. and Park, J. and Yoo, J. Y. and Breuer, K.
- S.},
- title = {Near-surface velocimetry using evanescent wave illumination},
- journal = {Experiments in Fluids},
- year = {2004},
- volume = {37},
- pages = {825-833},
- affiliation = {School of Mechanical and Aerospace Engineering Seoul National University
- Seoul 151-742 Korea},
- doi = {10.1007/s00348-004-0870-7},
- issn = {0723-4864},
- issue = {6},
- keyword = {Technik},
- owner = {paul},
- publisher = {Springer Berlin / Heidelberg},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Kannan2006,
- author = {Kannan, Balakrishnan and Har, Jia Yi and Liu, Ping and Maruyama,
- Ichiro and Ding, Jeak Ling and Wohland, Thorsten},
- title = {Electron Multiplying Charge-Coupled Device Camera Based Fluorescence
- Correlation Spectroscopy},
- journal = {Analytical Chemistry},
- year = {2006},
- volume = {78},
- pages = {3444-3451},
- number = {10},
- doi = {10.1021/ac0600959},
- owner = {paul},
- timestamp = {2012.11.07}
-}
-
- at INCOLLECTION{Kohl2005,
- author = {Kohl, Tobias and Schwille, Petra},
- title = {Fluorescence Correlation Spectroscopy with Autofluorescent Proteins},
- booktitle = {Microscopy Techniques},
- publisher = {Springer Berlin / Heidelberg},
- year = {2005},
- editor = {Rietdorf, Jens},
- volume = {95},
- series = {Advances in Biochemical Engineering/Biotechnology},
- pages = {1316-1317},
- affiliation = {Pastor-Sander-Bogen 92 37083 Göttingen Germany},
- doi = {10.1007/b102212},
- isbn = {978-3-540-23698-6},
- keyword = {Chemistry and Materials Science},
- owner = {paul},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Korson1969,
- author = {Korson, Lawrence and Drost-Hansen, Walter and Millero, Frank J.},
- title = {Viscosity of water at various temperatures},
- journal = {The Journal of Physical Chemistry},
- year = {1969},
- volume = {73},
- pages = {34-39},
- number = {1},
- doi = {10.1021/j100721a006},
- owner = {paul},
- timestamp = {2012.10.29}
-}
-
- at BOOK{LandauLifshitsStatPhys,
- title = {{Statistical Physics, Third Edition, Part 1: Volume 5 (Course of
- Theoretical Physics, Volume 5)}},
- publisher = {Butterworth-Heinemann},
- year = {1980},
- author = {Landau, L. D. and Lifshitz, E. M.},
- edition = {3},
- month = jan,
- abstract = {{A lucid presentation of statistical physics and thermodynamics which
- develops from the general principles to give a large number of applications
- of the theory.}},
- citeulike-article-id = {1284487},
- citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0750633727},
- citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0750633727},
- citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0750633727},
- citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0750633727},
- citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0750633727/citeulike00-21},
- citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0750633727},
- citeulike-linkout-6 = {http://www.worldcat.org/isbn/0750633727},
- citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0750633727},
- citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0750633727\&index=books\&linkCode=qs},
- citeulike-linkout-9 = {http://www.librarything.com/isbn/0750633727},
- day = {15},
- howpublished = {Paperback},
- isbn = {0750633727},
- keywords = {fermi\_statistics, statistical\_physics},
- owner = {paul},
- posted-at = {2011-03-03 11:38:41},
- priority = {2},
- timestamp = {2012.02.03}
-}
-
- at ARTICLE{Leutenegger2012,
- author = {Marcel Leutenegger and Christian Ringemann and Theo Lasser and Stefan
- W. Hell and Christian Eggeling},
- title = {Fluorescence correlation spectroscopy with a total internal reflection
- fluorescence STED microscope (TIRF-STED-FCS)},
- journal = {Optics Express},
- year = {2012},
- volume = {20},
- pages = {5243--5263},
- number = {5},
- month = {Feb},
- abstract = {We characterize a novel fluorescence microscope which combines the
- high spatial discrimination of a total internal reflection epi-fluorescence
- (epi-TIRF) microscope with that of stimulated emission depletion
- (STED) nanoscopy. This combination of high axial confinement and
- dynamic-active lateral spatial discrimination of the detected fluorescence
- emission promises imaging and spectroscopy of the structure and function
- of cell membranes at the macro-molecular scale. Following a full
- theoretical description of the sampling volume and the recording
- of images of fluorescent beads, we exemplify the performance and
- limitations of the TIRF-STED nanoscope with particular attention
- to the polarization state of the laser excitation light. We demonstrate
- fluorescence correlation spectroscopy (FCS) with the TIRF-STED nanoscope
- by observing the diffusion of dye molecules in aqueous solutions
- and of fluorescent lipid analogs in supported lipid bilayers in the
- presence of background signal. The nanoscope reduced the out-of-focus
- background signal. A lateral resolution down to 40--50 nm was attained
- which was ultimately limited by the low lateral signal-to-background
- ratio inherent to the confocal epi-TIRF scheme. Together with the
- estimated axial confinement of about 55 nm, our TIRF-STED nanoscope
- achieved an almost isotropic and less than 1 attoliter small all-optically
- induced measurement volume.},
- doi = {10.1364/OE.20.005243},
- keywords = {Diffraction; Fluorescence microscopy; Fluorescence},
- owner = {paul},
- publisher = {OSA},
- timestamp = {2012.09.21}
-}
-
- at ARTICLE{Lieto2003a,
- author = {Lieto, Alena M. and Cush, Randall C. and Thompson, Nancy L.},
- title = {Ligand-Receptor Kinetics Measured by Total Internal Reflection with
- Fluorescence Correlation Spectroscopy},
- journal = {Biophysical Journal},
- year = {2003},
- volume = {85},
- pages = {3294--3302},
- number = {5},
- month = nov,
- doi = {10.1016/S0006-3495(03)74748-1},
- issn = {0006-3495},
- owner = {paul},
- publisher = {Cell Press},
- refid = {S0006-3495(03)74748-1 DOI - 10.1016/S0006-3495(03)74748-1},
- timestamp = {2012.09.21}
-}
-
- at ARTICLE{Lieto2003,
- author = {Lieto, Alena M. and Lagerholm, B. Christoffer and Thompson, Nancy
- L.},
- title = {Lateral Diffusion from Ligand Dissociation and Rebinding at Surfaces†},
- journal = {Langmuir},
- year = {2003},
- volume = {19},
- pages = {1782-1787},
- number = {5},
- doi = {10.1021/la0261601},
- owner = {paul},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Lieto2004,
- author = {Alena M. Lieto and Nancy L. Thompson},
- title = {Total Internal Reflection with Fluorescence Correlation Spectroscopy:
- Nonfluorescent Competitors},
- journal = {Biophysical Journal},
- year = {2004},
- volume = {87},
- pages = {1268 - 1278},
- number = {2},
- doi = {10.1529/biophysj.103.035030},
- issn = {0006-3495},
- owner = {paul},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Magde1972,
- author = {Magde, Douglas and Elson, Elliot and Webb, W. W.},
- title = {Thermodynamic Fluctuations in a Reacting System - Measurement by
- Fluorescence Correlation Spectroscopy},
- journal = {Physical Review Letters},
- year = {1972},
- volume = {29},
- pages = {705--708},
- month = {Sep},
- doi = {10.1103/PhysRevLett.29.705},
- issue = {11},
- owner = {paul},
- publisher = {American Physical Society},
- timestamp = {2012.11.01}
-}
-
- at ARTICLE{Magde1974,
- author = {Magde, Douglas and Elson, Elliot L. and Webb, Watt W.},
- title = {Fluorescence correlation spectroscopy. II. An experimental realization},
- journal = {Biopolymers},
- year = {1974},
- volume = {13},
- pages = {29--61},
- number = {1},
- doi = {10.1002/bip.1974.360130103},
- issn = {1097-0282},
- owner = {paul},
- publisher = {Wiley Subscription Services, Inc., A Wiley Company},
- timestamp = {2012.09.21}
-}
-
- at ARTICLE{Nitsche2004,
- author = {Johannes M. Nitsche and Hou-Chien Chang and Paul A. Weber and Bruce
- J. Nicholson},
- title = {A Transient Diffusion Model Yields Unitary Gap Junctional Permeabilities
- from Images of Cell-to-Cell Fluorescent Dye Transfer Between Xenopus
- Oocytes},
- journal = {Biophysical Journal},
- year = {2004},
- volume = {86},
- pages = {2058 - 2077},
- number = {4},
- doi = {10.1016/S0006-3495(04)74267-8},
- issn = {0006-3495},
- owner = {paul},
- timestamp = {2012.11.08}
-}
-
- at ARTICLE{Ohsugi2009,
- author = {Ohsugi, Yu and Kinjo, Masataka},
- title = {Multipoint fluorescence correlation spectroscopy with total internal
- reflection fluorescence microscope},
- journal = {Journal of Biomedical Optics},
- year = {2009},
- volume = {14},
- pages = {014030-014030-4},
- number = {1},
- doi = {10.1117/1.3080723},
- owner = {paul},
- timestamp = {2012.11.12}
-}
-
- at ARTICLE{Ohsugi2006,
- author = {Ohsugi, Yu and Saito, Kenta and Tamura, Mamoru and Kinjo, Masataka},
- title = {Lateral mobility of membrane-binding proteins in living cells measured
- by total internal reflection fluorescence correlation spectroscopy.},
- journal = {Biophysical Journal},
- year = {2006},
- volume = {91},
- pages = {3456--3464},
- number = {9},
- doi = {10.1529/biophysj.105.074625},
- owner = {paul},
- publisher = {Biophysical Society},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Palmer1987,
- author = {A. G. Palmer and N. L. Thompson},
- title = {Theory of sample translation in fluorescence correlation spectroscopy.},
- journal = {Biophysical Journal},
- year = {1987},
- volume = {51},
- pages = {339--343},
- number = {2},
- month = {Feb},
- abstract = {New applications of the technique of fluorescence correlation spectroscopy
- (FCS) require lateral translation of the sample through a focused
- laser beam (Peterson, N.O., D.C. Johnson, and M.J. Schlesinger, 1986,
- Biophys. J., 49:817-820). Here, the effect of sample translation
- on the shape of the FCS autocorrelation function is examined in general.
- It is found that if the lateral diffusion coefficients of the fluorescent
- species obey certain conditions, then the FCS autocorrelation function
- is a simple product of one function that depends only on transport
- coefficients and another function that depends only on the rate constants
- of chemical reactions that occur in the sample. This simple form
- should allow manageable data analyses in new FCS experiments that
- involve sample translation.},
- doi = {10.1016/S0006-3495(87)83340-4},
- keywords = {Kinetics; Lasers; Mathematics; Models, Theoretical; Spectrometry,
- Fluorescence, methods},
- language = {eng},
- medline-pst = {ppublish},
- owner = {paul},
- pii = {S0006-3495(87)83340-4},
- pmid = {3828464},
- timestamp = {2012.11.02}
-}
-
- at ARTICLE{Pero2006-06,
- author = {Pero, JK and Haas, EM and Thompson, NL},
- title = {Size dependence of protein diffusion very close to membrane surfaces:
- measurement by total internal reflection with fluorescence correlation
- spectroscopy.},
- journal = {The Journal of Physical Chemistry. B},
- year = {2006},
- volume = {110},
- pages = {10910-8},
- number = {5},
- doi = {10.1021/jp056990y},
- issn = {1520-6106},
- owner = {paul},
- timestamp = {2012.09.21}
-}
-
- at ARTICLE{Petrasek2008,
- author = {Petr\'{a}\v{s}ek, Zden\v{e}k and Schwille, Petra},
- title = {Precise Measurement of Diffusion Coefficients using Scanning Fluorescence
- Correlation Spectroscopy},
- journal = {Biophysical Journal},
- year = {2008},
- volume = {94},
- pages = {1437--1448},
- number = {4},
- month = feb,
- doi = {10.1529/biophysj.107.108811},
- issn = {0006-3495},
- owner = {paul},
- publisher = {Cell Press},
- refid = {S0006-3495(08)70660-X DOI - 10.1529/biophysj.107.108811},
- timestamp = {2012.05.20}
-}
-
- at INCOLLECTION{Petrov:2008,
- author = {Petrov, E. P. and Schwille, P.},
- title = {State of the Art and Novel Trends in Fluorescence Correlation Spectroscopy},
- booktitle = {Standardization and Quality Assurance in Fluorescence Measurements
- II},
- publisher = {Springer Berlin Heidelberg},
- year = {2008},
- editor = {Resch-Genger, Ute},
- volume = {6},
- series = {Springer Series on Fluorescence},
- pages = {145-197},
- affiliation = {Biophysics, BIOTEC, Technische Universität Dresden, Tatzberg 47–51,
- 01307 Dresden, Germany},
- doi = {10.1007/4243_2008_032},
- isbn = {978-3-540-70571-0},
- keyword = {Chemistry}
-}
-
- at ARTICLE{Qian1991,
- author = {Hong Qian and Elliot L. Elson},
- title = {Analysis of confocal laser-microscope optics for 3-D fluorescence
- correlation spectroscopy},
- journal = {Applied Optics},
- year = {1991},
- volume = {30},
- pages = {1185--1195},
- number = {10},
- month = {Apr},
- abstract = {Quantitative fluorescence correlation spectroscopy (FCS) and fluorescence
- photobleaching recovery (FPR) measurements in bulk solution require
- a well characterized confocal laser microscope optical system. The
- introduction of a characteristic function, the collection efficiency
- function (CEF), provides a quantitative theoretical analysis of this
- system, which yields an interpretation of the FCS and FPR measurements
- in three dimensions. We demonstrate that when the proper field diaphragm
- is introduced, the 3-D FCS measurements can be mimicked by a 2-D
- theory with only minor error. The FPR characteristic recovery time
- for diffusion is expected to be slightly longer than the corresponding
- time measured by FCS in the same conditions. This is because the
- profile of the laser beam used for photobleaching is not affected
- by the field diaphragm. The CEF is also important for quantitative
- analysis of standard scanning confocal microscopy when it is carried
- out using a finite detection pinhole.},
- doi = {10.1364/AO.30.001185},
- owner = {paul},
- publisher = {OSA},
- timestamp = {2012.11.02}
-}
-
- at ELECTRONIC{ImageJ,
- author = {Rasband, W.S.},
- year = {1997-2012},
- title = {ImageJ},
- organization = {U. S. National Institutes of Health},
- note = {\url{http://imagej.nih.gov/ij/}},
- owner = {paul},
- timestamp = {2012.10.16}
-}
-
- at ARTICLE{Richter2006,
- author = {Richter, Ralf P. and Bérat, Rémi and Brisson, Alain R.},
- title = {Formation of Solid-Supported Lipid Bilayers: An Integrated View},
- journal = {Langmuir},
- year = {2006},
- volume = {22},
- pages = {3497-3505},
- number = {8},
- doi = {10.1021/la052687c},
- owner = {paul},
- timestamp = {2012.11.12}
-}
-
- at PHDTHESIS{Ries:08,
- author = {Ries, E.},
- title = {Advanced Fluorescence Correlation Techniques to Study Membrane Dynamics},
- school = {Biophysics, BIOTEC, Technische Universität Dresden, Tatzberg 47–51,
- 01307 Dresden, Germany},
- year = {2008},
- note = {\url{http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1219846317196-73420}}
-}
-
- at ARTICLE{Ries2009,
- author = {Jonas Ries and Salvatore Chiantia and Petra Schwille},
- title = {Accurate Determination of Membrane Dynamics with Line-Scan FCS},
- journal = {Biophysical Journal},
- year = {2009},
- volume = {96},
- pages = {1999 - 2008},
- number = {5},
- doi = {10.1016/j.bpj.2008.12.3888},
- issn = {0006-3495},
- owner = {paul},
- timestamp = {2012.11.08}
-}
-
- at ARTICLE{Ries2008390,
- author = {Jonas Ries and Eugene P. Petrov and Petra Schwille},
- title = {Total Internal Reflection Fluorescence Correlation Spectroscopy:
- Effects of Lateral Diffusion and Surface-Generated Fluorescence},
- journal = {Biophysical Journal},
- year = {2008},
- volume = {95},
- pages = {390 - 399},
- number = {1},
- doi = {10.1529/biophysj.107.126193},
- issn = {0006-3495}
-}
-
- at ARTICLE{Ries2008,
- author = {Ries, Jonas and Schwille, Petra},
- title = {New concepts for fluorescence correlation spectroscopy on membranes},
- journal = {Physical Chemistry Chemical Physics},
- year = {2008},
- volume = {10},
- pages = {--},
- number = {24},
- abstract = {Fluorescence correlation spectroscopy (FCS) is a powerful tool to
- measure useful physical quantities such as concentrations, diffusion
- coefficients, diffusion modes or binding parameters, both in model
- and cell membranes. However, it can suffer from severe artifacts,
- especially in non-ideal systems. Here we assess the potential and
- limitations of standard confocal FCS on lipid membranes and present
- recent developments which facilitate accurate and quantitative measurements
- on such systems. In particular, we discuss calibration-free diffusion
- and concentration measurements using z-scan FCS and two focus FCS
- and present several approaches using scanning FCS to accurately measure
- slow dynamics. We also show how surface confined FCS enables the
- study of membrane dynamics even in presence of a strong cytosolic
- background and how FCS with a variable detection area can reveal
- submicroscopic heterogeneities in cell membranes.},
- issn = {1463-9076},
- owner = {paul},
- publisher = {The Royal Society of Chemistry},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Rigler1993,
- author = {Rigler, R. and Mets, {\"U}. and Widengren, J. and Kask, P.},
- title = {Fluorescence correlation spectroscopy with high count rate and low
- background: analysis of translational diffusion},
- journal = {European Biophysics Journal},
- year = {1993},
- volume = {22},
- pages = {169-175},
- doi = {10.1007/BF00185777},
- issn = {0175-7571},
- issue = {3},
- keywords = {Fluorescence correlation spectroscopy; Fluorescence intensity fluctuations;
- Translational diffusion; Epifluorescence microscope; Silicon photon
- counter},
- language = {English},
- owner = {paul},
- publisher = {Springer-Verlag},
- timestamp = {2012.11.02}
-}
-
- at ARTICLE{Ruan2004,
- author = {Ruan, Qiaoqiao and Cheng, Melanie A. and Levi, Moshe and Gratton,
- Enrico and Mantulin, William W.},
- title = {Spatial-Temporal Studies of Membrane Dynamics: Scanning Fluorescence
- Correlation Spectroscopy (SFCS)},
- journal = {Biophysical Journal},
- year = {2004},
- volume = {87},
- pages = {1260--1267},
- number = {2},
- month = aug,
- issn = {0006-3495},
- owner = {paul},
- publisher = {Cell Press},
- refid = {S0006-3495(04)73605-X DOI - 10.1529/biophysj.103.036483},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Sankaran2009,
- author = {Sankaran, Jagadish and Manna, Manoj and Guo, Lin and Kraut, Rachel
- and Wohland, Thorsten},
- title = {Diffusion, Transport, and Cell Membrane Organization Investigated
- by Imaging Fluorescence Cross-Correlation Spectroscopy},
- journal = {Biophysical Journal},
- year = {2009},
- volume = {97},
- pages = {2630--2639},
- number = {9},
- month = nov,
- doi = {10.1016/j.bpj.2009.08.025},
- issn = {0006-3495},
- owner = {paul},
- publisher = {Cell Press},
- refid = {S0006-3495(09)01387-3 DOI - 10.1016/j.bpj.2009.08.025},
- timestamp = {2012.09.21}
-}
-
- at ARTICLE{Sankaran2010,
- author = {Jagadish Sankaran and Xianke Shi and Liang Yoong Ho and Ernst H K
- Stelzer and Thorsten Wohland},
- title = {ImFCS: a software for imaging FCS data analysis and visualization.},
- journal = {Optics Express},
- year = {2010},
- volume = {18},
- pages = {25468--25481},
- number = {25},
- month = {Dec},
- abstract = {The multiplexing of fluorescence correlation spectroscopy (FCS), especially
- in imaging FCS using fast, sensitive array detectors, requires the
- handling of large amounts of data. One can easily collect in excess
- of 100,000 FCS curves a day, too many to be treated manually. Therefore,
- ImFCS, an open-source software which relies on standard image files
- was developed and provides a wide range of options for the calculation
- of spatial and temporal auto- and cross-correlations, as well as
- differences in Cross-Correlation Functions (ΔCCF). ImFCS permits
- fitting of standard models to correlation functions and provides
- optimized histograms of fitted parameters. Applications include the
- measurement of diffusion and flow with Imaging Total Internal Reflection
- FCS (ITIR-FCS) and Single Plane Illumination Microscopy FCS (SPIM-FCS)
- in biologically relevant samples. As a compromise between ITIR-FCS
- and SPIM-FCS, we extend the applications to Imaging Variable Angle-FCS
- (IVA-FCS) where sub-critical oblique illumination provides sample
- sectioning close to the cover slide.},
- doi = {10.1364/OE.18.025468},
- institution = {Singapore-MIT Alliance, National University of Singapore, E4-04-10,
- 4 Engineering Drive 3, 117576 Singapore.},
- keywords = {Algorithms; Pattern Recognition, Automated, methods; Software; Spectrometry,
- Fluorescence, methods},
- language = {eng},
- medline-pst = {ppublish},
- owner = {paul},
- pii = {208325},
- pmid = {21164894},
- timestamp = {2012.10.24}
-}
-
- at ARTICLE{SbalzariniSPT,
- author = {I. F. Sbalzarini and P. Koumoutsakos},
- title = {Feature Point Tracking and Trajectory Analysis for Video Imaging
- in Cell Biology},
- journal = {Journal of Structural Biology},
- year = {2005},
- volume = {151(2)},
- pages = {182-195},
- doi = {10.1016/j.jsb.2005.06.002},
- owner = {paul},
- timestamp = {2012.10.16}
-}
-
- at ARTICLE{Schwille2000,
- author = {Schwille, Petra and Kummer, Susanne and Heikal, Ahmed A. and Moerner,
- W. E. and Webb, Watt W.},
- title = {Fluorescence correlation spectroscopy reveals fast optical excitation-driven
- intramolecular dynamics of yellow fluorescent proteins},
- journal = {Proceedings of the National Academy of Sciences},
- year = {2000},
- volume = {97},
- pages = {151-156},
- number = {1},
- abstract = {Fast excitation-driven fluctuations in the fluorescence emission of
- yellow-shifted green fluorescent protein mutants T203Y and T203F,
- with S65G/S72A, are discovered in the 10−6–10−3-s time range, by
- using fluorescence correlation spectroscopy at 10−8 M. This intensity-dependent
- flickering is conspicuous at high pH, with rate constants independent
- of pH and viscosity with a minor temperature effect. The mean flicker
- rate increases linearly with excitation intensity for at least three
- decades, but the mean dark fraction of the molecules undergoing these
- dynamics is independent of illumination intensity over ≈6 × 102 to
- 5 × 106 W/cm2. These results suggest that optical excitation establishes
- an equilibration between two molecular states of different spectroscopic
- properties that are coupled only via the excited state as a gateway.
- This reversible excitation-driven transition has a quantum efficiency
- of ≈10−3. Dynamics of external protonation, reversibly quenching
- the fluorescence, are also observed at low pH in the 10- to 100-μs
- time range. The independence of these two bright–dark flicker processes
- implies the existence of at least two separate dark states of these
- green fluorescent protein mutants. Time-resolved fluorescence measurements
- reveal a single exponential decay of the excited state population
- with 3.8-ns lifetime, after 500-nm excitation, that is pH independent.
- Our fluorescence correlation spectroscopy results are discussed in
- terms of recent theoretical studies that invoke isomerization of
- the chromophore as a nonradiative channel of the excited state relaxation.},
- doi = {10.1073/pnas.97.1.151},
- owner = {paul},
- timestamp = {2012.09.24}
-}
-
- at ARTICLE{Schwille1997,
- author = {Schwille, P. and Meyer-Almes, F.J. and Rigler, R.},
- title = {Dual-color fluorescence cross-correlation spectroscopy for multicomponent
- diffusional analysis in solution},
- journal = {Biophysical Journal},
- year = {1997},
- volume = {72},
- pages = {1878--1886},
- number = {4},
- month = apr,
- issn = {0006-3495},
- owner = {paul},
- publisher = {Cell Press},
- refid = {S0006-3495(97)78833-7 DOI - 10.1016/S0006-3495(97)78833-7},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Schatzel1990,
- author = {K. Sch{\"a}tzel},
- title = {Noise on photon correlation data. I. Autocorrelation functions},
- journal = {Quantum Optics: Journal of the European Optical Society Part B},
- year = {1990},
- volume = {2},
- pages = {287},
- number = {4},
- abstract = {An adequate analysis of photon correlation data requires knowledge
- about the statistical accuracy of the measured data. For the model
- of gamma-distributed intensities, that is including the effect of
- a finite intercept, the full covariance matrix is calculated for
- all the channels of the photon autocorrelation functions. A thorough
- discussion of multiple sample time correlation illuminates the importance
- of temporal averaging effects at large lag times. A practical estimation
- scheme is given for the noise in photon correlation data from a multiple
- sample time measurement.},
- doi = {10.1088/0954-8998/2/4/002},
- owner = {paul},
- timestamp = {2012.11.02}
-}
-
- at ARTICLE{Scomparin2009,
- author = {Scomparin, C. and Lecuyer, S. and Ferreira, M. and Charitat, T. and
- Tinland, B.},
- title = {Diffusion in supported lipid bilayers: Influence of substrate and
- preparation technique on the internal dynamics},
- journal = {The European Physical Journal E: Soft Matter and Biological Physics},
- year = {2009},
- volume = {28},
- pages = {211-220},
- affiliation = {CNRS UPR 3118 CINAM 13288 Marseille Cedex 09 France},
- doi = {10.1140/epje/i2008-10407-3},
- issn = {1292-8941},
- issue = {2},
- keyword = {Physik und Astronomie},
- owner = {paul},
- publisher = {Springer Berlin / Heidelberg},
- timestamp = {2012.10.22}
-}
-
- at ARTICLE{Seu2007,
- author = {Seu, Kalani J. and Pandey, Anjan P. and Haque, Farzin and Proctor,
- Elizabeth A. and Ribbe, Alexander E. and Hovis, Jennifer S.},
- title = {Effect of Surface Treatment on Diffusion and Domain Formation in
- Supported Lipid Bilayers},
- journal = {Biophysical Journal},
- year = {2007},
- volume = {92},
- pages = {2445--2450},
- number = {7},
- month = apr,
- doi = {10.1529/biophysj.106.099721},
- issn = {0006-3495},
- owner = {paul},
- publisher = {Cell Press},
- refid = {S0006-3495(07)71049-4 DOI - 10.1529/biophysj.106.099721},
- timestamp = {2012.10.22}
-}
-
- at ARTICLE{Shannon1984,
- author = {Shannon, C.E.},
- title = {Communication in the presence of noise},
- journal = {Proceedings of the IEEE},
- year = {1984},
- volume = {72},
- pages = { 1192 - 1201},
- number = {9},
- month = {sept.},
- doi = {10.1109/PROC.1984.12998},
- issn = {0018-9219},
- owner = {paul},
- timestamp = {2012.11.12}
-}
-
- at ARTICLE{Skinner2005,
- author = {Joseph P Skinner and Yan Chen and Joachim D Müller},
- title = {Position-sensitive scanning fluorescence correlation spectroscopy.},
- journal = {Biophysical Journal},
- year = {2005},
- volume = {89},
- pages = {1288--1301},
- number = {2},
- month = {Aug},
- abstract = {Fluorescence correlation spectroscopy (FCS) uses a stationary laser
- beam to illuminate a small sample volume and analyze the temporal
- behavior of the fluorescence fluctuations within the stationary observation
- volume. In contrast, scanning FCS (SFCS) collects the fluorescence
- signal from a moving observation volume by scanning the laser beam.
- The fluctuations now contain both temporal and spatial information
- about the sample. To access the spatial information we synchronize
- scanning and data acquisition. Synchronization allows us to evaluate
- correlations for every position along the scanned trajectory. We
- use a circular scan trajectory in this study. Because the scan radius
- is constant, the phase angle is sufficient to characterize the position
- of the beam. We introduce position-sensitive SFCS (PSFCS), where
- correlations are calculated as a function of lag time and phase.
- We present the theory of PSFCS and derive expressions for diffusion,
- diffusion in the presence of flow, and for immobilization. To test
- PSFCS we compare experimental data with theory. We determine the
- direction and speed of a flowing dye solution and the position of
- an immobilized particle. To demonstrate the feasibility of the technique
- for applications in living cells we present data of enhanced green
- fluorescent protein measured in the nucleus of COS cells.},
- doi = {10.1529/biophysj.105.060749},
- institution = {School of Physics and Astronomy, University of Minnesota, Minneapolis,
- 55455, USA. josephs at physics.umn.edu},
- keywords = {Algorithms; Image Enhancement, methods; Image Interpretation, Computer-Assisted,
- methods; Information Storage and Retrieval, methods; Microscopy,
- Confocal, methods; Reproducibility of Results; Sensitivity and Specificity;
- Spectrometry, Fluorescence, methods},
- language = {eng},
- medline-pst = {ppublish},
- owner = {paul},
- pii = {S0006-3495(05)72776-4},
- pmid = {15894645},
- timestamp = {2012.10.28}
-}
-
- at ARTICLE{Starr2001,
- author = {Tammy E. Starr and Nancy L. Thompson},
- title = {Total Internal Reflection with Fluorescence Correlation Spectroscopy:
- Combined Surface Reaction and Solution Diffusion},
- journal = {Biophysical Journal},
- year = {2001},
- volume = {80},
- pages = {1575 - 1584},
- number = {3},
- doi = {10.1016/S0006-3495(01)76130-9},
- issn = {0006-3495}
-}
-
- at ARTICLE{Sutherland1905,
- author = {Sutherland, William},
- title = {A dynamical theory of diffusion for non-electrolytes and the molecular
- mass of albumin},
- journal = {Philosophical Magazine Series 6},
- year = {1905},
- volume = {9},
- pages = {781-785},
- number = {54},
- __markedentry = {[paul]},
- doi = {10.1080/14786440509463331},
- owner = {paul},
- timestamp = {2012.11.14}
-}
-
- at ARTICLE{Tamm1985,
- author = {Tamm, L.K. and McConnell, H.M.},
- title = {Supported phospholipid bilayers},
- journal = {Biophysical Journal},
- year = {1985},
- volume = {47},
- pages = {105--113},
- number = {1},
- month = jan,
- doi = {10.1016/S0006-3495(85)83882-0},
- issn = {0006-3495},
- owner = {paul},
- publisher = {Cell Press},
- refid = {S0006-3495(85)83882-0 DOI - 10.1016/S0006-3495(85)83882-0},
- timestamp = {2012.10.29}
-}
-
- at INCOLLECTION{Thomps:bookFCS2002,
- author = {Thompson, Nancy},
- title = {Fluorescence Correlation Spectroscopy},
- booktitle = {Topics in Fluorescence Spectroscopy},
- publisher = {Springer US},
- year = {2002},
- editor = {Lakowicz, Joseph and Geddes, Chris D. and Lakowicz, Joseph R.},
- volume = {1},
- series = {Topics in Fluorescence Spectroscopy},
- pages = {337-378},
- affiliation = {University of North Carolina at Chapel Hill Department of Chemistry
- Chapel Hill North Carolina 27599-3290 USA},
- doi = {10.1007/0-306-47057-8_6},
- isbn = {978-0-306-47057-8},
- keyword = {Biomedical and Life Sciences},
- owner = {paul},
- timestamp = {2012.01.10}
-}
-
- at ARTICLE{Thompson1983,
- author = {N.L. Thompson and D. Axelrod},
- title = {Immunoglobulin surface-binding kinetics studied by total internal
- reflection with fluorescence correlation spectroscopy},
- journal = {Biophysical Journal},
- year = {1983},
- volume = {43},
- pages = {103 - 114},
- number = {1},
- doi = {10.1016/S0006-3495(83)84328-8},
- issn = {0006-3495},
- owner = {paul},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Thompson1981,
- author = {N.L. Thompson and T.P. Burghardt and D. Axelrod},
- title = {Measuring surface dynamics of biomolecules by total internal reflection
- fluorescence with photobleaching recovery or correlation spectroscopy},
- journal = {Biophysical Journal},
- year = {1981},
- volume = {33},
- pages = {435 - 454},
- number = {3},
- doi = {10.1016/S0006-3495(81)84905-3},
- issn = {0006-3495},
- owner = {paul},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Thompson1997,
- author = {Thompson, Nancy L. and Drake, Andrew W. and Chen, Lixin and Broek,
- Willem Vanden},
- title = {Equilibrium, Kinetics, Diffusion and Self-Association of Proteins
- at Membrane Surfaces: Measurement by Total Internal Reflection Fluorescence
- Microscopy},
- journal = {Photochemistry and Photobiology},
- year = {1997},
- volume = {65},
- pages = {39--46},
- number = {1},
- doi = {10.1111/j.1751-1097.1997.tb01875.x},
- issn = {1751-1097},
- owner = {paul},
- publisher = {Blackwell Publishing Ltd},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Thompson1997a,
- author = {Nancy L Thompson and B Christoffer Lagerholm},
- title = {Total internal reflection fluorescence: applications in cellular
- biophysics},
- journal = {Current Opinion in Biotechnology},
- year = {1997},
- volume = {8},
- pages = {58 - 64},
- number = {1},
- doi = {10.1016/S0958-1669(97)80158-9},
- issn = {0958-1669},
- owner = {paul},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Toomre2001,
- author = {Derek Toomre and Dietmar J. Manstein},
- title = {Lighting up the cell surface with evanescent wave microscopy},
- journal = {Trends in Cell Biology},
- year = {2001},
- volume = {11},
- pages = {298 - 303},
- number = {7},
- doi = {10.1016/S0962-8924(01)02027-X},
- issn = {0962-8924},
- keywords = {green-fluorescent protein (GFP)},
- owner = {paul},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Unruh2008,
- author = {Unruh, Jay R. and Gratton, Enrico},
- title = {Analysis of Molecular Concentration and Brightness from Fluorescence
- Fluctuation Data with an Electron Multiplied CCD Camera},
- journal = {Biophysical Journal},
- year = {2008},
- volume = {95},
- pages = {5385--5398},
- number = {11},
- month = dec,
- doi = {10.1529/biophysj.108.130310},
- issn = {0006-3495},
- owner = {paul},
- publisher = {Cell Press},
- refid = {S0006-3495(08)78962-8 DOI - 10.1529/biophysj.108.130310},
- timestamp = {2012.09.21}
-}
-
- at ARTICLE{Vacha2009,
- author = {V\'{a}cha, Robert and Siu, Shirley W. I. and Petrov, Michal and Böckmann,
- Rainer A. and Barucha-Kraszewska, Justyna and Jurkiewicz, Piotr and
- Hof, Martin and Berkowitz, Max L. and Jungwirth, Pavel},
- title = {Effects of Alkali Cations and Halide Anions on the DOPC Lipid Membrane},
- journal = {The Journal of Physical Chemistry A},
- year = {2009},
- volume = {113},
- pages = {7235-7243},
- number = {26},
- note = {PMID: 19290591},
- doi = {10.1021/jp809974e},
- owner = {paul},
- timestamp = {2012.10.24}
-}
-
- at ELECTRONIC{VisserRol,
- author = {G. Visser and J. Rolinski},
- year = {2010},
- title = {Basic Photophysics},
- note = {Photobiological Sciences Online (KC Smith, ed.) American Society
- for Photobiology \url{http://www.photobiology.info}.},
- owner = {paul},
- timestamp = {2012.02.14}
-}
-
- at ARTICLE{Widengren1995,
- author = {Widengren, Jerker and Mets, {\"U}lo and Rigler, Rudolf},
- title = {Fluorescence correlation spectroscopy of triplet states in solution:
- a theoretical and experimental study},
- journal = {The Journal of Physical Chemistry},
- year = {1995},
- volume = {99},
- pages = {13368-13379},
- number = {36},
- doi = {10.1021/j100036a009},
- owner = {paul},
- timestamp = {2012.02.20}
-}
-
- at ARTICLE{Widengren1994,
- author = {Widengren, Jerker and Rigler, Rudolf and Mets, {\"U}lo},
- title = {Triplet-state monitoring by fluorescence correlation spectroscopy},
- journal = {Journal of Fluorescence},
- year = {1994},
- volume = {4},
- pages = {255-258},
- affiliation = {Department of Medical Biochemistry and Biophysics Karolinska Institute
- S-171 77 Stockholm Sweden},
- doi = {10.1007/BF01878460},
- issn = {1053-0509},
- issue = {3},
- keyword = {Biomedizin & Life Sciences},
- owner = {paul},
- publisher = {Springer Netherlands},
- timestamp = {2012.09.24}
-}
-
- at ARTICLE{Wohland2001,
- author = {Wohland, Thorsten and Rigler, Rudolf and Vogel, Horst},
- title = {The Standard Deviation in Fluorescence Correlation Spectroscopy},
- journal = {Biophysical Journal},
- year = {2001},
- volume = {80},
- pages = {2987--2999},
- number = {6},
- month = jun,
- doi = {10.1016/S0006-3495(01)76264-9},
- issn = {0006-3495},
- owner = {paul},
- timestamp = {2012.09.08}
-}
-
- at ARTICLE{Wohland2010,
- author = {Thorsten Wohland and Xianke Shi and Jagadish Sankaran and Ernst H.K.
- Stelzer},
- title = {Single Plane Illumination Fluorescence Correlation Spectroscopy (SPIM-FCS)
- probes inhomogeneous three-dimensional environments},
- journal = {Optics Express},
- year = {2010},
- volume = {18},
- pages = {10627--10641},
- number = {10},
- month = {May},
- abstract = {The life sciences require new highly sensitive imaging tools, which
- allow the quantitative measurement of molecular parameters within
- a physiological three-dimensional (3D) environment. Therefore, we
- combined single plane illumination microscopy (SPIM) with camera
- based fluorescence correlation spectroscopy (FCS). SPIM-FCS provides
- contiguous particle number and diffusion coefficient images with
- a high spatial resolution in homo- and heterogeneous 3D specimens
- and live zebrafish embryos. Our SPIM-FCS recorded up to 4096 spectra
- within 56 seconds at a laser power of 60 \&\#x03BC;W without damaging
- the embryo. This new FCS modality provides more measurements per
- time and more, less photo-toxic measurements per sample than confocal
- based methods. In essence, SPIM-FCS offers new opportunities to observe
- biomolecular interactions quantitatively and functions in a highly
- multiplexed manner within a physiologically relevant 3D environment.},
- doi = {10.1364/OE.18.010627},
- keywords = {Fluorescence microscopy; Three-dimensional microscopy; Spectroscopy,
- fluorescence and luminescence},
- owner = {paul},
- publisher = {OSA},
- timestamp = {2012.11.07}
-}
-
- at ARTICLE{Yordanov2009,
- author = {Stoyan Yordanov and Andreas Best and Hans-J\"{u}rgen Butt and Kaloian
- Koynov},
- title = {Direct studies of liquid flows near solid surfaces by total internal
- reflection fluorescence cross-correlation spectroscopy},
- journal = {Optics Express},
- year = {2009},
- volume = {17},
- pages = {21149--21158},
- number = {23},
- month = {Nov},
- abstract = {We present a new method to study flow of liquids near solid surface:
- Total internal reflection fluorescence cross-correlation spectroscopy
- (TIR-FCCS). Fluorescent tracers flowing with the liquid are excited
- by evanescent light, produced by epi-illumination through the periphery
- of a high numerical aperture oil-immersion objective. The time-resolved
- fluorescence intensity signals from two laterally shifted observation
- volumes, created by two confocal pinholes are independently measured.
- The cross-correlation of these signals provides information of the
- tracers' velocities. By changing the evanescent wave penetration
- depth, flow profiling at distances less than 200 nm from the interface
- can be performed. Due to the high sensitivity of the method fluorescent
- species with different size, down to single dye molecules can be
- used as tracers. We applied this method to study the flow of aqueous
- electrolyte solutions near a smooth hydrophilic surface and explored
- the effect of several important parameters, e.g. tracer size, ionic
- strength, and distance between the observation volumes.},
- doi = {10.1364/OE.17.021149},
- keywords = {Velocimetry; Fluorescence, laser-induced; Spectroscopy, surface},
- owner = {paul},
- publisher = {OSA},
- timestamp = {2012.09.21}
-}
-
- at ARTICLE{Yordanov2011,
- author = {Stoyan Yordanov and Andreas Best and Klaus Weisshart and Kaloian
- Koynov},
- title = {Note: An easy way to enable total internal reflection-fluorescence
- correlation spectroscopy (TIR-FCS) by combining commercial devices
- for FCS and TIR microscopy},
- journal = {Review of Scientific Instruments},
- year = {2011},
- volume = {82},
- pages = {036105},
- number = {3},
- eid = {036105},
- doi = {10.1063/1.3557412},
- keywords = {fluorescence spectroscopy; optical microscopy},
- numpages = {3},
- owner = {paul},
- publisher = {AIP},
- timestamp = {2012.05.02}
-}
-
- at ARTICLE{Zhang2007,
- author = {Bo Zhang and Josiane Zerubia and Jean-Christophe Olivo-Marin},
- title = {Gaussian approximations of fluorescence microscope point-spread function
- models},
- journal = {Applied Optics},
- year = {2007},
- volume = {46},
- pages = {1819--1829},
- number = {10},
- month = {Apr},
- abstract = {We comprehensively study the least-squares Gaussian approximations
- of the diffraction-limited 2D-3D paraxial-nonparaxial point-spread
- functions (PSFs)of the wide field fluorescence microscope (WFFM),
- the laser scanning confocal microscope(LSCM), and the disk scanning
- confocal microscope (DSCM). The PSFs are expressed using the Debye
- integral. Under anL$\infty$ constraint imposing peak matching, optimal
- and near-optimal Gaussian parameters are derived for the PSFs. With
- anL1 constraint imposing energy conservation, an optimal Gaussian
- parameter is derived for the 2D paraxial WFFM PSF. We found that
- (1) the 2D approximations are all very accurate; (2) no accurate
- Gaussian approximation exists for 3D WFFM PSFs; and (3) with typical
- pinhole sizes, the 3D approximations are accurate for the DSCM and
- nearly perfect for the LSCM. All the Gaussian parameters derived
- in this study are in explicit analytical form, allowing their direct
- use in practical applications.},
- doi = {10.1364/AO.46.001819},
- keywords = {Numerical approximation and analysis; Microscopy; Confocal microscopy;
- Fluorescence microscopy; Three-dimensional microscopy},
- owner = {paul},
- publisher = {OSA},
- timestamp = {2012.09.20}
-}
-
- at BOOK{Rigler:FCSbook,
- title = {Fluorescence Correlation Spectroscopy, Theory and Applications},
- publisher = {Springer Berlin Heidelberg},
- year = {2001},
- editor = {R. Rigler and E.S. Elson},
- edition = {1},
- howpublished = {Paperback},
- isbn = {978-3540674337},
- owner = {paul},
- timestamp = {2012.11.02}
-}
-
- at ELECTRONIC{AndorNeoSpec,
- title = {Andor Technology, Neo sCMOS Specifications},
- organization = {Andor Technology},
- note = {\url{http://www.andor.com/pdfs/specifications/Andor_Neo_sCMOS_Specifications.pdf}
- (Okt. 2012)},
- citeseerurl = {http://www.andor.com/pdfs/specifications/Andor_Neo_sCMOS_Specifications.pdf},
- owner = {paul},
- timestamp = {2012.10.08}
-}
-
- at ELECTRONIC{HamamatsuOrcaSpec,
- title = {Hamamatsu, ORCA-Flash4.0 CMOS datasheet},
- organization = {Hamamatsu},
- note = {\url{http://sales.hamamatsu.com/assets/pdf/hpspdf/e_flash4.pdf} (Okt.
- 2012)},
- citeseerurl = {http://www.andor.com/pdfs/specifications/Andor_Neo_sCMOS_Specifications.pdf},
- owner = {paul},
- timestamp = {2012.10.08}
-}
-
- at ELECTRONIC{InvitrogenDiO,
- month = {November},
- title = {Invitrogen, catalog number D-275 (DiO)},
- note = {\url{http://products.invitrogen.com/ivgn/product/D275} (Okt. 2012)},
- owner = {paul},
- timestamp = {2012.10.18}
-}
-
- at ELECTRONIC{vaxavis,
- title = {Dynamic viscosity of liquid water from 0 \degC},
- note = {\url{http://www.vaxasoftware.com/doc_eduen/qui/viscoh2o.pdf} (Okt.
- 2012)},
- owner = {paul},
- timestamp = {2012.10.29}
-}
-
- at ELECTRONIC{WikipediaBrown,
- title = {Brownian motion, Wikipedia - The Free Encyclopedia},
- note = {\url{http://en.wikipedia.org/wiki/Brownian_motion} (Okt. 2012)},
- owner = {paul},
- timestamp = {2012.10.18}
-}
-
- at ELECTRONIC{AndorNeo,
- year = {2011},
- title = {Andor Technology, Neo sCMOS Hardware Guide},
- organization = {Andor Technology},
- owner = {paul},
- timestamp = {2012.10.06}
+
+ at Article{Aragon1976,
+ Title = {Fluorescence correlation spectroscopy as a probe of molecular dynamics},
+ Author = {S. R. Aragon and R. Pecora},
+ Journal = {The Journal of Chemical Physics},
+ Year = {1976},
+ Number = {4},
+ Pages = {1791-1803},
+ Volume = {64},
+
+ Doi = {10.1063/1.432357},
+ Owner = {paul},
+ Publisher = {AIP},
+ Timestamp = {2012.11.02}
+}
+
+ at Article{Ashkin1970,
+ Title = {Acceleration and Trapping of Particles by Radiation Pressure},
+ Author = {Ashkin, A.},
+ Journal = {Physical Review Letters},
+ Year = {1970},
+
+ Month = {Jan},
+ Pages = {156--159},
+ Volume = {24},
+
+ Doi = {10.1103/PhysRevLett.24.156},
+ Issue = {4},
+ Owner = {paul},
+ Publisher = {American Physical Society},
+ Timestamp = {2012.11.13}
+}
+
+ at Article{Axelrod1984,
+ Title = {Total Internal Reflection Fluorescence},
+ Author = {Axelrod, D and Burghardt, T P and Thompson, N L},
+ Journal = {Annual Review of Biophysics and Biomolecular Structure},
+ Year = {1984},
+
+ Month = jun,
+ Number = {1},
+ Pages = {247--268},
+ Volume = {13},
+
+ Booktitle = {Annual Review of Biophysics and Bioengineering},
+ Comment = {doi: 10.1146/annurev.bb.13.060184.001335},
+ Doi = {10.1146/annurev.bb.13.060184.001335},
+ ISSN = {0084-6589},
+ Owner = {paul},
+ Publisher = {Annual Reviews},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Bacia2006,
+ Title = {Fluorescence cross-correlation spectroscopy in living cells},
+ Author = {Bacia, K. and Kim, S. A. and Schwille, P.},
+ Journal = {Nat Methods},
+ Year = {2006},
+ Number = {2},
+ Pages = {83--9},
+ Volume = {3},
+
+ Abstract = {Cell biologists strive to characterize molecular interactions directly in the intracellular environment. The intrinsic resolution of optical microscopy, however, allows visualization of only coarse subcellular localization. By extracting information from molecular dynamics, fluorescence cross-correlation spectroscopy (FCCS) grants access to processes on a molecular scale, such as diffusion, binding, enzymatic reactions and codiffusion, and has become a valua [...]
+ Doi = {10.1038/nmeth822},
+ Keywords = {Algorithms Animals Biological Transport Diffusion Endocytosis/physiology Enzymes/metabolism Fluorescence Resonance Energy Transfer/methods Humans Laser Scanning Cytometry/instrumentation/*methods Oligonucleotides/metabolism Protein Binding Protein Transport Proteins/metabolism Signal Transduction/physiology Spectrometry, Fluorescence/instrumentation/methods},
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at Article{Bacia2012,
+ Title = {Correcting for spectral cross-talk in dual-color fluorescence cross-correlation spectroscopy},
+ Author = {Bacia, K. and Petr\'{a}\v{s}ek, Zden\v{e}k and Schwille, P.},
+ Journal = {Chemphyschem},
+ Year = {2012},
+ Number = {5},
+ Pages = {1221--31},
+ Volume = {13},
+
+ Abstract = {Dual-color fluorescence cross-correlation spectroscopy (dcFCCS) allows one to quantitatively assess the interactions of mobile molecules labeled with distinct fluorophores. The technique is widely applied to both reconstituted and live-cell biological systems. A major drawback of dcFCCS is the risk of an artifactual false-positive or overestimated cross-correlation amplitude arising from spectral cross-talk. Cross-talk can be reduced or prevented by fast alt [...]
+ Doi = {10.1002/cphc.201100801},
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at Article{Bag2012,
+ Title = {Calibration and Limits of Camera-Based Fluorescence Correlation Spectroscopy: A Supported Lipid Bilayer Study},
+ Author = {Bag, Nirmalya and Sankaran, Jagadish and Paul, Alexandra and Kraut, Rachel S. and Wohland, Thorsten},
+ Journal = {ChemPhysChem},
+ Year = {2012},
+ Number = {11},
+ Pages = {2784--2794},
+ Volume = {13},
+
+ Doi = {10.1002/cphc.201200032},
+ ISSN = {1439-7641},
+ Keywords = {fluorescence spectroscopy, membrane, multiplexing, point spread function, total internal reflection},
+ Owner = {paul},
+ Publisher = {WILEY-VCH Verlag},
+ Timestamp = {2012.09.20}
+}
+
+ at Article{Bestvater2010,
+ Title = {EMCCD-based spectrally resolved fluorescence correlation spectroscopy},
+ Author = {Felix Bestvater and Zahir Seghiri and Moon Sik Kang and Nadine Gr\"{o}ner and Ji Young Lee and Kang-Bin Im and Malte Wachsmuth},
+ Journal = {Optics Express},
+ Year = {2010},
+
+ Month = {Nov},
+ Number = {23},
+ Pages = {23818--23828},
+ Volume = {18},
+
+ Abstract = {We present an implementation of fluorescence correlation spectroscopy with spectrally resolved detection based on a combined commercial confocal laser scanning/fluorescence correlation spectroscopy microscope. We have replaced the conventional detection scheme by a prism-based spectrometer and an electron-multiplying charge-coupled device camera used to record the photons. This allows us to read out more than 80,000 full spectra per second with a signal-to-n [...]
+ Doi = {10.1364/OE.18.023818},
+ Keywords = {CCD, charge-coupled device; Confocal microscopy; Spectroscopy, fluorescence and luminescence},
+ Owner = {paul},
+ Publisher = {OSA},
+ Timestamp = {2012.11.07}
+}
+
+ at Article{Blom2009,
+ Title = {Triplet-State Investigations of Fluorescent Dyes at Dielectric Interfaces Using Total Internal Reflection Fluorescence Correlation Spectroscopy},
+ Author = {Blom, Hans and Chmyrov, Andriy and Hassler, Kai and Davis, Lloyd M. and Widengren, Jerker},
+ Journal = {The Journal of Physical Chemistry A},
+ Year = {2009},
+ Number = {19},
+ Pages = {5554-5566},
+ Volume = {113},
+
+ Doi = {10.1021/jp8110088},
+ Owner = {paul},
+ Timestamp = {2012.11.02}
+}
+
+ at Article{Blom2002,
+ Title = {Parallel Fluorescence Detection of Single Biomolecules in Microarrays by a Diffractive-Optical-Designed 2 x 2 Fan-Out Element},
+ Author = {Hans Blom and Mathias Johansson and Anna-Sara Hedman and Liselotte Lundberg and Anders Hanning and Sverker H{\aa}rd and Rudolf Rigler},
+ Journal = {Applied Optics},
+ Year = {2002},
+
+ Month = {Jun},
+ Number = {16},
+ Pages = {3336--3342},
+ Volume = {41},
+
+ Abstract = {We have developed a multifocal diffractive-optical fluorescence correlation spectroscopy system for parallel excitation and detection of single tetramethylrhodamine biomolecules in microarrays. Multifocal excitation was made possible through the use of a 2 {\texttimes} 2 fan-out diffractive-optical element with uniform intensity in all foci. Characterization of the 2 {\texttimes} 2 fan-out diffractive-optical element shows formation of almost perfect Gaussia [...]
+ Doi = {10.1364/AO.41.003336},
+ Keywords = {Diffractive optics; Confocal microscopy; Fluorescence microscopy; Fluorescence, laser-induced},
+ Owner = {paul},
+ Publisher = {OSA},
+ Timestamp = {2012.11.07}
+}
+
+ at Article{Brinkmeier1999,
+ Title = {Two-beam cross-correlation: a method to characterize transport phenomena in micrometer-sized structures.},
+ Author = {M. Brinkmeier and K. Dörre and J. Stephan and M. Eigen},
+ Journal = {Analytical Chemistry},
+ Year = {1999},
+
+ Month = {Feb},
+ Number = {3},
+ Pages = {609--616},
+ Volume = {71},
+
+ Abstract = {To determine flow properties, namely, the velocity and angle of the flow in microstructured channels, an experimental realization based on fluorescence correlation spectroscopy is described. For this purpose, two micrometer-sized spatially separated volume elements have been created. The cross-correlation signal from these has been recorded and evaluated mathematically. In addition to previous results, two-beam cross-correlation allows for fast and easy dete [...]
+ Doi = {10.1021/ac980820i},
+ Institution = {Max-Planck-Institut für biophysikalische Chemie, Am Fassberg, D-37077 Göttingen, Germany.},
+ Language = {eng},
+ Medline-pst = {ppublish},
+ Owner = {paul},
+ Pmid = {21662718},
+ Timestamp = {2012.11.07}
+}
+
+ at Article{Brutzer2012,
+ Title = {Scanning Evanescent Fields Using a pointlike Light Source and a Nanomechanical DNA Gear},
+ Author = {Brutzer, Hergen and Schwarz, Friedrich W. and Seidel, Ralf},
+ Journal = {Nano Letters},
+ Year = {2012},
+ Number = {1},
+ Pages = {473-478},
+ Volume = {12},
+
+ Doi = {10.1021/nl203876w},
+ Owner = {paul},
+ Timestamp = {2012.08.09}
+}
+
+ at Article{Buchholz2012,
+ Title = {FPGA implementation of a 32x32 autocorrelator array for analysis of fast image series},
+ Author = {Jan Buchholz and Jan Wolfgang Krieger and G\'{a}bor Mocs\'{a}r and Bal\'{a}zs Kreith and Edoardo Charbon and Gy\"{o}rgy V\'{a}mosi and Udo Kebschull and J\"{o}rg Langowski},
+ Journal = {Optics Express},
+ Year = {2012},
+
+ Month = {Jul},
+ Number = {16},
+ Pages = {17767--17782},
+ Volume = {20},
+
+ Abstract = {With the evolving technology in CMOS integration, new classes of 2D-imaging detectors have recently become available. In particular, single photon avalanche diode (SPAD) arrays allow detection of single photons at high acquisition rates (\&\#x02265; 100kfps), which is about two orders of magnitude higher than with currently available cameras. Here we demonstrate the use of a SPAD array for imaging fluorescence correlation spectroscopy (imFCS), a tool to crea [...]
+ Doi = {10.1364/OE.20.017767},
+ Keywords = {Detectors; Arrays; Cameras; Correlators ; Fluorescence microscopy; Three-dimensional microscopy; Spectroscopy, fluorescence and luminescence; Avalanche photodiodes (APDs)},
+ Owner = {paul},
+ Publisher = {OSA},
+ Timestamp = {2012.10.24}
+}
+
+ at PhdThesis{Burkhardt2010,
+ Title = {Electron multiplying CCD – based detection in Fluorescence Correlation Spectroscopy and measurements in living zebrafish embryos},
+ Author = {Burkhardt, Markus},
+ School = {Biophysics, BIOTEC, Technische Universität Dresden, Tatzberg 47–51, 01307 Dresden, Germany},
+ Year = {2010},
+ Note = {\url{http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-61021}},
+
+ Owner = {paul},
+ Timestamp = {2012.10.24}
+}
+
+ at Article{Burkhardt:06,
+ Title = {Electron multiplying CCD based detection for spatially resolved fluorescence correlation spectroscopy},
+ Author = {Markus Burkhardt and Petra Schwille},
+ Journal = {Optics Express},
+ Year = {2006},
+
+ Month = {Jun},
+ Number = {12},
+ Pages = {5013--5020},
+ Volume = {14},
+
+ Abstract = {Fluorescence correlation spectroscopy (FCS) is carried out with an electron multiplying CCD (EMCCD). This new strategy is compared to standard detection by an avalanche photo diode showing good agreement with respect to the resulting autocorrelation curves. Applying different readout modes, a time resolution of 20 {\textmu}s can be achieved, which is sufficient to resolve the diffusion of free dye in solution. The advantages of implementing EMCCD cameras in [...]
+ Doi = {10.1364/OE.14.005013},
+ Keywords = {CCD, charge-coupled device; Medical optics and biotechnology; Fluorescence, laser-induced},
+ Publisher = {OSA}
+}
+
+ at Article{Chiantia2006,
+ Title = {Combined AFM and Two-Focus SFCS Study of Raft-Exhibiting Model Membranes},
+ Author = {Chiantia , Salvatore and Ries , Jonas and Kahya, Nicoletta and Schwille, Petra},
+ Journal = {ChemPhysChem},
+ Year = {2006},
+ Number = {11},
+ Pages = {2409--2418},
+ Volume = {7},
+
+ Doi = {10.1002/cphc.200600464},
+ ISSN = {1439-7641},
+ Keywords = {fluorescent probes, force measurements, membranes, sphingolipids},
+ Owner = {paul},
+ Publisher = {WILEY-VCH Verlag},
+ Timestamp = {2012.10.24}
+}
+
+ at Article{Dertinger2007,
+ Title = {Two-Focus Fluorescence Correlation Spectroscopy: A New Tool for Accurate and Absolute Diffusion Measurements},
+ Author = {Dertinger, Thomas and Pacheco, Victor and von der Hocht, Iris and Hartmann, Rudolf and Gregor, Ingo and Enderlein, Jörg},
+ Journal = {ChemPhysChem},
+ Year = {2007},
+ Number = {3},
+ Pages = {433--443},
+ Volume = {8},
+
+ Doi = {10.1002/cphc.200600638},
+ ISSN = {1439-7641},
+ Keywords = {diffusion coefficients, fluorescence spectroscopy, fluorescent dyes, time-resolved spectroscopy},
+ Owner = {paul},
+ Publisher = {WILEY-VCH Verlag},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Einstein1905,
+ Title = {Über die von der molekularkinetischen Theorie der Wärme geforderte Bewegung von in ruhenden Flüssigkeiten suspendierten Teilchen},
+ Author = {Einstein, A.},
+ Journal = {Annalen der Physik},
+ Year = {1905},
+ Number = {8},
+ Pages = {549--560},
+ Volume = {322},
+
+ Doi = {10.1002/andp.19053220806},
+ ISSN = {1521-3889},
+ Owner = {paul},
+ Publisher = {WILEY-VCH Verlag},
+ Timestamp = {2012.11.02}
+}
+
+ at Article{Elson1974,
+ Title = {Fluorescence correlation spectroscopy. I. Conceptual basis and theory},
+ Author = {Elson, Elliot L. and Magde, Douglas},
+ Journal = {Biopolymers},
+ Year = {1974},
+ Number = {1},
+ Pages = {1--27},
+ Volume = {13},
+
+ Doi = {10.1002/bip.1974.360130102},
+ ISSN = {1097-0282},
+ Owner = {paul},
+ Publisher = {Wiley Subscription Services, Inc., A Wiley Company},
+ Timestamp = {2012.09.24}
+}
+
+ at Article{Enderlein1999,
+ Title = {Highly Efficient Optical Detection of Surface-Generated Fluorescence},
+ Author = {J\"{o}rg Enderlein and Thomas Ruckstuhl and Stefan Seeger},
+ Journal = {Applied Optics},
+ Year = {1999},
+
+ Month = {Feb},
+ Number = {4},
+ Pages = {724--732},
+ Volume = {38},
+
+ Abstract = {We present a theoretical study of a new highly efficient system for optical light collection, designed for ultrasensitive fluorescence detection of surface-bound molecules. The main core of the system is a paraboloid glass segment acting as a mirror for collecting the fluorescence. A special feature of the system is its ability to sample not only fluorescence that is emitted below the angle of total internal reflection (the critical angle) but also particula [...]
+ Doi = {10.1364/AO.38.000724},
+ Keywords = {Geometric optical design; Microscopy; Detection; Fluorescence microscopy},
+ Owner = {paul},
+ Publisher = {OSA},
+ Timestamp = {2012.11.02}
+}
+
+ at Article{Foo2012,
+ Title = {Factors Affecting the Quantification of Biomolecular Interactions by Fluorescence Cross-Correlation Spectroscopy},
+ Author = {Foo, Y. H. and Naredi-Rainer, N. and Lamb, D. C. and Ahmed, S. and Wohland, T.},
+ Journal = {Biophys J},
+ Year = {2012},
+ Number = {5},
+ Pages = {1174--83},
+ Volume = {102},
+
+ Abstract = {Fluorescence cross-correlation spectroscopy (FCCS) is used to determine interactions and dissociation constants (K(d)s) of biomolecules. The determination of a K(d) depends on the accurate measurement of the auto- and cross-correlation function (ACF and CCF) amplitudes. In the case of complete binding, the ratio of the CCF/ACF amplitudes is expected to be 1. However, measurements performed on tandem fluorescent proteins (FPs), in which two different FPs are [...]
+ Doi = {10.1016/j.bpj.2012.01.040},
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at Article{Hansen1998,
+ Title = {Measuring Reversible Adsorption Kinetics of Small Molecules at Solid/Liquid Interfaces by Total Internal Reflection Fluorescence Correlation Spectroscopy},
+ Author = {Hansen, Richard L and Harris, Joel M},
+ Journal = {Analytical Chemistry},
+ Year = {1998},
+ Number = {20},
+ Pages = {4247--4256},
+ Volume = {70},
+
+ Doi = {10.1021/ac980925l},
+ Owner = {paul},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Hashmi2007,
+ Title = {Spatially extended FCS for visualizing and quantifying high-speed multiphase flows in microchannels},
+ Author = {Sara M. Hashmi and Michael Loewenberg and Eric R. Dufresne},
+ Journal = {Optics Express},
+ Year = {2007},
+
+ Month = {May},
+ Number = {10},
+ Pages = {6528--6533},
+ Volume = {15},
+
+ Abstract = {We report the development of spatially extended fluorescence correlation spectroscopy for visualizing and quantifying multiphase flows in microchannels. We employ simultaneous detection with a high-speed camera across the width of the channel, enabling investigation of the dynamics of the flow at short time scales. We take advantage of the flow to scan the sample past the fixed illumination, capturing frames up to 100 KHz. At these rates, we can resolve the [...]
+ Doi = {10.1364/OE.15.006528},
+ Keywords = {Velocimetry; Flow diagnostics; Fluorescence, laser-induced},
+ Owner = {paul},
+ Publisher = {OSA},
+ Timestamp = {2012.11.07}
+}
+
+ at Article{Hassler2005,
+ Title = {High Count Rates with Total Internal Reflection Fluorescence Correlation Spectroscopy},
+ Author = {Hassler, Kai and Anhut, Tiemo and Rigler, Rudolf and G\"{o}sch, Michael and Lasser, Theo},
+ Journal = {Biophysical Journal},
+ Year = {2005},
+
+ Month = jan,
+ Number = {1},
+ Pages = {L01--L03},
+ Volume = {88},
+
+ Doi = {10.1529/biophysj.104.053884},
+ ISSN = {0006-3495},
+ Owner = {paul},
+ Publisher = {Cell Press},
+ Refid = {S0006-3495(05)73079-4 DOI - 10.1529/biophysj.104.053884},
+ Timestamp = {2012.05.02}
+}
+
+ at Article{Hassler2005a,
+ Title = {Total internal reflection fluorescence correlation spectroscopy (TIR-FCS) with low background and high count-rate per molecule},
+ Author = {Kai Hassler and Marcel Leutenegger and Per Rigler and Ramachandra Rao and Rudolf Rigler and Michael G\"{o}sch and Theo Lasser},
+ Journal = {Optics Express},
+ Year = {2005},
+
+ Month = {Sep},
+ Number = {19},
+ Pages = {7415--7423},
+ Volume = {13},
+
+ Abstract = {We designed a fluorescence correlation spectroscopy (FCS) system for measurements on surfaces. The system consists of an objective-type total internal reflection fluorescence (TIRF) microscopy setup, adapted to measure FCS. Here, the fluorescence exciting evanescent wave is generated by epi-illumination through the periphery of a high NA oil-immersion objective. The main advantages with respect to conventional FCS systems are an improvement in terms of count [...]
+ Doi = {10.1364/OPEX.13.007415},
+ Keywords = {Spectroscopy, fluorescence and luminescence; Spectroscopy, surface; Fluorescence, laser-induced},
+ Owner = {paul},
+ Publisher = {OSA},
+ Timestamp = {2012.09.21}
+}
+
+ at Article{Haupts1998,
+ Title = {Dynamics of fluorescence fluctuations in green fluorescent protein observed by fluorescence correlation spectroscopy},
+ Author = {Haupts, Ulrich and Maiti, Sudipta and Schwille, Petra and Webb, Watt W.},
+ Journal = {Proceedings of the National Academy of Sciences},
+ Year = {1998},
+ Number = {23},
+ Pages = {13573-13578},
+ Volume = {95},
+
+ Abstract = {We have investigated the pH dependence of the dynamics of conformational fluctuations of green fluorescent protein mutants EGFP (F64L/S65T) and GFP-S65T in small ensembles of molecules in solution by using fluorescence correlation spectroscopy (FCS). FCS utilizes time-resolved measurements of fluctuations in the molecular fluorescence emission for determination of the intrinsic dynamics and thermodynamics of all processes that affect the fluorescence. Fluore [...]
+ Doi = {10.1073/pnas.95.23.13573},
+ Owner = {paul},
+ Timestamp = {2012.11.01}
+}
+
+ at Article{Haustein2007,
+ Title = {Fluorescence Correlation Spectroscopy: Novel Variations of an Established Technique},
+ Author = {Haustein, Elke and Schwille, Petra},
+ Journal = {Annual Review of Biophysics and Biomolecular Structure},
+ Year = {2007},
+ Number = {1},
+ Pages = {151-169},
+ Volume = {36},
+
+ Doi = {10.1146/annurev.biophys.36.040306.132612},
+ Owner = {paul},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Helmers2003,
+ Title = {CMOS vs. CCD sensors in speckle interferometry},
+ Author = {Heinz Helmers and Markus Schellenberg},
+ Journal = {Optics \& Laser Technology},
+ Year = {2003},
+ Number = {8},
+ Pages = {587 - 595},
+ Volume = {35},
+
+ Doi = {10.1016/S0030-3992(03)00078-1},
+ ISSN = {0030-3992},
+ Keywords = {CCD sensors},
+ Owner = {paul},
+ Timestamp = {2012.10.06}
+}
+
+ at Article{Holekamp2008,
+ Title = {Fast Three-Dimensional Fluorescence Imaging of Activity in Neural Populations by Objective-Coupled Planar Illumination Microscopy},
+ Author = {Terrence F. Holekamp and Diwakar Turaga and Timothy E. Holy},
+ Journal = {Neuron},
+ Year = {2008},
+ Number = {5},
+ Pages = {661 - 672},
+ Volume = {57},
+
+ Doi = {10.1016/j.neuron.2008.01.011},
+ ISSN = {0896-6273},
+ Keywords = {SYSBIO},
+ Owner = {paul},
+ Timestamp = {2012.11.13}
+}
+
+ at Article{Humpolickova2006,
+ Title = {Probing Diffusion Laws within Cellular Membranes by Z-Scan Fluorescence Correlation Spectroscopy},
+ Author = {Jana Humpol\'{i}\v{c}kov\'{a} and Ellen Gielen and Ale\v{s} Benda and Veronika Fagulova and Jo Vercammen and Martin vandeVen and Martin Hof and Marcel Ameloot and Yves Engelborghs},
+ Journal = {Biophysical Journal},
+ Year = {2006},
+ Number = {3},
+ Pages = {L23 - L25},
+ Volume = {91},
+
+ Doi = {10.1529/biophysj.106.089474},
+ ISSN = {0006-3495},
+ Owner = {paul},
+ Timestamp = {2012.10.25}
+}
+
+ at Article{Jin2004,
+ Title = {Near-surface velocimetry using evanescent wave illumination},
+ Author = {Jin, S. and Huang, P. and Park, J. and Yoo, J. Y. and Breuer, K. S.},
+ Journal = {Experiments in Fluids},
+ Year = {2004},
+ Pages = {825-833},
+ Volume = {37},
+
+ Affiliation = {School of Mechanical and Aerospace Engineering Seoul National University Seoul 151-742 Korea},
+ Doi = {10.1007/s00348-004-0870-7},
+ ISSN = {0723-4864},
+ Issue = {6},
+ Keyword = {Technik},
+ Owner = {paul},
+ Publisher = {Springer Berlin / Heidelberg},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Kannan2006,
+ Title = {Electron Multiplying Charge-Coupled Device Camera Based Fluorescence Correlation Spectroscopy},
+ Author = {Kannan, Balakrishnan and Har, Jia Yi and Liu, Ping and Maruyama, Ichiro and Ding, Jeak Ling and Wohland, Thorsten},
+ Journal = {Analytical Chemistry},
+ Year = {2006},
+ Number = {10},
+ Pages = {3444-3451},
+ Volume = {78},
+
+ Doi = {10.1021/ac0600959},
+ Owner = {paul},
+ Timestamp = {2012.11.07}
+}
+
+ at Article{Kim2007,
+ Title = {Fluorescence correlation spectroscopy in living cells},
+ Author = {Kim, S. A. and Heinze, K. G. and Schwille, P.},
+ Journal = {Nat Methods},
+ Year = {2007},
+ Number = {11},
+ Pages = {963--73},
+ Volume = {4},
+
+ Abstract = {Fluorescence correlation spectroscopy (FCS) is an ideal analytical tool for studying concentrations, propagation, interactions and internal dynamics of molecules at nanomolar concentrations in living cells. FCS analyzes minute fluorescence-intensity fluctuations about the equilibrium of a small ensemble (<10(3)) of molecules. These fluctuations act like a 'fingerprint' of a molecular species detected when entering and leaving a femtoliter-sized optically def [...]
+ Doi = {10.1038/nmeth1104},
+ Keywords = {Animals Biological Transport Cytophotometry/instrumentation/*methods Eukaryotic Cells/*metabolism Fluorescent Dyes/chemistry Humans Kinetics Models, Biological Proteins/chemistry/metabolism Spectrometry, Fluorescence/instrumentation/methods Staining and Labeling},
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at InCollection{Kohl2005,
+ Title = {Fluorescence Correlation Spectroscopy with Autofluorescent Proteins},
+ Author = {Kohl, Tobias and Schwille, Petra},
+ Booktitle = {Microscopy Techniques},
+ Publisher = {Springer Berlin / Heidelberg},
+ Year = {2005},
+ Editor = {Rietdorf, Jens},
+ Pages = {1316-1317},
+ Series = {Advances in Biochemical Engineering/Biotechnology},
+ Volume = {95},
+
+ Affiliation = {Pastor-Sander-Bogen 92 37083 Göttingen Germany},
+ Doi = {10.1007/b102212},
+ ISBN = {978-3-540-23698-6},
+ Keyword = {Chemistry and Materials Science},
+ Owner = {paul},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Koppel1974,
+ Title = {Statistical accuracy in fluorescence correlation spectroscopy},
+ Author = {Koppel, D.},
+ Journal = {Phys Rev A},
+ Year = {1974},
+ Pages = {1938--1945},
+ Volume = {10},
+
+ Doi = {10.1103/physreva.10.1938},
+ Keywords = {FCS},
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at Article{Korlach1999,
+ Title = {Characterization of lipid bilayer phases by confocal microscopy and fluorescence correlation spectroscopy},
+ Author = {Korlach, J. and Schwille, P. and Webb, W. W. and Feigenson, G. W.},
+ Journal = {Proc Natl Acad Sci U S A},
+ Year = {1999},
+ Number = {15},
+ Pages = {8461--6},
+ Volume = {96},
+
+ Abstract = {We report the application of confocal imaging and fluorescence correlation spectroscopy (FCS) to characterize chemically well-defined lipid bilayer models for biomembranes. Giant unilamellar vesicles of dilauroyl phosphatidylcholine/dipalmitoyl phosphatidylcholine (DLPC/DPPC)/cholesterol were imaged by confocal fluorescence microscopy with two fluorescent probes, 1, 1'-dieicosanyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI-C(20)) and 2-(4,4-diflu [...]
+ Doi = {10.1073/pnas.96.15.8461},
+ Keywords = {Carbocyanines Cholesterol/chemistry Diffusion Fluorescent Dyes Lipid Bilayers/*chemistry Liposomes/chemistry Microscopy, Confocal Phospholipids/chemistry Spectrometry, Fluorescence},
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at Article{Korson1969,
+ Title = {Viscosity of water at various temperatures},
+ Author = {Korson, Lawrence and Drost-Hansen, Walter and Millero, Frank J.},
+ Journal = {The Journal of Physical Chemistry},
+ Year = {1969},
+ Number = {1},
+ Pages = {34-39},
+ Volume = {73},
+
+ Doi = {10.1021/j100721a006},
+ Owner = {paul},
+ Timestamp = {2012.10.29}
+}
+
+ at Book{LandauLifshitsStatPhys,
+ Title = {{Statistical Physics, Third Edition, Part 1: Volume 5 (Course of Theoretical Physics, Volume 5)}},
+ Author = {Landau, L. D. and Lifshitz, E. M.},
+ Publisher = {Butterworth-Heinemann},
+ Year = {1980},
+ Edition = {3},
+ Month = jan,
+
+ Abstract = {{A lucid presentation of statistical physics and thermodynamics which develops from the general principles to give a large number of applications of the theory.}},
+ Citeulike-article-id = {1284487},
+ Citeulike-linkout-0 = {http://www.amazon.ca/exec/obidos/redirect?tag=citeulike09-20\&path=ASIN/0750633727},
+ Citeulike-linkout-1 = {http://www.amazon.de/exec/obidos/redirect?tag=citeulike01-21\&path=ASIN/0750633727},
+ Citeulike-linkout-2 = {http://www.amazon.fr/exec/obidos/redirect?tag=citeulike06-21\&path=ASIN/0750633727},
+ Citeulike-linkout-3 = {http://www.amazon.jp/exec/obidos/ASIN/0750633727},
+ Citeulike-linkout-4 = {http://www.amazon.co.uk/exec/obidos/ASIN/0750633727/citeulike00-21},
+ Citeulike-linkout-5 = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0750633727},
+ Citeulike-linkout-6 = {http://www.worldcat.org/isbn/0750633727},
+ Citeulike-linkout-7 = {http://books.google.com/books?vid=ISBN0750633727},
+ Citeulike-linkout-8 = {http://www.amazon.com/gp/search?keywords=0750633727\&index=books\&linkCode=qs},
+ Citeulike-linkout-9 = {http://www.librarything.com/isbn/0750633727},
+ Day = {15},
+ HowPublished = {Paperback},
+ ISBN = {0750633727},
+ Keywords = {fermi\_statistics, statistical\_physics},
+ Owner = {paul},
+ Posted-at = {2011-03-03 11:38:41},
+ Priority = {2},
+ Timestamp = {2012.02.03}
+}
+
+ at Article{Leutenegger2012,
+ Title = {Fluorescence correlation spectroscopy with a total internal reflection fluorescence STED microscope (TIRF-STED-FCS)},
+ Author = {Marcel Leutenegger and Christian Ringemann and Theo Lasser and Stefan W. Hell and Christian Eggeling},
+ Journal = {Optics Express},
+ Year = {2012},
+
+ Month = {Feb},
+ Number = {5},
+ Pages = {5243--5263},
+ Volume = {20},
+
+ Abstract = {We characterize a novel fluorescence microscope which combines the high spatial discrimination of a total internal reflection epi-fluorescence (epi-TIRF) microscope with that of stimulated emission depletion (STED) nanoscopy. This combination of high axial confinement and dynamic-active lateral spatial discrimination of the detected fluorescence emission promises imaging and spectroscopy of the structure and function of cell membranes at the macro-molecular [...]
+ Doi = {10.1364/OE.20.005243},
+ Keywords = {Diffraction; Fluorescence microscopy; Fluorescence},
+ Owner = {paul},
+ Publisher = {OSA},
+ Timestamp = {2012.09.21}
+}
+
+ at Article{Lieto2003a,
+ Title = {Ligand-Receptor Kinetics Measured by Total Internal Reflection with Fluorescence Correlation Spectroscopy},
+ Author = {Lieto, Alena M. and Cush, Randall C. and Thompson, Nancy L.},
+ Journal = {Biophysical Journal},
+ Year = {2003},
+
+ Month = nov,
+ Number = {5},
+ Pages = {3294--3302},
+ Volume = {85},
+
+ Doi = {10.1016/S0006-3495(03)74748-1},
+ ISSN = {0006-3495},
+ Owner = {paul},
+ Publisher = {Cell Press},
+ Refid = {S0006-3495(03)74748-1 DOI - 10.1016/S0006-3495(03)74748-1},
+ Timestamp = {2012.09.21}
+}
+
+ at Article{Lieto2003,
+ Title = {Lateral Diffusion from Ligand Dissociation and Rebinding at Surfaces†},
+ Author = {Lieto, Alena M. and Lagerholm, B. Christoffer and Thompson, Nancy L.},
+ Journal = {Langmuir},
+ Year = {2003},
+ Number = {5},
+ Pages = {1782-1787},
+ Volume = {19},
+
+ Doi = {10.1021/la0261601},
+ Owner = {paul},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Lieto2004,
+ Title = {Total Internal Reflection with Fluorescence Correlation Spectroscopy: Nonfluorescent Competitors},
+ Author = {Alena M. Lieto and Nancy L. Thompson},
+ Journal = {Biophysical Journal},
+ Year = {2004},
+ Number = {2},
+ Pages = {1268 - 1278},
+ Volume = {87},
+
+ Doi = {10.1529/biophysj.103.035030},
+ ISSN = {0006-3495},
+ Owner = {paul},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Muller2014,
+ Title = {Scanning fluorescence correlation spectroscopy ({SFCS}) with a scan path perpendicular to the membrane plane},
+ Author = {M\"{u}ller, P. and Schwille, P. and Weidemann, T.},
+ Journal = {Methods Mol Biol},
+ Year = {2014},
+ Pages = {635--51},
+ Volume = {1076},
+
+ __markedentry = {[paul:6]},
+ Abstract = {Scanning fluorescence correlation spectroscopy (SFCS) with a scan path perpendicular to the membrane plane was introduced to measure diffusion and interactions of fluorescent components in free-standing biomembranes. Using a confocal laser scanning microscope (CLSM), the open detection volume is repeatedly scanned through the membrane at a kHz frequency. The fluorescence photons emitted from the detection volume are continuously recorded and stored in a file [...]
+ Doi = {10.1007/978-1-62703-649-8_29},
+ Owner = {paul},
+ Timestamp = {2014.01.25}
+}
+
+ at Article{Magde1972,
+ Title = {Thermodynamic Fluctuations in a Reacting System - Measurement by Fluorescence Correlation Spectroscopy},
+ Author = {Magde, Douglas and Elson, Elliot and Webb, W. W.},
+ Journal = {Physical Review Letters},
+ Year = {1972},
+
+ Month = {Sep},
+ Pages = {705--708},
+ Volume = {29},
+
+ Doi = {10.1103/PhysRevLett.29.705},
+ Issue = {11},
+ Owner = {paul},
+ Publisher = {American Physical Society},
+ Timestamp = {2012.11.01}
+}
+
+ at Article{Magde1974,
+ Title = {Fluorescence correlation spectroscopy. II. An experimental realization},
+ Author = {Magde, Douglas and Elson, Elliot L. and Webb, Watt W.},
+ Journal = {Biopolymers},
+ Year = {1974},
+ Number = {1},
+ Pages = {29--61},
+ Volume = {13},
+
+ Doi = {10.1002/bip.1974.360130103},
+ ISSN = {1097-0282},
+ Owner = {paul},
+ Publisher = {Wiley Subscription Services, Inc., A Wiley Company},
+ Timestamp = {2012.09.21}
+}
+
+ at Article{Magde1978,
+ Title = {Fluorescence correlation spectroscopy. III. Uniform translation and laminar flow},
+ Author = {Magde, D. and Webb, W. W. and Elson, E. L.},
+ Journal = {Biopolymers},
+ Year = {1978},
+ Pages = {361--376},
+ Volume = {17},
+
+ Doi = {10.1002/bip.1978.360170208},
+ Keywords = {FCS; laminar flow; capillary electrophoresis},
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at Article{Meseth1999,
+ Title = {Resolution of fluorescence correlation measurements},
+ Author = {Meseth, U. and Wohland, T. and Rigler, R. and Vogel, H.},
+ Journal = {Biophys J},
+ Year = {1999},
+ Pages = {1619--1631},
+ Volume = {76},
+
+ Doi = {10.1016/S0006-3495(99)77321-2},
+ Keywords = {Diffusion, Multiple components},
+
+ Abstract = {The resolution limit of fluorescence correlation spectroscopy for two-component solutions is investigated theoretically and experimentally. The autocorrelation function for two different particles in solution were computed, statistical noise was added, and the resulting curve was fitted with a least squares fit. These simulations show that the ability to distinguish between two different molecular species in solution depends strongly on the number of photons [...]
+ Owner = {TW},
+ Timestamp = {2014.01.27}
+}
+
+ at Article{Nitsche2004,
+ Title = {A Transient Diffusion Model Yields Unitary Gap Junctional Permeabilities from Images of Cell-to-Cell Fluorescent Dye Transfer Between Xenopus Oocytes},
+ Author = {Johannes M. Nitsche and Hou-Chien Chang and Paul A. Weber and Bruce J. Nicholson},
+ Journal = {Biophysical Journal},
+ Year = {2004},
+ Number = {4},
+ Pages = {2058 - 2077},
+ Volume = {86},
+
+ Doi = {10.1016/S0006-3495(04)74267-8},
+ ISSN = {0006-3495},
+ Owner = {paul},
+ Timestamp = {2012.11.08}
+}
+
+ at Article{Ohsugi2009,
+ Title = {Multipoint fluorescence correlation spectroscopy with total internal reflection fluorescence microscope},
+ Author = {Ohsugi, Yu and Kinjo, Masataka},
+ Journal = {Journal of Biomedical Optics},
+ Year = {2009},
+ Number = {1},
+ Pages = {014030-014030-4},
+ Volume = {14},
+
+ Doi = {10.1117/1.3080723},
+ Owner = {paul},
+ Timestamp = {2012.11.12}
+}
+
+ at Article{Ohsugi2006,
+ Title = {Lateral mobility of membrane-binding proteins in living cells measured by total internal reflection fluorescence correlation spectroscopy.},
+ Author = {Ohsugi, Yu and Saito, Kenta and Tamura, Mamoru and Kinjo, Masataka},
+ Journal = {Biophysical Journal},
+ Year = {2006},
+ Number = {9},
+ Pages = {3456--3464},
+ Volume = {91},
+
+ Doi = {10.1529/biophysj.105.074625},
+ Owner = {paul},
+ Publisher = {Biophysical Society},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Palmer1987,
+ Title = {Theory of sample translation in fluorescence correlation spectroscopy.},
+ Author = {A. G. Palmer and N. L. Thompson},
+ Journal = {Biophysical Journal},
+ Year = {1987},
+
+ Month = {Feb},
+ Number = {2},
+ Pages = {339--343},
+ Volume = {51},
+
+ Abstract = {New applications of the technique of fluorescence correlation spectroscopy (FCS) require lateral translation of the sample through a focused laser beam (Peterson, N.O., D.C. Johnson, and M.J. Schlesinger, 1986, Biophys. J., 49:817-820). Here, the effect of sample translation on the shape of the FCS autocorrelation function is examined in general. It is found that if the lateral diffusion coefficients of the fluorescent species obey certain conditions, then t [...]
+ Doi = {10.1016/S0006-3495(87)83340-4},
+ Keywords = {Kinetics; Lasers; Mathematics; Models, Theoretical; Spectrometry, Fluorescence, methods},
+ Language = {eng},
+ Medline-pst = {ppublish},
+ Owner = {paul},
+ Pii = {S0006-3495(87)83340-4},
+ Pmid = {3828464},
+ Timestamp = {2012.11.02}
+}
+
+ at Article{Pero2006-06,
+ Title = {Size dependence of protein diffusion very close to membrane surfaces: measurement by total internal reflection with fluorescence correlation spectroscopy.},
+ Author = {Pero, JK and Haas, EM and Thompson, NL},
+ Journal = {The Journal of Physical Chemistry. B},
+ Year = {2006},
+ Number = {5},
+ Pages = {10910-8},
+ Volume = {110},
+
+ Doi = {10.1021/jp056990y},
+ ISSN = {1520-6106},
+ Owner = {paul},
+ Timestamp = {2012.09.21}
+}
+
+ at Article{Petrasek2010,
+ Title = {Scanning {FCS} for the characterization of protein dynamics in live cells},
+ Author = {Petr\'{a}\v{s}ek, Zden\v{e}k and Ries, J. and Schwille, P.},
+ Journal = {Methods Enzymol},
+ Year = {2010},
+ Pages = {317--43},
+ Volume = {472},
+
+ Abstract = {Scanning fluorescence correlation spectroscopy (sFCS) is the generic term for a group of fluorescence correlation techniques where the measurement volume is moved across the sample in a defined way. The introduction of scanning is motivated by its ability to alleviate or remove several distinct problems often encountered in standard FCS, and thus, to extend the range of applicability of fluorescence correlation methods in biological systems. These problems i [...]
+ Doi = {10.1016/s0076-6879(10)72005-x},
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at Article{Petrasek2008,
+ Title = {Precise Measurement of Diffusion Coefficients using Scanning Fluorescence Correlation Spectroscopy},
+ Author = {Petr\'{a}\v{s}ek, Zden\v{e}k and Schwille, Petra},
+ Journal = {Biophysical Journal},
+ Year = {2008},
+
+ Month = feb,
+ Number = {4},
+ Pages = {1437--1448},
+ Volume = {94},
+
+ Doi = {10.1529/biophysj.107.108811},
+ ISSN = {0006-3495},
+ Owner = {paul},
+ Publisher = {Cell Press},
+ Refid = {S0006-3495(08)70660-X DOI - 10.1529/biophysj.107.108811},
+ Timestamp = {2012.05.20}
+}
+
+ at InCollection{Petrov:2008,
+ Title = {State of the Art and Novel Trends in Fluorescence Correlation Spectroscopy},
+ Author = {Petrov, E. P. and Schwille, P.},
+ Booktitle = {Standardization and Quality Assurance in Fluorescence Measurements II},
+ Publisher = {Springer Berlin Heidelberg},
+ Year = {2008},
+ Editor = {Resch-Genger, Ute},
+ Pages = {145-197},
+ Series = {Springer Series on Fluorescence},
+ Volume = {6},
+
+ Affiliation = {Biophysics, BIOTEC, Technische Universität Dresden, Tatzberg 47–51, 01307 Dresden, Germany},
+ Doi = {10.1007/4243_2008_032},
+ ISBN = {978-3-540-70571-0},
+ Keyword = {Chemistry}
+}
+
+ at Article{Qian1991,
+ Title = {Analysis of confocal laser-microscope optics for 3-D fluorescence correlation spectroscopy},
+ Author = {Hong Qian and Elliot L. Elson},
+ Journal = {Applied Optics},
+ Year = {1991},
+
+ Month = {Apr},
+ Number = {10},
+ Pages = {1185--1195},
+ Volume = {30},
+
+ Abstract = {Quantitative fluorescence correlation spectroscopy (FCS) and fluorescence photobleaching recovery (FPR) measurements in bulk solution require a well characterized confocal laser microscope optical system. The introduction of a characteristic function, the collection efficiency function (CEF), provides a quantitative theoretical analysis of this system, which yields an interpretation of the FCS and FPR measurements in three dimensions. We demonstrate that whe [...]
+ Doi = {10.1364/AO.30.001185},
+ Owner = {paul},
+ Publisher = {OSA},
+ Timestamp = {2012.11.02}
+}
+
+ at Article{Richter2006,
+ Title = {Formation of Solid-Supported Lipid Bilayers: An Integrated View},
+ Author = {Richter, Ralf P. and Bérat, Rémi and Brisson, Alain R.},
+ Journal = {Langmuir},
+ Year = {2006},
+ Number = {8},
+ Pages = {3497-3505},
+ Volume = {22},
+
+ Doi = {10.1021/la052687c},
+ Owner = {paul},
+ Timestamp = {2012.11.12}
+}
+
+ at PhdThesis{Ries:08,
+ Title = {Advanced Fluorescence Correlation Techniques to Study Membrane Dynamics},
+ Author = {Ries, E.},
+ School = {Biophysics, BIOTEC, Technische Universität Dresden, Tatzberg 47–51, 01307 Dresden, Germany},
+ Year = {2008},
+ Note = {\url{http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1219846317196-73420}}
+}
+
+ at Article{Ries2009,
+ Title = {Accurate Determination of Membrane Dynamics with Line-Scan FCS},
+ Author = {Jonas Ries and Salvatore Chiantia and Petra Schwille},
+ Journal = {Biophysical Journal},
+ Year = {2009},
+ Number = {5},
+ Pages = {1999 - 2008},
+ Volume = {96},
+
+ Doi = {10.1016/j.bpj.2008.12.3888},
+ ISSN = {0006-3495},
+ Owner = {paul},
+ Timestamp = {2012.11.08}
+}
+
+ at Article{Ries2010,
+ Title = {A comprehensive framework for fluorescence cross-correlation spectroscopy},
+ Author = {Ries, J. and Petr\'{a}\v{s}ek, Zden\v{e}k and Garcia-Saez, A. J. and Schwille, P.},
+ Journal = {New Journal of Physics},
+ Year = {2010},
+ Number = {11},
+ Pages = {113009},
+ Volume = {12},
+
+ Abstract = {Dual-colour fluorescence cross-correlation spectroscopy is a powerful method of studying binding between labelled biomolecules in vitro as well as in vivo. However, numerous artefacts and experimental complexities complicate quantitative measurements. Here, we show that a combination of dual-colour fluorescence correlation spectroscopy (FCS) with dual-focus FCS avoids artefacts due to chromatic aberrations or saturation and circumvents the calibration of the [...]
+ Doi = {10.1088/1367-2630/12/11/113009},
+ Keywords = {living cells membrane dynamics diffusion molecules accurate fret fcs},
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at Article{Ries2008390,
+ Title = {Total Internal Reflection Fluorescence Correlation Spectroscopy: Effects of Lateral Diffusion and Surface-Generated Fluorescence},
+ Author = {Jonas Ries and Eugene P. Petrov and Petra Schwille},
+ Journal = {Biophysical Journal},
+ Year = {2008},
+ Number = {1},
+ Pages = {390 - 399},
+ Volume = {95},
+
+ Doi = {10.1529/biophysj.107.126193},
+ ISSN = {0006-3495}
+}
+
+ at Article{Ries2008,
+ Title = {New concepts for fluorescence correlation spectroscopy on membranes},
+ Author = {Ries, Jonas and Schwille, Petra},
+ Journal = {Physical Chemistry Chemical Physics},
+ Year = {2008},
+ Number = {24},
+ Pages = {--},
+ Volume = {10},
+
+ Abstract = {Fluorescence correlation spectroscopy (FCS) is a powerful tool to measure useful physical quantities such as concentrations, diffusion coefficients, diffusion modes or binding parameters, both in model and cell membranes. However, it can suffer from severe artifacts, especially in non-ideal systems. Here we assess the potential and limitations of standard confocal FCS on lipid membranes and present recent developments which facilitate accurate and quantitati [...]
+ Doi = {10.1039/b718132a},
+ ISSN = {1463-9076},
+ Owner = {paul},
+ Publisher = {The Royal Society of Chemistry},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Ries2006,
+ Title = {Studying slow membrane dynamics with continuous wave scanning fluorescence correlation spectroscopy},
+ Author = {Ries, J. and Schwille, P.},
+ Journal = {Biophys J},
+ Year = {2006},
+ Number = {5},
+ Pages = {1915--24},
+ Volume = {91},
+
+ __markedentry = {[paul:6]},
+ Abstract = {Here we discuss the application of scanning fluorescence correlation spectroscopy (SFCS) using continuous wave excitation to analyze membrane dynamics. The high count rate per molecule enables the study of very slow diffusion in model and cell membranes, as well as the application of two-foci fluorescence cross-correlation spectroscopy for parameter-free determination of diffusion constants. The combination with dual-color fluorescence cross-correlation spec [...]
+ Doi = {10.1529/biophysj.106.082297},
+ Keywords = {Biological Transport, Active/physiology Cell Membrane/*chemistry/*metabolism Diffusion Membrane Proteins/analysis/*chemistry/*metabolism Spectrometry, Fluorescence/*methods Time Factors},
+ Owner = {paul},
+ Timestamp = {2014.01.25}
+}
+
+ at Article{Rigler1993,
+ Title = {Fluorescence correlation spectroscopy with high count rate and low background: analysis of translational diffusion},
+ Author = {Rigler, R. and Mets, {\"U}. and Widengren, J. and Kask, P.},
+ Journal = {European Biophysics Journal},
+ Year = {1993},
+ Pages = {169-175},
+ Volume = {22},
+
+ Doi = {10.1007/BF00185777},
+ ISSN = {0175-7571},
+ Issue = {3},
+ Keywords = {Fluorescence correlation spectroscopy; Fluorescence intensity fluctuations; Translational diffusion; Epifluorescence microscope; Silicon photon counter},
+ Language = {English},
+ Owner = {paul},
+ Publisher = {Springer-Verlag},
+ Timestamp = {2012.11.02}
+}
+
+ at Article{Rippe2000,
+ Title = {Simultaneous binding of two {DNA} duplexes to the NtrC-enhancer complex studied by two-color fluorescence cross-correlation spectroscopy},
+ Author = {Rippe, K.},
+ Journal = {Biochemistry},
+ Year = {2000},
+ Number = {9},
+ Pages = {2131--9},
+ Volume = {39},
+
+ Abstract = {The transcription activator protein NtrC (nitrogen regulatory protein C, also termed NR(I)) can catalyze the transition of Escherichia coli RNA polymerase complexed with the sigma(54) factor (RNAP x sigma(54)) from the closed complex (RNAP x sigma(54) bound at the promoter) to the open complex (melting of the promoter DNA). This process involves phosphorylation of NtrC (NtrC-P), assembly of an octameric NtrC-P complex at the enhancer DNA sequence, interactio [...]
+ Doi = {10.1021/bi9922190},
+ Keywords = {Bacterial Proteins/chemistry/*metabolism Base Sequence DNA, Bacterial/chemistry/*metabolism DNA-Binding Proteins/chemistry/*metabolism Diffusion *Enhancer Elements (Genetics) Escherichia coli/chemistry/genetics Escherichia coli Proteins Models, Chemical Models, Molecular Molecular Sequence Data Nucleic Acid Heteroduplexes/chemistry/*metabolism PII Nitrogen Regulatory Proteins Phosphorylation Protein Binding Reproducibility of Results Spectrometry, Fluorescen [...]
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at Article{Ruan2004,
+ Title = {Spatial-Temporal Studies of Membrane Dynamics: Scanning Fluorescence Correlation Spectroscopy (SFCS)},
+ Author = {Ruan, Qiaoqiao and Cheng, Melanie A. and Levi, Moshe and Gratton, Enrico and Mantulin, William W.},
+ Journal = {Biophysical Journal},
+ Year = {2004},
+
+ Month = aug,
+ Number = {2},
+ Pages = {1260--1267},
+ Volume = {87},
+
+ Doi = {10.1529/biophysj.103.036483},
+ ISSN = {0006-3495},
+ Owner = {paul},
+ Publisher = {Cell Press},
+ Refid = {S0006-3495(04)73605-X DOI - 10.1529/biophysj.103.036483},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Sankaran2009,
+ Title = {Diffusion, Transport, and Cell Membrane Organization Investigated by Imaging Fluorescence Cross-Correlation Spectroscopy},
+ Author = {Sankaran, Jagadish and Manna, Manoj and Guo, Lin and Kraut, Rachel and Wohland, Thorsten},
+ Journal = {Biophysical Journal},
+ Year = {2009},
+
+ Month = nov,
+ Number = {9},
+ Pages = {2630--2639},
+ Volume = {97},
+
+ Doi = {10.1016/j.bpj.2009.08.025},
+ ISSN = {0006-3495},
+ Owner = {paul},
+ Publisher = {Cell Press},
+ Refid = {S0006-3495(09)01387-3 DOI - 10.1016/j.bpj.2009.08.025},
+ Timestamp = {2012.09.21}
+}
+
+ at Article{Sankaran2010,
+ Title = {ImFCS: a software for imaging FCS data analysis and visualization.},
+ Author = {Jagadish Sankaran and Xianke Shi and Liang Yoong Ho and Ernst H K Stelzer and Thorsten Wohland},
+ Journal = {Optics Express},
+ Year = {2010},
+
+ Month = {Dec},
+ Number = {25},
+ Pages = {25468--25481},
+ Volume = {18},
+
+ Abstract = {The multiplexing of fluorescence correlation spectroscopy (FCS), especially in imaging FCS using fast, sensitive array detectors, requires the handling of large amounts of data. One can easily collect in excess of 100,000 FCS curves a day, too many to be treated manually. Therefore, ImFCS, an open-source software which relies on standard image files was developed and provides a wide range of options for the calculation of spatial and temporal auto- and cross [...]
+ Doi = {10.1364/OE.18.025468},
+ Institution = {Singapore-MIT Alliance, National University of Singapore, E4-04-10, 4 Engineering Drive 3, 117576 Singapore.},
+ Keywords = {Algorithms; Pattern Recognition, Automated, methods; Software; Spectrometry, Fluorescence, methods},
+ Language = {eng},
+ Medline-pst = {ppublish},
+ Owner = {paul},
+ Pii = {208325},
+ Pmid = {21164894},
+ Timestamp = {2012.10.24}
+}
+
+ at Article{SbalzariniSPT,
+ Title = {Feature Point Tracking and Trajectory Analysis for Video Imaging in Cell Biology},
+ Author = {I. F. Sbalzarini and P. Koumoutsakos},
+ Journal = {Journal of Structural Biology},
+ Year = {2005},
+ Pages = {182-195},
+ Volume = {151(2)},
+
+ Doi = {10.1016/j.jsb.2005.06.002},
+ Owner = {paul},
+ Timestamp = {2012.10.16}
+}
+
+ at Article{Schatzel1990,
+ Title = {Noise on photon correlation data. I. Autocorrelation functions},
+ Author = {K. Sch{\"a}tzel},
+ Journal = {Quantum Optics: Journal of the European Optical Society Part B},
+ Year = {1990},
+ Number = {4},
+ Pages = {287},
+ Volume = {2},
+
+ Abstract = {An adequate analysis of photon correlation data requires knowledge about the statistical accuracy of the measured data. For the model of gamma-distributed intensities, that is including the effect of a finite intercept, the full covariance matrix is calculated for all the channels of the photon autocorrelation functions. A thorough discussion of multiple sample time correlation illuminates the importance of temporal averaging effects at large lag times. A pr [...]
+ Doi = {10.1088/0954-8998/2/4/002},
+ Owner = {paul},
+ Timestamp = {2012.11.02}
+}
+
+ at Article{Schwille1999,
+ Title = {Molecular dynamics in living cells observed by fluorescence correlation spectroscopy with one- and two-photon excitation},
+ Author = {Schwille, P. and Haupts, U. and Maiti, S. and Webb, W. W.},
+ Journal = {Biophys J},
+ Year = {1999},
+ Number = {4},
+ Pages = {2251--65},
+ Volume = {77},
+
+ Abstract = {Multiphoton excitation (MPE) of fluorescent probes has become an attractive alternative in biological applications of laser scanning microscopy because many problems encountered in spectroscopic measurements of living tissue such as light scattering, autofluorescence, and photodamage can be reduced. The present study investigates the characteristics of two-photon excitation (2PE) in comparison with confocal one-photon excitation (1PE) for intracellular appli [...]
+ Doi = {10.1016/s0006-3495(99)77065-7},
+ Keywords = {Animals Calibration Cell Line Cell Membrane/*metabolism/radiation effects Cell Wall/*metabolism/radiation effects Cytoplasm/*metabolism/radiation effects Diffusion Fluorescence Fluorescent Dyes/*metabolism Green Fluorescent Proteins Humans Kinetics Luminescent Proteins/metabolism Photochemistry *Photons Plant Leaves/cytology/radiation effects Plants, Toxic Rhodamines/metabolism Spectrometry, Fluorescence/instrumentation/*methods Tobacco},
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at Article{Schwille2000,
+ Title = {Fluorescence correlation spectroscopy reveals fast optical excitation-driven intramolecular dynamics of yellow fluorescent proteins},
+ Author = {Schwille, Petra and Kummer, Susanne and Heikal, Ahmed A. and Moerner, W. E. and Webb, Watt W.},
+ Journal = {Proceedings of the National Academy of Sciences},
+ Year = {2000},
+ Number = {1},
+ Pages = {151-156},
+ Volume = {97},
+
+ Abstract = {Fast excitation-driven fluctuations in the fluorescence emission of yellow-shifted green fluorescent protein mutants T203Y and T203F, with S65G/S72A, are discovered in the 10−6–10−3-s time range, by using fluorescence correlation spectroscopy at 10−8 M. This intensity-dependent flickering is conspicuous at high pH, with rate constants independent of pH and viscosity with a minor temperature effect. The mean flicker rate increases linearly with excitation int [...]
+ Doi = {10.1073/pnas.97.1.151},
+ Owner = {paul},
+ Timestamp = {2012.09.24}
+}
+
+ at Article{Schwille1997,
+ Title = {Dual-color fluorescence cross-correlation spectroscopy for multicomponent diffusional analysis in solution},
+ Author = {Schwille, P. and Meyer-Almes, F.J. and Rigler, R.},
+ Journal = {Biophysical Journal},
+ Year = {1997},
+
+ Month = apr,
+ Number = {4},
+ Pages = {1878--1886},
+ Volume = {72},
+
+ Doi = {10.1016/s0006-3495(97)78833-7},
+ ISSN = {0006-3495},
+ Owner = {paul},
+ Publisher = {Cell Press},
+ Refid = {S0006-3495(97)78833-7 DOI - 10.1016/S0006-3495(97)78833-7},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Scomparin2009,
+ Title = {Diffusion in supported lipid bilayers: Influence of substrate and preparation technique on the internal dynamics},
+ Author = {Scomparin, C. and Lecuyer, S. and Ferreira, M. and Charitat, T. and Tinland, B.},
+ Journal = {The European Physical Journal E: Soft Matter and Biological Physics},
+ Year = {2009},
+ Pages = {211-220},
+ Volume = {28},
+
+ Affiliation = {CNRS UPR 3118 CINAM 13288 Marseille Cedex 09 France},
+ Doi = {10.1140/epje/i2008-10407-3},
+ ISSN = {1292-8941},
+ Issue = {2},
+ Keyword = {Physik und Astronomie},
+ Owner = {paul},
+ Publisher = {Springer Berlin / Heidelberg},
+ Timestamp = {2012.10.22}
+}
+
+ at Article{Seu2007,
+ Title = {Effect of Surface Treatment on Diffusion and Domain Formation in Supported Lipid Bilayers},
+ Author = {Seu, Kalani J. and Pandey, Anjan P. and Haque, Farzin and Proctor, Elizabeth A. and Ribbe, Alexander E. and Hovis, Jennifer S.},
+ Journal = {Biophysical Journal},
+ Year = {2007},
+
+ Month = apr,
+ Number = {7},
+ Pages = {2445--2450},
+ Volume = {92},
+
+ Doi = {10.1529/biophysj.106.099721},
+ ISSN = {0006-3495},
+ Owner = {paul},
+ Publisher = {Cell Press},
+ Refid = {S0006-3495(07)71049-4 DOI - 10.1529/biophysj.106.099721},
+ Timestamp = {2012.10.22}
+}
+
+ at Article{Shannon1984,
+ Title = {Communication in the presence of noise},
+ Author = {Shannon, C.E.},
+ Journal = {Proceedings of the IEEE},
+ Year = {1984},
+
+ Month = {sept.},
+ Number = {9},
+ Pages = { 1192 - 1201},
+ Volume = {72},
+
+ Doi = {10.1109/PROC.1984.12998},
+ ISSN = {0018-9219},
+ Owner = {paul},
+ Timestamp = {2012.11.12}
+}
+
+ at Article{Skinner2005,
+ Title = {Position-sensitive scanning fluorescence correlation spectroscopy.},
+ Author = {Joseph P Skinner and Yan Chen and Joachim D Müller},
+ Journal = {Biophysical Journal},
+ Year = {2005},
+
+ Month = {Aug},
+ Number = {2},
+ Pages = {1288--1301},
+ Volume = {89},
+
+ Abstract = {Fluorescence correlation spectroscopy (FCS) uses a stationary laser beam to illuminate a small sample volume and analyze the temporal behavior of the fluorescence fluctuations within the stationary observation volume. In contrast, scanning FCS (SFCS) collects the fluorescence signal from a moving observation volume by scanning the laser beam. The fluctuations now contain both temporal and spatial information about the sample. To access the spatial informatio [...]
+ Doi = {10.1529/biophysj.105.060749},
+ Institution = {School of Physics and Astronomy, University of Minnesota, Minneapolis, 55455, USA. josephs at physics.umn.edu},
+ Keywords = {Algorithms; Image Enhancement, methods; Image Interpretation, Computer-Assisted, methods; Information Storage and Retrieval, methods; Microscopy, Confocal, methods; Reproducibility of Results; Sensitivity and Specificity; Spectrometry, Fluorescence, methods},
+ Language = {eng},
+ Medline-pst = {ppublish},
+ Owner = {paul},
+ Pii = {S0006-3495(05)72776-4},
+ Pmid = {15894645},
+ Timestamp = {2012.10.28}
+}
+
+ at Article{Starr2001,
+ Title = {Total Internal Reflection with Fluorescence Correlation Spectroscopy: Combined Surface Reaction and Solution Diffusion},
+ Author = {Tammy E. Starr and Nancy L. Thompson},
+ Journal = {Biophysical Journal},
+ Year = {2001},
+ Number = {3},
+ Pages = {1575 - 1584},
+ Volume = {80},
+
+ Doi = {10.1016/S0006-3495(01)76130-9},
+ ISSN = {0006-3495}
+}
+
+ at Article{Sutherland1905,
+ Title = {A dynamical theory of diffusion for non-electrolytes and the molecular mass of albumin},
+ Author = {Sutherland, William},
+ Journal = {Philosophical Magazine Series 6},
+ Year = {1905},
+ Number = {54},
+ Pages = {781-785},
+ Volume = {9},
+
+ __markedentry = {[paul]},
+ Doi = {10.1080/14786440509463331},
+ Owner = {paul},
+ Timestamp = {2012.11.14}
+}
+
+ at Article{Tamm1985,
+ Title = {Supported phospholipid bilayers},
+ Author = {Tamm, L.K. and McConnell, H.M.},
+ Journal = {Biophysical Journal},
+ Year = {1985},
+
+ Month = jan,
+ Number = {1},
+ Pages = {105--113},
+ Volume = {47},
+
+ Doi = {10.1016/S0006-3495(85)83882-0},
+ ISSN = {0006-3495},
+ Owner = {paul},
+ Publisher = {Cell Press},
+ Refid = {S0006-3495(85)83882-0 DOI - 10.1016/S0006-3495(85)83882-0},
+ Timestamp = {2012.10.29}
+}
+
+ at InCollection{Thomps:bookFCS2002,
+ Title = {Fluorescence Correlation Spectroscopy},
+ Author = {Thompson, Nancy},
+ Booktitle = {Topics in Fluorescence Spectroscopy},
+ Publisher = {Springer US},
+ Year = {2002},
+ Editor = {Lakowicz, Joseph and Geddes, Chris D. and Lakowicz, Joseph R.},
+ Pages = {337-378},
+ Series = {Topics in Fluorescence Spectroscopy},
+ Volume = {1},
+
+ Affiliation = {University of North Carolina at Chapel Hill Department of Chemistry Chapel Hill North Carolina 27599-3290 USA},
+ Doi = {10.1007/0-306-47057-8_6},
+ ISBN = {978-0-306-47057-8},
+ Keyword = {Biomedical and Life Sciences},
+ Owner = {paul},
+ Timestamp = {2012.01.10}
+}
+
+ at InBook{Thompson1991,
+ Title = {Fluorescence Correlation Spectroscopy},
+ Author = {Thompson, N.L.},
+ Editor = {Lankowicz, J.R.},
+ Pages = {337--378},
+ Publisher = {Plenum Press},
+ Year = {1991},
+
+ Address = {New York},
+ Edition = {Techniques},
+ Series = {Topics in Fluorescence Spectroscopy},
+ Volume = {1},
+
+ Booktitle = {Topics in Fluorescence Spectroscopy},
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at Article{Thompson1983,
+ Title = {Immunoglobulin surface-binding kinetics studied by total internal reflection with fluorescence correlation spectroscopy},
+ Author = {N.L. Thompson and D. Axelrod},
+ Journal = {Biophysical Journal},
+ Year = {1983},
+ Number = {1},
+ Pages = {103 - 114},
+ Volume = {43},
+
+ Doi = {10.1016/S0006-3495(83)84328-8},
+ ISSN = {0006-3495},
+ Owner = {paul},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Thompson1981,
+ Title = {Measuring surface dynamics of biomolecules by total internal reflection fluorescence with photobleaching recovery or correlation spectroscopy},
+ Author = {N.L. Thompson and T.P. Burghardt and D. Axelrod},
+ Journal = {Biophysical Journal},
+ Year = {1981},
+ Number = {3},
+ Pages = {435 - 454},
+ Volume = {33},
+
+ Doi = {10.1016/S0006-3495(81)84905-3},
+ ISSN = {0006-3495},
+ Owner = {paul},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Thompson1997,
+ Title = {Equilibrium, Kinetics, Diffusion and Self-Association of Proteins at Membrane Surfaces: Measurement by Total Internal Reflection Fluorescence Microscopy},
+ Author = {Thompson, Nancy L. and Drake, Andrew W. and Chen, Lixin and Broek, Willem Vanden},
+ Journal = {Photochemistry and Photobiology},
+ Year = {1997},
+ Number = {1},
+ Pages = {39--46},
+ Volume = {65},
+
+ Doi = {10.1111/j.1751-1097.1997.tb01875.x},
+ ISSN = {1751-1097},
+ Owner = {paul},
+ Publisher = {Blackwell Publishing Ltd},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Thompson1997a,
+ Title = {Total internal reflection fluorescence: applications in cellular biophysics},
+ Author = {Nancy L Thompson and B Christoffer Lagerholm},
+ Journal = {Current Opinion in Biotechnology},
+ Year = {1997},
+ Number = {1},
+ Pages = {58 - 64},
+ Volume = {8},
+
+ Doi = {10.1016/S0958-1669(97)80158-9},
+ ISSN = {0958-1669},
+ Owner = {paul},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Thompson2007,
+ Title = {Total internal reflection with fluorescence correlation spectroscopy},
+ Author = {Thompson, N. L. and Steele, B. L.},
+ Journal = {Nat Protoc},
+ Year = {2007},
+ Number = {4},
+ Pages = {878--90},
+ Volume = {2},
+
+ __markedentry = {[paul:6]},
+ Abstract = {Total internal reflection-fluorescence correlation spectroscopy (TIR-FCS) is an emerging technique that is used to measure events at or near an interface, including local fluorophore concentrations, local translational mobilities and the kinetic rate constants that describe the association and dissociation of fluorophores at the interface. TIR-FCS is also an extremely promising method for studying dynamics at or near the basal membranes of living cells. This [...]
+ Doi = {10.1038/nprot.2007.110},
+ Keywords = {Fluorescent Dyes/analysis Kinetics Ligands Spectrometry, Fluorescence/instrumentation/*methods},
+ Owner = {paul},
+ Timestamp = {2014.01.25}
+}
+
+ at Article{Toomre2001,
+ Title = {Lighting up the cell surface with evanescent wave microscopy},
+ Author = {Derek Toomre and Dietmar J. Manstein},
+ Journal = {Trends in Cell Biology},
+ Year = {2001},
+ Number = {7},
+ Pages = {298 - 303},
+ Volume = {11},
+
+ Doi = {10.1016/S0962-8924(01)02027-X},
+ ISSN = {0962-8924},
+ Keywords = {green-fluorescent protein (GFP)},
+ Owner = {paul},
+ Timestamp = {2012.02.14}
+}
+
+ at Article{Unruh2008,
+ Title = {Analysis of Molecular Concentration and Brightness from Fluorescence Fluctuation Data with an Electron Multiplied CCD Camera},
+ Author = {Unruh, Jay R. and Gratton, Enrico},
+ Journal = {Biophysical Journal},
+ Year = {2008},
+
+ Month = dec,
+ Number = {11},
+ Pages = {5385--5398},
+ Volume = {95},
+
+ Doi = {10.1529/biophysj.108.130310},
+ ISSN = {0006-3495},
+ Owner = {paul},
+ Publisher = {Cell Press},
+ Refid = {S0006-3495(08)78962-8 DOI - 10.1529/biophysj.108.130310},
+ Timestamp = {2012.09.21}
+}
+
+ at Article{Vacha2009,
+ Title = {Effects of Alkali Cations and Halide Anions on the DOPC Lipid Membrane},
+ Author = {V\'{a}cha, Robert and Siu, Shirley W. I. and Petrov, Michal and Böckmann, Rainer A. and Barucha-Kraszewska, Justyna and Jurkiewicz, Piotr and Hof, Martin and Berkowitz, Max L. and Jungwirth, Pavel},
+ Journal = {The Journal of Physical Chemistry A},
+ Year = {2009},
+ Number = {26},
+ Pages = {7235-7243},
+ Volume = {113},
+
+ Doi = {10.1021/jp809974e},
+ Owner = {paul},
+ Timestamp = {2012.10.24}
+}
+
+ at Article{Wachsmuth2000,
+ Title = {Anomalous diffusion of fluorescent probes inside living cell nuclei investigated by spatially-resolved fluorescence correlation spectroscopy},
+ Author = {Wachsmuth, M. and Waldeck, W. and Langowski, J.},
+ Journal = {J Mol Biol},
+ Year = {2000},
+ Number = {4},
+ Pages = {677--89},
+ Volume = {298},
+
+ Abstract = {We have investigated spatial variations of the diffusion behavior of the green fluorescent protein mutant EGFP (F64L/S65T) and of the EGFP-beta-galactosidase fusion protein in living cells with fluorescence correlation spectroscopy. Our fluorescence correlation spectroscopy device, in connection with a precision x-y translation stage, provides submicron spatial resolution and a detection volume smaller than a femtoliter. The fluorescence fluctuations in cell [...]
+ Doi = {10.1006/jmbi.2000.3692},
+ Keywords = {Animals COS Cells Cell Line Cell Nucleus/chemistry/*metabolism Cell Survival Cytoplasm/chemistry/metabolism Diffusion Fluorescence Fluorescent Dyes/*metabolism Genetic Vectors/genetics Green Fluorescent Proteins Hydrogen-Ion Concentration Kinetics Luminescent Proteins/chemistry/genetics/metabolism Models, Biological Protein Conformation Protons Recombinant Fusion Proteins/chemistry/genetics/metabolism Solutions Spectrometry, Fluorescence Statistics Transfection},
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at Article{Weidemann2013,
+ Title = {Dual-color fluorescence cross-correlation spectroscopy with continuous laser excitation in a confocal setup},
+ Author = {Weidemann, T. and Schwille, P.},
+ Journal = {Methods Enzymol},
+ Year = {2013},
+ Pages = {43--70},
+ Volume = {518},
+
+ Abstract = {Fluorescence correlation spectroscopy evaluates local signal fluctuations arising from stochastic movements of fluorescent particles in solution. The measured fluctuating signal is correlated in time and analyzed with appropriate model functions containing the parameters that describe the underlying molecular behavior. The dual-color extension, fluorescence cross-correlation spectroscopy (FCCS) allows for a comparison between spectrally well-separated channe [...]
+ Doi = {10.1016/B978-0-12-388422-0.00003-0},
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at Book{Weidemann2009,
+ Title = {Fluorescence Correlation Spectroscopy in Living Cells},
+ Author = {Weidemann, T. and Schwille, P.},
+ Publisher = {Springer},
+ Year = {2009},
+
+ Address = {Heidelberg},
+ Series = {Handbook of Single-Molecule Biophysics},
+
+ Owner = {paul},
+ Pages = {648},
+ Timestamp = {2014.01.15}
+}
+
+ at Article{Weidemann2002,
+ Title = {Analysis of Ligand Binding by Two-Colour Fluorescence Cross-Correlation Spectroscopy},
+ Author = {Weidemann, T. and Wachsmuth, M. and Tewes, M and Rippe, K. and Langowski, J.},
+ Journal = {Single Mol},
+ Year = {2002},
+ Number = {1},
+ Pages = {49--61},
+ Volume = {3},
+
+ Abstract = {Fluorescence correlation spectroscopy (FCS) is a well-established method for the analysis of freely diffusing fluorescent particles in solution. In a two-colour setup, simultaneous detection of two different dyes allows the acquisition of both the autocorrelation of the signal of each channel and the cross-correlation of the two channels (fluorescence cross correlation spectroscopy, FCCS). The cross-correlation function is related to the amount of diffusing [...]
+ Doi = {10.1002/1438-5171(200204)3:1<49::aid-simo49>3.0.co;2-t},
+ Keywords = {FCS FCCS receptor-ligand binding protein-DNA interactions},
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at Article{Weiss2003,
+ Title = {Anomalous protein diffusion in living cells as seen by fluorescence correlation spectroscopy},
+ Author = {Weiss, M. and Hashimoto, H. and Nilsson, T.},
+ Journal = {Biophys J},
+ Year = {2003},
+ Number = {6},
+ Pages = {4043--4052},
+ Volume = {84},
+
+ Abstract = {We investigate the challenges and limitations that are encountered when studying membrane protein dynamics in vivo by means of fluorescence correlation spectroscopy (FCS). Based on theoretical arguments and computer simulations, we show that, in general, the fluctuating fluorescence has a fractal dimension D(0) >or= 1.5, which is determined by the anomality alpha of the diffusional motion of the labeled particles, i.e., by the growth of their mean square dis [...]
+ Doi = {10.1016/s0006-3495(03)75130-3},
+ Keywords = {Algorithms ARE Biology Biophysics Cell Membrane Cells Comparative Study COMPLEXES Computer Simulation CORRELATION SPECTROSCOPY Diffusion DYNAMICS Endoplasmic Reticulum Fluorescence FLUORESCENCE CORRELATION SPECTROSCOPY Fractals Germany Golgi Apparatus Hela Cells Humans IN-VIVO LIVING CELLS Membrane Proteins metabolism methods Microscopy,Confocal Models,Biological Molecular Biology Motion N-Acetylgalactosaminyltransferases physiology Protein Protein Transport [...]
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at Article{Widengren1995,
+ Title = {Fluorescence correlation spectroscopy of triplet states in solution: a theoretical and experimental study},
+ Author = {Widengren, Jerker and Mets, {\"U}lo and Rigler, Rudolf},
+ Journal = {The Journal of Physical Chemistry},
+ Year = {1995},
+ Number = {36},
+ Pages = {13368-13379},
+ Volume = {99},
+
+ Doi = {10.1021/j100036a009},
+ Owner = {paul},
+ Timestamp = {2012.02.20}
+}
+
+ at Article{Widengren1998,
+ Title = {Fluorescence correlation spectroscopy as a tool to investigate chemical reactions in solutions and on cell surfaces},
+ Author = {Widengren, J. and Rigler, R.},
+ Journal = {Cell Mol Biol (Noisy-le-grand)},
+ Year = {1998},
+ Note = {Retrieved from \url{http://europepmc.org/abstract/MED/9764752}},
+ Number = {5},
+ Pages = {857--79},
+ Volume = {44},
+
+ Abstract = {Taking advantage of the present day possibilities for ultrasensitive detection by fluorescence, fluorescence correlation spectroscopy (FCS) has over the last ten years emerged as a potentially very powerful technique. In this article we present some results to illustrate the use of FCS for monitoring chemical kinetics on a molecular level and show how, for a wide range of chemical processes, the theoretical treatment can be strongly simplified. The experimen [...]
+ Owner = {paul},
+ Timestamp = {2014.01.15}
+}
+
+ at Article{Widengren1994,
+ Title = {Triplet-state monitoring by fluorescence correlation spectroscopy},
+ Author = {Widengren, Jerker and Rigler, Rudolf and Mets, {\"U}lo},
+ Journal = {Journal of Fluorescence},
+ Year = {1994},
+ Pages = {255-258},
+ Volume = {4},
+
+ Affiliation = {Department of Medical Biochemistry and Biophysics Karolinska Institute S-171 77 Stockholm Sweden},
+ Doi = {10.1007/BF01878460},
+ ISSN = {1053-0509},
+ Issue = {3},
+ Keyword = {Biomedizin & Life Sciences},
+ Owner = {paul},
+ Publisher = {Springer Netherlands},
+ Timestamp = {2012.09.24}
+}
+
+ at Article{Wohland2001,
+ Title = {The Standard Deviation in Fluorescence Correlation Spectroscopy},
+ Author = {Wohland, Thorsten and Rigler, Rudolf and Vogel, Horst},
+ Journal = {Biophysical Journal},
+ Year = {2001},
+
+ Month = jun,
+ Number = {6},
+ Pages = {2987--2999},
+ Volume = {80},
+
+ Doi = {10.1016/S0006-3495(01)76264-9},
+ ISSN = {0006-3495},
+ Owner = {paul},
+ Timestamp = {2012.09.08}
+}
+
+ at Article{Wohland2010,
+ Title = {Single Plane Illumination Fluorescence Correlation Spectroscopy (SPIM-FCS) probes inhomogeneous three-dimensional environments},
+ Author = {Thorsten Wohland and Xianke Shi and Jagadish Sankaran and Ernst H.K. Stelzer},
+ Journal = {Optics Express},
+ Year = {2010},
+
+ Month = {May},
+ Number = {10},
+ Pages = {10627--10641},
+ Volume = {18},
+
+ Abstract = {The life sciences require new highly sensitive imaging tools, which allow the quantitative measurement of molecular parameters within a physiological three-dimensional (3D) environment. Therefore, we combined single plane illumination microscopy (SPIM) with camera based fluorescence correlation spectroscopy (FCS). SPIM-FCS provides contiguous particle number and diffusion coefficient images with a high spatial resolution in homo- and heterogeneous 3D specime [...]
+ Doi = {10.1364/OE.18.010627},
+ Keywords = {Fluorescence microscopy; Three-dimensional microscopy; Spectroscopy, fluorescence and luminescence},
+ Owner = {paul},
+ Publisher = {OSA},
+ Timestamp = {2012.11.07}
+}
+
+ at Article{Yordanov2009,
+ Title = {Direct studies of liquid flows near solid surfaces by total internal reflection fluorescence cross-correlation spectroscopy},
+ Author = {Stoyan Yordanov and Andreas Best and Hans-J\"{u}rgen Butt and Kaloian Koynov},
+ Journal = {Optics Express},
+ Year = {2009},
+
+ Month = {Nov},
+ Number = {23},
+ Pages = {21149--21158},
+ Volume = {17},
+
+ Abstract = {We present a new method to study flow of liquids near solid surface: Total internal reflection fluorescence cross-correlation spectroscopy (TIR-FCCS). Fluorescent tracers flowing with the liquid are excited by evanescent light, produced by epi-illumination through the periphery of a high numerical aperture oil-immersion objective. The time-resolved fluorescence intensity signals from two laterally shifted observation volumes, created by two confocal pinholes [...]
+ Doi = {10.1364/OE.17.021149},
+ Keywords = {Velocimetry; Fluorescence, laser-induced; Spectroscopy, surface},
+ Owner = {paul},
+ Publisher = {OSA},
+ Timestamp = {2012.09.21}
+}
+
+ at Article{Yordanov2011,
+ Title = {Note: An easy way to enable total internal reflection-fluorescence correlation spectroscopy ({TIR-FCS}) by combining commercial devices for {FCS} and {TIR} microscopy},
+ Author = {Stoyan Yordanov and Andreas Best and Klaus Weisshart and Kaloian Koynov},
+ Journal = {Review of Scientific Instruments},
+ Year = {2011},
+ Number = {3},
+ Pages = {036105},
+ Volume = {82},
+
+ Doi = {10.1063/1.3557412},
+ Eid = {036105},
+ Keywords = {fluorescence spectroscopy; optical microscopy},
+ Numpages = {3},
+ Owner = {paul},
+ Publisher = {AIP},
+ Timestamp = {2012.05.02}
+}
+
+ at Article{Zhang2007,
+ Title = {Gaussian approximations of fluorescence microscope point-spread function models},
+ Author = {Bo Zhang and Josiane Zerubia and Jean-Christophe Olivo-Marin},
+ Journal = {Applied Optics},
+ Year = {2007},
+
+ Month = {Apr},
+ Number = {10},
+ Pages = {1819--1829},
+ Volume = {46},
+
+ Abstract = {We comprehensively study the least-squares Gaussian approximations of the diffraction-limited 2D-3D paraxial-nonparaxial point-spread functions (PSFs)of the wide field fluorescence microscope (WFFM), the laser scanning confocal microscope(LSCM), and the disk scanning confocal microscope (DSCM). The PSFs are expressed using the Debye integral. Under anL$\infty$ constraint imposing peak matching, optimal and near-optimal Gaussian parameters are derived for the [...]
+ Doi = {10.1364/AO.46.001819},
+ Keywords = {Numerical approximation and analysis; Microscopy; Confocal microscopy; Fluorescence microscopy; Three-dimensional microscopy},
+ Owner = {paul},
+ Publisher = {OSA},
+ Timestamp = {2012.09.20}
+}
+
+ at Book{Rigler:FCSbook,
+ Title = {Fluorescence Correlation Spectroscopy, Theory and Applications},
+ Editor = {R. Rigler and E.S. Elson},
+ Publisher = {Springer Berlin Heidelberg},
+ Year = {2001},
+ Edition = {1},
+
+ HowPublished = {Paperback},
+ ISBN = {978-3540674337},
+ Owner = {paul},
+ Timestamp = {2012.11.02}
}
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--- a/doc-src/PyCorrFit_doc.tex
+++ b/doc-src/PyCorrFit_doc.tex
@@ -144,18 +144,18 @@
\newpage
\graphicspath{{Images/}}
+
\include{PyCorrFit_doc_content}
\section*{Acknowledgements}
\addcontentsline{toc}{section}{Acknowledgements}
-I thank André Scholich (TU Dresden, Germany) for initial proof reading of the manuscript and Grzegorz Chwastek, Franziska Thomas, and Thomas Weidemann (Biotec, TU Dresden, Germany) for critical feedback on PyCorrFit.
+I thank André Scholich (TU Dresden, Germany) for initial proof reading of the manuscript.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Literaturverzeichnis
\pagestyle{plain} % nur Nummerierung in der Fuzeile
-
\bibliographystyle{plainurl} % Zitierstil: alphadin = [Nam88] apt-get install bibtex-extras
\bibliography{Bibliography} % BibTeX-Datei name.bib ohne .bib hier einfgen
%\nocite{*} % Listet alle Eintrge der Datei auf, wenn aktiv
diff --git a/doc-src/PyCorrFit_doc_content.tex b/doc-src/PyCorrFit_doc_content.tex
index 2557a6f..5f6a894 100755
--- a/doc-src/PyCorrFit_doc_content.tex
+++ b/doc-src/PyCorrFit_doc_content.tex
@@ -1,7 +1,8 @@
\section{Introduction}
-
+\label{sec:intro}
\subsection{Preface}
-\textit{PyCorrFit} emerged from my work in the Schwille Lab\footnote{\url{http://www.biochem.mpg.de/en/rd/schwille/}} at the Biotechnology Center of the TU Dresden in 2011/2012. The program source code is available at GitHub\footnote{\url{https://github.com/paulmueller/PyCorrFit}}. Please do not hesitate to sign up and add a feature request. If you you found a bug, please let me know via GitHub.\\
+\label{sec:intro.prefa}
+\textit{PyCorrFit} emerged from my work in the Schwille Lab\footnote{\url{http://www.biochem.mpg.de/en/rd/schwille/}} at the Biotechnology Center of the TU Dresden in 2011/2012. Since then, the program has been further developed based on numerous input from FCS users, in particular Franziska Thomas, Grzesiek Chwastek, Janine Tittel, and Thomas Weidemann. The program source code is available at GitHub\footnote{\url{https://github.com/paulmueller/PyCorrFit}}. Please do not hesitate to sign [...]
\noindent \textit{PyCorrFit} was written to simplify the work with experimentally obtained correlation curves. These can be processed independently (operating system, location, time). PyCorrFit supports commonly used file formats and enables users to allocate and organize their data in a simple way.\\
@@ -13,11 +14,12 @@ or (at your option) any later version\footnote{\url{http://www.gnu.org/licenses/
\subsubsection*{What \textit{PyCorrFit} can do}
\begin{itemize}
\item Load correlation curves from numerous correlators
-\item Process these curves (\hyref{Section}{sec:tm})
+\item Process these curves
\item Fit a model function (many included) to an experimental curve
\item Import user defined models for fitting
\item Many batch processing features
\item Save/load entire \textit{PyCorrFit} sessions
+\item \textbf{\LaTeX} support for data export
\end{itemize}
\subsubsection*{What \textit{PyCorrFit} is not}
@@ -27,8 +29,10 @@ or (at your option) any later version\footnote{\url{http://www.gnu.org/licenses/
\end{itemize}
\subsection{System prerequisites}
+\label{sec:intro.prere}
\subsubsection{Hardware}
-This documentation addresses the processing of correlation curves with \textit{PyCorrFit}. \textit{PyCorrFit} was successfully used with the following setups:
+\label{sec:intro.prere.hardw}
+This documentation addresses the processing of correlation curves with \textit{PyCorrFit} and was successfully used with the following setups:
\begin{itemize}
\item[1.]
APD: Photon Counting Device from PerkinElmer Optoelectronics, Model: \texttt{SPCM-CD3017}\\
@@ -41,17 +45,19 @@ This documentation addresses the processing of correlation curves with \textit{P
\end{itemize}
\subsubsection{Software}
-\label{cha:soft}
+\label{sec:intro.prere.softw}
The latest version of \textit{PyCorrFit} can be obtained from the internet at \url{http://pycorrfit.craban.de}.
\begin{itemize}
-\item \textbf{MacOSx}.
-Binary files for MacOSx $>$10.6.8 are available from the download page but have not yet been fully tested for stability.
-\item \textbf{Windows}.
-For Windows XP or Windows 7, stand-alone binary executables are available from the download page.
-\item \textbf{Linux}.
-There are executable binaries for widely used distributions (e.g. Ubuntu).
-\item \textbf{Sources}
-The program was written in Python, keeping the concept of cross-platform programming in mind. To run \textit{PyCorrFit} on any other operating system, the installation of Python v.2.7 is required. To obtain the latest source, visit \textit{PyCorrFit} at GitHub (\url{https://github.com/paulmueller/PyCorrFit}). \textit{PyCorrFit} depends on the following python modules:\\
+\item \textbf{MacOSx.}
+Binary files for Mac OSx 10.6.8 and later are available from the download page.
+\item \textbf{Windows.}
+For Windows XP and later, stand-alone binary executables are available from the download page.
+\item \textbf{Ubuntu/Debian.}
+PyCorrFit is available from the Debian repositories and can be installed via the operating systems packaging tool (e.g. \texttt{apt-get install pycorrfit}). There are also binaries for Ubuntu at the PyCorrFit download page.
+\item\textbf{Pypi.} The program was written in Python, keeping the concept of cross-platform programming in mind. To run \textit{PyCorrFit} on any other operating system, the installation of Python v.2.7 is required. \textit{PyCorrFit} is included in the package index of \texttt{python-pip} (\url{http://pypi.python.org/pypi/pip}) and can be installed via
+\texttt{pip~install~pycorrfit}\footnote{See also the wiki article at \url{https://github.com/paulmueller/PyCorrFit/wiki/Installation_pip}}.
+\item \textbf{Sources.}
+You can also directly download the source code at any developmental stage. Visit \textit{PyCorrFit} at GitHub (\url{https://github.com/paulmueller/PyCorrFit}). \textit{PyCorrFit} depends on the following python modules:\\
\texttt{\\
python-matplotlib ($\geq$ 1.0.1) \\
python-numpy ($\geq$ 1.5.1) \\
@@ -61,39 +67,27 @@ python-yaml \\
python-wxtools \\
python-wxgtk2.8-dbg \\
}
-\\
-For older versions of Ubuntu, some of the above package versions are not listed in the package repository. To enable the use of \textit{PyCorrFit} on those systems, the following tasks have to be performed:
-\begin{itemize}
-\item[ ] \textbf{matplotlib}. The tukss-ppa includes version 1.0.1. After adding the repository (\texttt{apt-add-repository ppa:tukss/ppa}), matplotlib can be installed as usual.
-\item[ ] \textbf{numpy}. The package from a later version of Ubuntu can be installed: \url{https://launchpad.net/ubuntu/+source/python-numpy/}
-\item[ ] \textbf{scipy}. The package from a later version of Ubuntu can be installed: \url{https://launchpad.net/ubuntu/+source/python-scipy/}
-\item[ ] \textbf{sympy}. To enable importing external model functions, sympy is required. It is available from \url{http://code.google.com/p/sympy/downloads/list}. Unpacking the archive and executing \texttt{python setup.py install} within the unpacked directory will install sympy.
\end{itemize}
-\end{itemize}
-Alternatively \texttt{python-pip} (\url{http://pypi.python.org/pypi/pip}) can be used to install up-to-date python modules.
-\noindent \textbf{\LaTeX}.
-\textit{PyCorrFit} can save correlation curves as images using matplotlib. It is also possible to utilize Latex to generate these plots. On Windows, installing MiKTeX with ``automatic package download'' will enable this feature. On MacOSx, the MacTeX distribution can be used. On other systems, the packages LaTeX, dvipng, Ghostscript and the scientific latex packages \texttt{texlive-science} and \texttt{texlive-math-extra} need to be installed.
-\subsection{Running \textit{PyCorrFit}}
-\label{sec:run}
-\paragraph*{Windows}
+\vspace{1em}
+\noindent \textbf{\LaTeX .} \textit{PyCorrFit} can save correlation curves as images using matplotlib. It is also possible to utilize \LaTeX to generate these plots. On Windows, installing MiKTeX with ``automatic package download'' will enable this feature. On MacOSx, the MacTeX distribution can be used. On other systems, the packages \LaTeX \, dvipng, Ghostscript and the scientific \LaTeX \,packages \texttt{texlive-science} and \texttt{texlive-math-extra} need to be installed.
+
+\subsubsection{Running \textit{PyCorrFit}}
+\label{sec:intro.runni}
+\paragraph*{Windows.}
Download the executable file and double-click on the \texttt{PyCorrFit.exe} icon.
-\paragraph*{Linux/Ubuntu}
-Make sure the binary has the executable bit set, then simply double-click on the binary \texttt{PyCorrFit}.
-\paragraph*{Mac OSx}
+\paragraph*{Ubuntu/Debian.}
+\texttt{PyCorrFit} is integrated into Debian and thus behaves like any other application.
+\paragraph*{Mac OSx.}
When downloading the archive \texttt{PyCorrFit.zip}, the binary should be extracted automatically (if not, extract the archive) and you can double-click it to run \textit{PyCorrFit}.
-\paragraph*{from source}
+\paragraph*{from source.}
Invoke \texttt{python PyCorrFit.py} from the command line.
-
-\section{Working with \textit{PyCorrFit}}
-
\subsection{Workflow}
-\label{cha_graphint}
-\label{sec:PyCorrFitUserInterface}
+\label{sec:intro.workf}
-The following chapter introduces the general idea of how to start and accomplish a fitting project. FCS experiments produce different sets of experimental correlation functions which must be interpreted with appropriate physical models. Each correlation function refers to a single contiguous signal trace or ``run''. In \textit{PyCorrFit}, the user must assign a mathematical model function to each correlation function during the loading procedure. The assignment is irreversible in the sen [...]
+The following chapter introduces the general idea of how to start and accomplish a fitting project. FCS experiments produce different sets of experimental correlation functions which must be interpreted with appropriate physical models (\hyref{Chapter}{sec:theor}). Each correlation function refers to a single contiguous signal trace or ``run''. In \textit{PyCorrFit}, the user must assign a mathematical model function to each correlation function during the loading procedure. The assignme [...]
Let's briefly discuss a typical example: To determine the diffusion coefficient of a fluorescently labeled protein in free solution, one has to deal with two sets of autocorrelation data: measurements of a diffusion standard (e.g. free dye for which a diffusion coefficient has been published) to calibrate the detection volume and measurements of the protein sample. The protein sample may contain small amounts of slowly diffusing aggregates. While the calibration measurements can be fitte [...]
@@ -105,142 +99,51 @@ Let's briefly discuss a typical example: To determine the diffusion coefficient
\end{enumerate}
-The first approach is straightforward, however, it requires homogeneous diffusion behavior for each data set. The second strategy has the advantage that the dye and the protein curves, as well as the obtained parameters can be visually compared during the fitting analysis within the same session. In this case, batch fitting is still possible because it discriminates data sets assigned to different models. In the third case, simultaneous batch fitting is also possible. However, for each d [...]
-
-The fitting itself is usually explored with a representative data set. Here, the user has to decide on starting parameters, the range in which they should be varied, corrections like background, and other fitting options. Once the fit looks good, the chosen settings can be transferred at once to all other pages assigned to the same model using the \textit{Batch control} tool (\hyref{Section}{sec:tm.bc}). After flipping through the data for visual inspection one may check the parameters a [...]
+The first approach is straightforward, however, it requires homogeneous diffusion behavior for each data set. The second strategy has the advantage that the dye and the protein curves, as well as the obtained parameters, can be visually compared during the fitting analysis within the same session. In this case, batch fitting is still possible because it discriminates data sets assigned to different models. In the third case, simultaneous batch fitting is also possible. However, for each [...]
-\subsection{The \textit{main window}}
+The fitting itself is usually explored with a representative data set. Here, the user has to decide on starting parameters, the range in which they should be varied, corrections like background, and other fitting options. Once the fit looks good, the chosen settings can be transferred at once to all other pages assigned to the same model using the \textit{Batch control} tool (\hyref{Section}{sec:menub.tools.batch}). After flipping through the data for visual inspection one may check the [...]
-%\hyref{Figure}{fig:PyCorrFitMain} shows the main window of PyCorrFit. It contains a menu bar to access all tools, a notebook with tabs, each tab representing a single curve, and a page - the content of the currently selected tab.
+\subsection{Graphical user interface (GUI)}
+\label{sec:intro.graph}
+Together with a system's terminal of the platform on which \textit{PyCorrFit} was installed (Windows, Linux, MacOS), the \textit{main window} opens when starting the program as described in \hyref{Section}{sec:intro.runni}. The window title bar contains the version of \textit{PyCorrFit} and, if a session was re-opened or saved, the name of the fitting session. A menu bar provides access to many supporting tools and additional information as thoroughly described in \hyref{Chapter}{sec:menub}.
-Together with a system's terminal of the platform on which PyCorrFit was installed (Windows, Linux, MacOS), the \textit{main window} opens when starting the program as described in \hyref{section}{sec:run}. The window title bar contains the version of \textit{PyCorrFit} and, if a session was re-opened or saved, the name of the fitting session. A menu bar provides access to many supporting tools and additional information as thoroughly described in \hyref{Chapter}{sec:mb}.
-
-There are three gateways for experimental data into a pre-existing or a new \textit{PyCorrFit} session (\textit{File / Load data}, \textit{File / Open session}, and \textit{Current page / Import data}). When a session has been opened or correlation data have been loaded, each correlation curve is displayed on a separate page of a notebook. For quick identification of the active data set, a tab specifies the page number, the correlated channels (AC/CC), and the run number in case there ar [...]
+There are three gateways for experimental data into a pre-existing or a new \textit{PyCorrFit} session (\textit{File/Load data}, \textit{File/Open session}, and \textit{Current page/Import data}). When a session has been opened or correlation data have been loaded, each correlation curve is displayed on a separate page of a notebook. For quick identification of the active data set, a tab specifies the page number, the correlated channels (AC/CC), and the run number in cases where multip [...]
\begin{figure}[h]
\centering
\includegraphics[width=\linewidth]{PyCorrFit_Screenshot_Main.png}
- \mycaption{user interface of PyCorrFit}{A circular scanning FCS (CS-FCS) curve of DiO on a supported lipid bilayer (glass substrate) is shown. The measurement yields a diffusion coefficient of \SI{0.28}{\mu m^2s^{-1}} ($F1=1$, so only one component is fitted). Note that a 2D diffusion model is used and not a 3D model (as shown in \hyref{figure}{fig:extxt}). \label{fig:PyCorrFitMain}}
+ \mycaption{user interface of PyCorrFit}{Confocal measurement of nanomolar Alexa488 in aqueous solution. To avoid after-pulsing, the autocorrelation curve was measured by cross-correlating signals from two detection channels using a 50 \% beamsplitter. Fitting reveals the average number of observed particles ($n \approx 6$) and their residence time in the detection volume ($\tau_{\rm diff} = \SI{28}{\mu s})$. \label{fig:mainwin} }
\end{figure}
-The page containing a correlation function is divided in two halves. At the left hand side the page\textit{ }shows a pile of boxes containing values or fitting options associated to the current model and data set:
-
-
+The active page displaying a correlation function is divided in two panels (\hyref{Figure}{fig:mainwin}). At the left hand side the page shows a pile of boxes containing values or fitting options associated with the current model and data set:
\begin{itemize}
-\item \textit{Data set}, a unique identifier for each correlation curve which is automatically assembled from different fields during the loading procedure (\hyref{Section}{sec:fm.ld}). This window can also be manually edited, thereby allowing to re-name or flag certain data during the fitting analysis.
-\item \textit{Model parameters} displays the values which determine the current shape of the assigned model function. Initially, starting values are loaded as they were defined in the model description (\hyref{Section}{sec:fm.im}). Little buttons allow a stepwise increase or decrease in units of 1/10\textsuperscript{th}. It is also possible to directly enter some numbers. A checkbox is used to set the parameter status to ``varied'' (checked) or ``fixed'' (unchecked) during the fitting. A [...]
-\item \textit{Amplitude corrections} applies additional rescaling to amplitude related parameters like the number of particles $n$ or fractions thereof associated with different correlation times ($n_1$, $n_2$, etc.). Experimental values of non-correlated background intensity can be manually entered for each channel. In addition, the correlation curves can be normalized, to facilitate a visual comparison of their time dependence.
-\item \textit{Fitting options} offers weighted fitting. The underlying idea is that data points with higher accuracy should also have a higher impact on model parameters. To derive weights, \textit{PyCorrFit} calculates the variance of the difference between the actual data and a smooth, empiric representation of the curve for a certain neighborhood. The number of neighboring data points at each side ($j > 0$) can be set. For such a smooth representation a 5-knot spline function or the m [...]
+\item \textit{Data set} specifies the assigned model abbreviation in parentheses and shows a unique identifier for the correlation curve containing the file name, the number of the ``run'', and the data channel. This string is automatically assembled during the loading procedure (\hyref{Section}{sec:menub.filem.loadd}). However, during the session it can be manually edited, thereby allowing to re-name or flag certain data during the fitting analysis.
+\item \textit{Model parameters} displays the values which determine the current shape of the assigned model function (\hyref{Chapter}{sec:theor}). Initially, starting values are loaded as they were defined in the model description (\hyref{Section}{sec:menub.filem.impor}). Little buttons allow a stepwise increase or decrease in units of 1/10\textsuperscript{th}. It is also possible to directly enter some numbers. A checkbox is used to set the parameter status to ``varied'' (checked) or `` [...]
+\item \textit{Amplitude corrections} applies additional rescaling to amplitude related parameters like the number of particles $n$ or amplitude fractions associated with different correlation times ($n_1$, $n_2$, etc.). Experimental values of non-correlated background intensity can be manually entered for each channel. In addition, the correlation curves can be normalized, to facilitate a visual comparison of the decay.
+\item \textit{Fitting options} offers weighted fitting. The underlying idea is that data points with higher accuracy should also have a higher impact on model parameters. To derive weights, \textit{PyCorrFit} calculates the variance of the difference between the actual data and a smooth, empiric representation of the curve for a certain neighbourhood. The number of neighbouring data points at each side ($j > 0$) can be set. For such a smooth representation a spline function or the model [...]
\end{itemize}
-At the right hand side are two graphics windows. The dimensionless correlation functions $G(\tau)$ are plotted against the lag time ($\tau$) in logarithmic scale. Below, a second window shows the residuals, the actual numerical difference between the correlation data and the model function. Fitting with appropriate models will scatter the residuals symmetrically around zero ($x$-axis). When weighted fitting was performed, the weighted residuals are shown. A good fit will not leave residu [...]
+At the right hand side are two graphics windows. The dimensionless correlation functions $G(\tau)$ are plotted against the lag time ($\tau$) on a logarithmic scale. Below, a second window shows the residuals, the actual numerical difference between the correlation data and the model function. Fitting with appropriate models will scatter the residuals symmetrically around zero ($x$-axis). When weighted fitting was performed, the weighted residuals are shown. A good fit will not leave resi [...]
The main window can be rescaled as a whole to improve data representation. In addition, to zoom in, one can drag a rectangle within the plot area; a double click then restores the initial scale. Experimental data points are linked by grey lines, the state of the model function is shown in blue. When a weighted fit was applied, the variance of the fit is calculated for each data point and displayed in cyan.
\section{The menu bar}
-\label{sec:mb}
-
-PyCorrFit is organized in panels which group certain functions. The menu organizes data management (File), data analysis (Tools), display of correlation functions (Current Page), numerical examples (Model), software settings (Preferences), and software metadata (Help).
+\label{sec:menub}
+The menu bar organizes data management (File), data analysis (Tools), display of correlation functions (Current Page), numerical examples (Model), software settings (Preferences), and software metadata (Help).
\subsection{File menu}
-\label{sec:fm}
-The File menu organizes the import of theoretical models, experimental correlation data, and opening and saving of entire \textit{PyCorrFit} fitting sessions. However, the numerical fit results are exported from the \textit{Statistics view} panel which can be found under \textit{Tools} (\hyref{Section}{sec:tm.sv}).
+\label{sec:menub.filem}
+The File menu organizes the import of theoretical models, experimental correlation data, and opening and saving of entire \textit{PyCorrFit} fitting sessions. However, the numerical fit results are exported from the \textit{Statistics view} panel which can be found under \textit{Tools} (\hyref{Section}{sec:menub.tools.stati}).
\subsubsection{File / Import model}
-\label{sec:fm.im}
-Correlation data must be fitted to models describing the underlying physical processes which give rise to a particular time dependence and magnitude of the recorded signal fluctuations. Models are mathematical expressions containing parameters with physical meaning, like the molecular brightness or the dwell time through an illuminated volume etc. While a number of standard functions are built-in, the user can define new expressions. Some examples can be found at GitHub in the \textit{Py [...]
-
-Model functions are imported as text files (*.txt) using certain syntax:
-
-\begin{itemize}
-\item \textbf{Encoding}: PyCorrFit can interpret the standard Unicode character set (UTF-8).
-\item \textbf{Comments}: Lines starting with a hash (\texttt{\#}), empty lines, or lines containing only white space characters are ignored. The only exception is the first line starting with a hash followed by a white space and a short name of the model. This line is evaluated to complement the list of models in the dialogue\textit{ Choose }\textit{model}, when loading the data.
-\item \textbf{Units}: PyCorrFit works with internal units for:
-
-\begin{itemize}
-\item Time: \SI{1}{ms}
-\item Distance: \SI{100}{nm}
-\item Diffusion coefficient: \SI{10}{\mu m^2s^{-1}}
-\item Inverse time: \SI{1000}{s^{-1}}
-\item Inverse area: \SI{100}{\mu m^{-2}}
-\item Inverse volume: \SI{1000}{\mu m^{-3}}
-\end{itemize}
-\item \textbf{Parameters:} To define a new model function new parameters can be introduced. Parameters are defined by a sequence of strings separated by white spaces containing name, the dimension in angular brackets, the equal sign, and a starting value which appears in the main window for fitting. For example: \texttt{D [\SI{10}{\mu m^ 2 s^{-1}}] = 5.0}.
-%It is important to note that when the dimensions differ from the internal units (\SI{10}{\mu m^ 2 s^{-1}}), the expression must contain some adjusting factor; here a factor of 5.
-%Thus, user defined dimensions are only for display and cannot be processed numerically.
- The parameter names contain only alphabetic (not numerical) characters. \texttt{G} and \texttt{g}, as well as the numbers \texttt{e} and \texttt{pi} are already mapped and cannot be used freely.
-\item \textbf{Placeholder:} When defining composite mathematical expressions for correlation functions one can use placeholders. Placeholders start with a lowercase ‘g’. For example, the standard, Gaussian 3D diffusion in free solution may be written as
-
-\begin{itemize}
-\item \texttt{gTrp = 1+ T/(1-T)*exp(-tau/tautrip)}
-\item \texttt{gTwoD = 1/(1+tau/taudiff)}
-\item \texttt{gThrD = 1/sqrt(1+tau/(taudiff*S**2))}
-\end{itemize}
-\end{itemize}
-The individual parts are then combined in the last line of the *.txt file, where the correlation function is defined starting with uppercase ’G’:
-
-\begin{equation}
-\texttt{G = 1/n * gTrp * gTwoD * gThrD} \notag
-\end{equation}
-For reference of mathematical operators check for example \href{http://www.tutorialspoint.com/python/python_basic_operators.htm}{www.tutorialspoint.com / python / python\_basic\_operators.htm}. To illustrate a more complex example see the model function for circular scanning FCS in \hyref{figure}{fig:extxt}.
-
-
-\begin{figure}
-% for case sensitiver Verbatim, we need the package fancyvrb
-\begin{Verbatim}[frame = single]
-
-# CS-FCS 3D+S+T (Confocal)
-
-# Circular Scanning FCS model function. 3D diffusion + Triplet.
-
-## Definition of parameters:
-# First, the parameters and their starting values for the model function
-# need to be defined. If the parameter has a unit of measurement, then it
-# may be added separated by a white space before the "=" sign. The starting
-# value should be a floating point number. Floating point abbreviations
-# like "1e-3" instead of "0.001" may be used.
-
-# Diffusion coefficient
-D [10 µm²/s] = 200.0
-# Structural parameter
-w = 5.0
-# Waist of the lateral detection area
-a [100 nm] = 1.0
-# Particle number
-n = 5.0
-# Scan radius
-R [100 nm] = 5.0
-# Frequency
-f [kHz] = 20.0
-# Triplet fraction
-T = 0.1
-# Triplet time
-tautrip [ms] = 0.001
-
-# The user may wish to substitute certain parts of the correlation function
-# with other values to keep the formula simple. This can be done by using the
-# prefix "g". All common mathematical functions, such as "sqrt()" or "exp()"
-# may be used. For convenience, "pi" and "e" are available as well.
-
-gTrip = 1. + T/(1-T)*exp(-tau/tautrip)
-gScan = exp(-(R*sin(pi*f*tau))**2/(a**2+D*tau))
-gTwoD = 1./(1.+D*tau/a**2)
-gOneD = 1./sqrt(1.+D*tau/(w*a)**2)
-gThrD = gTwoD * gOneD
-
-# The final line with the correlation function should start with a "G"
-# before the "=" sign.
-
-G = 1./n * gThrD * gScan * gTrip
-
-\end{Verbatim}
-\mycaption{user defined model function for PyCorrFit}{The working example shows a model function for circular scanning FCS.\label{fig:extxt}}
-\end{figure}
+\label{sec:menub.filem.impor}
+Correlation data must be fitted to models describing the underlying physical processes which give rise to a particular time dependence and magnitude of the recorded signal fluctuations. Models are mathematical expressions containing parameters with physical meaning, like the molecular brightness or the dwell time through an illuminated volume. While the most commonly used standard functions are built-in, the user can define new expressions.
+Some examples can be found at GitHub in the \textit{PyCorrFit} repository, e.g. circular scanning FCS \cite{Petrasek2008} (\hyref{Figure}{fig:csfcs}) or a combination of diffusion and directed flow \cite{Brinkmeier1999}. External model functions are discussed in detail in \hyref{Section}{sec:hacke.extmod}.
\subsubsection{File / Load data}
-\label{sec:fm.ld}
+\label{sec:menub.filem.loadd}
\textit{Load data }is the first way to import multiple correlation data sets into a \textit{PyCorrFit} session. The supported file formats can be found in a drop-down list of supported file endings in the pop-up dialog \textit{Open data files}:
@@ -255,80 +158,47 @@ G = 1./n * gThrD * gScan * gTrip
\end{tabular}
\vspace{3ex}
\newline
-While (2)-(4) are file formats associated with commercial hardware, (5) refers to a MATLAB based FCS evaluation software developed by Jonas Ries in the Schwille lab at TU Dresden, (6) is the txt-file containing comma-separated values (csv) generated with PyCorrFit via the command \textit{Current Page / Save data}. Zip-files are automatically decompressed and can be imported when matching one of the above mentioned formats. In particular loading of zip files is a possibility to re-import [...]
-
-When loading data, the user is prompted to assign fit models in the \textit{Choose Models} dialogue window. There, curves are sorted according to channel (for example AC1, AC2, CC12, and CC21, as a typical outcome of a dual-color cross-correlation experiment). For each channel a fit model must be selected from the list (see \hyref{Section}{sec:models}):
-
-If a file format is not yet listed, the correlation data could be converted into a compatible text-file (*.csv) or bundles of *.csv files within a compressed archive *.zip. For reformatting the following points should be considered:
-
+While (2)-(4) are file formats associated with commercial hardware, (5) refers to a MATLAB based FCS evaluation software developed by Jonas Ries in the Schwille lab at TU Dresden, (6) is a text file containing comma-separated values (csv) generated by PyCorrFit via the command \textit{Current Page / Save data}. Zip-files are automatically decompressed and can be imported when matching one of the above mentioned formats. In particular loading of zip files is a possibility to re-import cor [...]
-\begin{itemize}
-\item \textbf{Encoding}: \textit{PyCorrFit} uses the standard Unicode character set (UTF-8). However, since no special characters are needed to save experimental data, other encodings may also work. New line characters are \texttt{{\textbackslash}r{\textbackslash}n} (Windows).
-\item \textbf{Comments}: Lines starting with a hash (\texttt{\#}), empty lines, or lines containing only white space characters are ignored. Exceptions are the keywords listed below.
-\item \textbf{Units}: PyCorrFit works with units/values for:
+During loading, the user is prompted to assign fit models in the \textit{Choose Models} dialogue window. There, curves are sorted according to channel (for example AC1, AC2, CC12, and CC21, as a typical outcome of a dual-color cross-correlation experiment). For each channel a fit model must be selected from the list (see \hyref{Section}{sec:menub.model}):
-\begin{itemize}
-\item Time: \SI{1}{ms}
-\item Intensity: \SI{1}{kHz}
-\item Amplitude offset: $G(0) = 0$ (not 1)
-\end{itemize}
-\item \textbf{Keywords:}\footnote{Keywords are case-insensitive.} \textit{PyCorrFit} reads the first two columns containing numerical values. The first table (non-hashed) is recognized as the correlation data containing the lag times in the first and the correlation data in the second column. (In case the *.csv file has been generated with \textit{PyCorrFit} up to three additional columns containing the fit function are ignored). The table ends, when the keyword \texttt{\# BEGIN TRACE} a [...]
-\item \textbf{Tags:}\footnote{Tags are case-insensitive.} Channel information can be entered using defined syntax in a header. The keyword
-\begin{center}
-\vspace{-1em}
- \texttt{\# Type AC/CC Autocorrelation}
-\vspace{-1em}
-\end{center}
- assigns the tag \texttt{AC} and the keyword
-\begin{center}
-\vspace{-1em}
- {\texttt{\# Type AC/CC Crosscorrelation}}
-\vspace{-1em}
-\end{center}
- assigns the tag \texttt{CC} to the correlation curve. These strings are consistently displayed in the user interface of the respective data page in \textit{PyCorrFit}. If no data type is specified, autocorrelation is assumed. Tags may be specified with additional information like channel numbers, e.g.
-\begin{center}
-\vspace{-1em}
- \texttt{\# Type AC/CC Autocorrelation \_01}.
-\vspace{-1em}
-\end{center}
-In this case the tag \texttt{AC\_01} is generated. This feature is useful to keep track of the type of curve during the fitting and when post-processing the numerical fit results.
-\end{itemize}
+If a file format is not yet listed, the correlation data could be converted into a compatible text-file (*.csv) or bundles of *.csv files within a compressed archive *.zip. For reformatting correlation data, have a look at \hyref{Section}{sec:hacke.csv}.
\subsubsection{File / Open session}
-\label{sec:fm.os}
-This command is the second way to import data into PyCorrFit. In contrast to \textit{Load data}, it opens an entire fitting project, which was previously saved with \textit{PyCorrFit}. Sessions are bundles of files named *.fcsfit-session.zip. Sessions contain, comments, model assigned correlation data, and the current state of parameters for each data page (\hyref{Section}{sec:fm.ss}).
+\label{sec:menub.filem.opens}
+This command is the second way to import data into PyCorrFit. In contrast to \textit{Load data}, it opens an entire fitting project, which was previously saved with \textit{PyCorrFit}. Session files are *.zip files named *.fcsfit-session.zip. These files contain all information to restore a session, including comments, model assigned correlation data, and the current state of parameters for each data set (\hyref{Section}{sec:menub.filem.saves}).
\subsubsection{File / Comment session}
-\label{sec:fm.cs}
+\label{sec:menub.filem.comme}
This command opens a window to place text messages that can be used to annotate a fitting session.
\subsubsection{File / Clear session}
-\label{sec:cls}
-This command closes all pages while the PyCorrFit.exe keeps running. The user is prompted to save the session under the same or a different name. At this stage both options \textit{No} or \textit{Cancel} lead to clearance and a potential loss of recent modifications.
+\label{sec:menub.filem.clear}
+This command closes all pages. The user is prompted to save the current session.
\subsubsection{File / Save session}
-\label{sec:fm.ss}
-In addition to display and fit individual curves, a strong feature of PyCorrFit is to save an entire fitting project as a single session. Sessions allow the user to revisit and explore different models, fitting strategies, and data sets. Importantly the work can be saved at any stage.
+\label{sec:menub.filem.saves}
+In addition to display and fit individual curves, a strong feature of \textit{PyCorrFit} is to save an entire fitting project as a single session. Sessions allow the user to revisit and explore different models, fitting strategies, and data sets. Importantly the work can be saved at any stage.
-The number of files bundled in a session varies depending on the number of data sets (pages), the number of used models, and what was done during the fitting. A detailed description can be found in the Readme.txt file attached to each session. For example, the numerical correlation and intensity data are saved separately as *.csv text files. However, in contrast to the \textit{Save data (*.csv)} command of the \textit{Current Page} menu, there are no metadata in the header, just tables c [...]
+The number of files bundled in a session varies depending on the number of data sets (pages), the number of used models, and what was done during the fitting. A detailed description can be found in the Readme.txt file attached to each session. For example, the numerical correlation and intensity data are saved separately as *.csv text files. However, in contrast to the \textit{Save data (*.csv)} command of the \textit{Current Page} menu, there are no metadata in the header, just tables c [...]
\subsubsection{File / Exit}
-\label{sec:fm.e}
-This command closes down \textit{PyCorrFit}. The user is prompted to save the session under the same or a different name. At this stage \textit{No} leads to the loss of recent changes, while \textit{Cancel} keeps \textit{PyCorrFit} running.
+\label{sec:menub.filem.exit}
+This command closes down \textit{PyCorrFit}. The user is prompted to save the session under the same or a different name.
\subsection{Tools menu}
-\label{sec:tm}
+\label{sec:menub.tools}
The \textit{Tools} menu provides access to a series of accessory panels which extent the capability of the main window. These accessory panels can stay open during the entire analysis. Open panels appear checked in the menu. Most operations can be executed across the entire data set with a single mouse click.
\subsubsection{Tools / Data range}
-\label{sec:tm.dr}
+\label{sec:menub.tools.datar}
This panel limits the range of lag times which are displayed in the main window panel. At the same time it defines the range of points which are used for fitting. For example, this feature can be applied to remove dominant after-pulsing of the avalanche photo diodes (APDs) which may interfere with Triplet blinking at short lag times. The user has the options to \textit{Apply} the channel settings only to the current page or he can \textit{Apply to all pages}. In contrast to \textit{Batch [...]
Power user, who frequently load and remove data sets, may take advantage of a checkbox to fix the channel selection for all newly loaded data sets.
\subsubsection{Tools / Overlay curves}
-\label{sec:tm.oc}
-This window displays the correlation data (not the fit curves) of all pages in a single plot. The curves can be discriminated by color. If only one curve is selected it appears in red. Curves with ambiguous shape can easily be identified, selected, and removed by clicking \textit{Apply}. A warning dialogue lists the pages which will be kept.
+\label{sec:menub.tools.overl}
+This window displays the correlation data (not the fit curves) of all pages in a single plot. The curves can be discriminated by color. If only one curve is selected, it appears in red. Curves with ambiguous shape can easily be identified, selected, and removed by clicking \textit{Apply}. A warning dialogue lists the pages which will be kept.
Data representation is synchronized with the page display in the \textit{Main window}. For example, narrowing the range of lag times by \textit{Data range }is immediately updated in the \textit{Overlay curves }tool. Likewise, their normalization of the amplitudes to unity.
@@ -337,22 +207,20 @@ The other way round, some tools directly respond to the selections made in the \
The tool is closed by the button \textit{Cancel}. All the listed data sets will be kept. However, the selections transferred to the \textit{Global fitting}, \textit{Average curves}, and \textit{Statistics view} tools are kept as well.
\subsubsection{Tools / Batch control}
-\label{sec:tm.bc}
-By default the current page is taken as a reference to perform automated fitting. A batch is defined as the ensemble of correlation data sets (pages) assigned to the same model function within a session. A session can therefore have several batches, even for the same data.
+\label{sec:menub.tools.batch}
+By default, the current page is taken as a reference to perform automated fitting. A batch is defined as the ensemble of correlation data sets (pages) assigned to the same model function within a session. A session can therefore have several batches, even for the same data.
-For fitting it is crucial to carefully define the starting parameters, whether parameters should be fixed or varied, the range of values which make physically sense, and other options offered within the \textit{Main window}. By executing \textit{Apply to applicable pages}, these settings are transferred to all other pages assigned to the same fit model. Note that this includes the range of lag times (lag time channels) which may have been changed with the \textit{Data range }tool for ind [...]
+For fitting, it is crucial to carefully define the starting parameters, whether parameters should be fixed or varied, the range of values which make physically sense, and other options offered within the \textit{Main window}. By executing \textit{Apply to applicable pages}, these settings are transferred to all other pages assigned to the same fit model. Note that this includes the range of lag times (lag time channels) which may have been changed with the \textit{Data range }tool for in [...]
-The button \textit{Fit applicable pages} then performs several cycles of fitting [how many cycles?] on all pages of the same batch. Alternatively, the user can define an external source of parameters as a reference, i.e. the first page of some \textit{Other session} (*.fcsfit-session.zip). However, this assumes a consistent assignment of model functions.
+The button \textit{Fit applicable pages} then performs fitting on all pages of the same batch. Alternatively, the user can define an external source of parameters as a reference, i.e. the first page of some \textit{Other session} (*.fcsfit-session.zip). However, this assumes a consistent assignment of model functions.
\subsubsection{Tools / Global fitting}
-\label{sec:tm.gf}
-Global fitting is useful when experimental curves share the same values for certain physical parameters. For example, due to physical constraints in two-focus FCS both autocorrelation curves and the cross-correlation curves should adopt the same values for the diffusion time \textit{taudiff} and the number of particles \textit{n}. A global fit can be applied such that \textit{n} and \textit{taudiff} are identical for all data sets. All curves are added to a single array. In contrast to f [...]
+\label{sec:menub.tools.globa}
+Global fitting is useful when experimental curves share the same values for certain physical parameters. For example, due to physical constraints in two-focus FCS both autocorrelation curves and cross-correlation curves should adopt the same values for the diffusion time $\tau_\mathrm{diff}$ and the number of particles $n$. A global fit can be applied such that $n$ and $\tau_\mathrm{diff}$ are identical for all data sets. All curves are added to a single array. In contrast to fixing the [...]
\subsubsection{Tools / Average data}
-\label{sec:tm.ad}
-Often in FCS, the measurement time at a particular spot is divided in several runs. This approach is taken when occasional, global intensity changes are superimposed on the molecular fluctuations of interest. Then the user has to sort out the bad runs. After fitting, one may want to re-combine the data, to export a cleaned, average correlation function. This can be done with the tool \textit{Average data}, for which a subset of curves has to be selected by typing the numbers into the inp [...]
-
-For averaging, there are constraints:
+\label{sec:menub.tools.avera}
+Often in FCS, the measurement time at a particular spot is divided in several runs. This approach is taken when occasional, global intensity changes are superimposed on the molecular fluctuations of interest. Then the user has to sort out the bad runs. After fitting, one may want to re-combine the data to export a cleaned average correlation function. This can be done with the tool \textit{Average data}, for which a subset of curves has to be selected by typing the numbers into the input [...]
\begin{enumerate}
@@ -363,11 +231,11 @@ For averaging, there are constraints:
The averaged curve is shown on a separate page. The new \textit{Filename/title} receives the entry \textit{Average [numbers of pages]}. The assigned model is by default the same as for the individual pages. However, while averaging, the user can choose a different model from a drop-down list.
\subsubsection{Tools / Trace view}
-\label{sec:tm.tv}
-FCS theory makes assumptions about the thermodynamic state of the system. Signal fluctuations can only be analyzed when the system is at equilibrium or at a sufficiently stable steady state. Global instabilities on the time scale of the measurement itself, e.g. photo-bleaching, have dramatic effect on the shape of the measured correlation curve. Therefore it is common practice to check the correlated intensity trace for each curve. Trace view simply displays the signal trace for each cor [...]
+\label{sec:menub.tools.trace}
+FCS theory makes assumptions about the thermodynamic state of the system. Signal fluctuations can only be analyzed when the system is at equilibrium or at a sufficiently stable steady state. Global instabilities on the time scale of the measurement itself, e.g. photo-bleaching, have dramatic effect on the shape of the measured correlation curve. Therefore, it is common practice to check the correlated intensity trace for each curve. Trace view simply displays the signal trace for each co [...]
\subsubsection{Tools / Statistics view}
-\label{sec:tm.sv}
+\label{sec:menub.tools.stati}
The goal of a correlation analysis is to determine experimental parameter values with sufficient statistical significance. However, especially for large data sets, it can get quite laborious to check all of the individual values on each page. We designed the \textit{Statistics view} panel to review the state of parameters across the experimental batch (pages assigned to the same model) in a single plot, thereby facilitating to the identification of outliers.
The current page is taken as a reference for the type of model parameters which can be displayed. The user can choose different \textit{Plot parameters} from a drop-down list. A subset of pages within the batch can be explicitly defined by typing the page numbers into the input field or by highlighting in the \textit{Overlay curves} tool. Note that page numbers which refer to different models than the current page are ignored.
@@ -375,60 +243,59 @@ The current page is taken as a reference for the type of model parameters which
The \textit{Statistics view} panel contains a separate \textit{Export} box, where parameters can be selected (checked) and saved as a comma separated text file (*.csv). Only selected page numbers are included.
\subsubsection{Tools / Page info}
-\label{sec:tm.pi}
+\label{sec:menub.tools.pagei}
Page info is a most verbose summary of a data set. The panel \textit{Page info} is synchronized with the current page. The following fields are listed:
\begin{enumerate}
-\item Version of PyCorrFit
+\item Version of \textit{PyCorrFit}
\item Field values from the main window (filename/title, model specifications, page number, type of correlation, normalizations)
\item Actual parameter values (as contained in the model function)
-\item Supplementary parameters (intensity, counts per particle, duration, etc.)
+\item Supplementary parameters (intensity, counts per particle, duration, background correction, etc.)
\item Fitting related information (Chi-square, channel selection, varied fit parameters) .
-\item Model doc string (\hyref{Section}{sec:models})
+\item Model doc string (\hyref{Section}{sec:menub.model})
\end{enumerate}
-The content of Page info is saved as a header when exporting correlation functions via the command \textit{Current page / Save data (*.csv)} (\hyref{Section}{sec:cp.sd}).
+The content of Page info is saved as a header when exporting correlation functions via the command \textit{Current page / Save data (*.csv)} (\hyref{Section}{sec:menub.curre.saved}).
\subsubsection{Tools / Slider simulation}
-\label{sec:tm.ss}
-This tool visualizes the impact of model parameters on the shape of the model function of a current page. Such insight may be useful to choose proper starting values for fitting or to develop new model functions. For example, in the case two of the parameters trade during the fitting one may explore to which extent a change in both values produces similar trends.
+\label{sec:menub.tools.slide}
+This tool visualizes the impact of model parameters on the shape of the model function of a current page. Such insight may be useful to choose proper starting values for fitting or to develop new model functions. For example, in the case of two parameters that trade during the fitting one may explore to which extent a change in both values produces similar trends.
-Two variables (A and B) have to be assigned from a drop-down list of parameters associated with the current model function. For each of these, the \textit{Slider simulation} panel shows initially the starting value (x) as a middle position of a certain range (from 0.1*x to 1.9*x). The accessible range can be manually edited and the actual value of the slider position is displayed at the right hand side of the panel. Dragging the slider to lower (left) or higher (right) values changes the [...]
+Two variables (A and B) have to be assigned from a drop-down list of parameters associated with the current model function. For each of these, the \textit{Slider simulation} panel shows initially the starting value (x) as a middle position of a certain range (from 0.1*x to 1.9*x). The accessible range can be manually edited and the actual value of the slider position is displayed at the right hand side of the panel. Dragging the slider to lower (left) or higher (right) values changes the [...]
In addition, the variables A and B can be linked by a mathematical relation. For this a mathematical operator can be selected from a small list and the option \textit{Fix relation} must be checked. Then, the variable B appears inactivated (greyed out) and the new variable combining values for A and B can be explored by dragging.
\subsection{Current Page}
-\label{sec:cp}
+\label{sec:menub.curre}
This menu compiles import and export operations referring exclusively to the active page in the main window.
\subsubsection{Current Page / Import Data}
-\label{sec:cp.id}
-This command is the third way to import data into a pre-existing session. Single files containing correlation data can be imported as long as they have the right format (\hyref{Section}{sec:fm.ld}). In contrast to \textit{Load data} from the \textit{File} menu, the model assignment and the state of the parameters remains. The purpose of this command is to compare different data sets to the very same model function for a given parameter values. After successful import, the previous correl [...]
+\label{sec:menub.curre.impor}
+This command is the third way to import data into a pre-existing session. Single files containing correlation data can be imported as long as they have the right format (\hyref{Section}{sec:menub.filem.loadd}). In contrast to \textit{Load data} from the \textit{File} menu, the model assignment and the state of the parameters remains. The purpose of this command is to compare different data sets to the very same model function for a given set of parameters. After successful import, the pr [...]
-To avoid this loss, one could first generate a new page via the menu (\hyref{Section}{sec:tm.m}), select a model function and import data there. This is also a possibility to assign the very same data to different models within the same session.
+To avoid this loss, one could first generate a new page via the menu \textit{Models} (\hyref{Section}{sec:menub.model}), select a model function and import data there. This is also a possibility to assign the very same data to different models within the same session.
\subsubsection{Current Page / Save data (*.csv)}
-\label{sec:cp.sd}
-For the documentation with graphics software of choice, correlation curves can be exported as a comma-separated table. A saved \textit{PyCorrFit} text-file (*.csv) will contain a hashed header with metadata from the \textit{Page info} tool (\hyref{Section}{sec:tm.pi}), followed by the correlation and fitting values in tab-separated columns: \textit{Channel (tau [s])}, \textit{Experimental correlation}, \textit{Fitted correlation}, \textit{Residuals}, and \textit{Weights (fit)}.
+\label{sec:menub.curre.saved}
+For the documentation with graphics software of choice, correlation curves can be exported as a comma-separated table. A saved \textit{PyCorrFit} text-file (*.csv) will contain a hashed header with metadata from the \textit{Page info} tool (\hyref{Section}{sec:menub.tools.pagei}), followed by the correlation and fitting values in tab-separated columns: \textit{Channel (tau [s])}, \textit{Experimental correlation}, \textit{Fitted correlation}, \textit{Residuals}, and \textit{Weights (fit)}.
Below the columns, there are again 5 rows of hashed comments followed by the intensity data in two columns: \textit{Time [s]} and \textit{Intensity trace [kHz]}. Note that there are no assemblies of ``multiple runs'', since \textit{PyCorrFit} treats these as individual correlation functions. A *.csv file therefore contains only a single fitted correlation curve and one intensity trace for autocorrelation or two intensity traces for cross-correlation.
\subsubsection{Current Page / Save correlation as image}
-\label{sec:cp.sc}
-For a quick documentation, the correlation curve can be exported as a compressed bitmap (*.png). The plot contains a legend and the actual values and errors of the varied parameters, however, not the fixed parameters. Note that the variable tau cannot be displayed using Unicode with Windows.
+\label{sec:menub.curre.savec}
+The correlation curve can be exported as bitmap (e.g. *.png for quick documentation) or as a scalable vector graphic (e.g. *.pdf for post-processing in \textit{Adobe Illustrator} or \textit{Inkscape}). The plot contains a legend and fitting parameters. Note that the variable $\tau$ (= tau) cannot be displayed using Unicode with Windows. A \LaTeX formatted image can be exported when the option \textit{Use Latex} is checked in the \textit{Preferences} menu (\hyref{Section}{sec:menub.prefe} [...]
\subsubsection{Current Page / Save trace view as image}
-\label{sec:cp.st}
-For a quick documentation the intensity from the \textit{Trace view} panel can be exported as a compressed bitmap (*.png).
+\label{sec:menub.curre.savet}
+An image of the trace can be exported in the same way as for the correlation curve (see above).
\subsubsection{Current Page / Close page}
-\label{sec:cp.cp}
+\label{sec:menub.curre.close}
Closes the page; the data set is removed from the session. The page numbers of all other pages remain the same. The command is equivalent with the closer (x) in the tab.
\subsection{Models}
-\label{sec:models}
-When choosing a model from the \textit{Models} menu a new page opens and the model function is plotted according to the set of starting values for parameters as they were defined in the model description. The lists contains all of the implemented model functions, which can be selected during \textit{File / Load data}. The parameters can be manipulated to explore different shapes; the tool \textit{Slider simulation} can also be used. Via \textit{Current page / Import data}, the model may [...]
-Standard model functions for a confocal setup are:
+\label{sec:menub.model}
+When choosing a model from the \textit{Models} menu, a new page opens and the model function is plotted according to the set of starting values for parameters as they were defined in the model description. The lists contains all of the implemented model functions, which can be selected during \textit{File / Load data}. The parameters can be manipulated to explore different shapes; the tool \textit{Slider simulation} can also be used. Via \textit{Current page / Import data}, the model may [...]
\begin{tabular}{l l}
%Confocal (Gaussian): 3D \ \ \ \ \ \ [Free diffusion in three dimensions]
@@ -442,7 +309,7 @@ Standard model functions for a confocal setup are:
\rule{0pt}{3ex}
\end{tabular}
-There is also a collection of models for FCS setups with TIR excitation:
+\noindent There is also a collection of models for FCS setups with TIR excitation (\hyref{Section}{sec:imple.tirfc}):
\begin{tabular}{l l}
\rule{0pt}{3ex} - TIR (Gaussian/Exp.): 3D & 3D diffusion \\
@@ -451,152 +318,369 @@ There is also a collection of models for FCS setups with TIR excitation:
\rule{0pt}{3ex}
\end{tabular}
-
-In addition, there are may be user defined model functions which have been uploaded previously via File / Import model (\hyref{Section}{sec:fm.im}).
+\noindent
+In addition, there are may be user defined model functions which have been imported previously via \textit{File / Import model} (\hyref{Section}{sec:menub.filem.impor}).
\subsection{Preferences}
-\paragraph*{Latex} If the user has a Tex distribution (e.g. MikTex for Windows) installed, checking the ``Latex'' option will open a separate, TeX formatted panel (\textit{Figure1}) via the \textit{Current page / Save […] as image} commands. The \textit{Figure1} contains some interactive options for display. From there, in a second step, the image can be exported as *.png or *.svg.
+\label{sec:menub.prefe}
+\paragraph*{Use Latex} If the user has a Tex distribution installed (e.g. MikTex for Windows), checking this option will generate \LaTeX formatted plots via the \textit{Current page / Save […] as image} commands.
-\paragraph*{Verbose} If checked, this will cause the \textit{PyCorrFit} to display graphs that would be hidden otherwise. In weighted fitting with a spline, the spline function used for calculating the weights for each data points is displayed\footnote{For obvious reasons, such a plot is not generated when using the iteratively improved \textit{Model function} or the actual \textit{Average} correlation curve for weighted fitting.}. When saving the correlation curve as an image (\hyref{Se [...]
+\paragraph*{Verbose mode} If checked, this will cause the \textit{PyCorrFit} to display graphs that would be hidden otherwise. In weighted fitting with a spline, the spline function used for calculating the weights for each data points is displayed\footnote{For obvious reasons, such a plot is not generated when using the iteratively improved \textit{Model function} or the actual \textit{Average} correlation curve for weighted fitting.}. When saving the correlation curve as an image (\hyr [...]
\paragraph*{Show weights}
-Checking the option \textit{Show weights} will produce two lines showing the weights for each data point of the correlation function in the plot, as well as in the exported image. Note that the weights are always exported when using the \textit{Save data (*.csv)} command from the \textit{Current page} menu.
+Checking this option will visualize the weights for each data point of the correlation function in the plot, as well as in the exported image. Note that the weights are always exported when using the \textit{Save data (*.csv)} command from the \textit{Current page} menu.
\subsection{Help}
-\paragraph*{Documentation}
+\label{sec:menub.help}
+\paragraph*{Documentation.}
This entry displays this documentation using the systems default PDF viewer.
-\paragraph*{Wiki}
+\paragraph*{Wiki.}
This entry displays the wiki of \textit{PyCorrFit} on \textit{GitHub}. Everyone who registers with \textit{GitHub} will be able to make additions and modifications. The wiki is intended for end-users of \textit{PyCorrFit} to share protocols or to add other useful information.
\paragraph*{Update}
-establishes a link to the GitHub website to check for a new release; it also provides a few web links associated with PyCorrFit
-\paragraph*{Shell}
+establishes a link to the \textit{GitHub} website to check for a new release; it also provides a few web links associated with \textit{PyCorrFit}
+\paragraph*{Shell.}
This gives Shell-access to the functions of \textit{PyCorrFit}. It is particularly useful for trouble-shooting.
-\paragraph*{Software}
-This lists the exact version of \textit{Python} and the corresponding modules with which PyCorrFit is currently running.
-\paragraph*{About}
+\paragraph*{Software.}
+This lists the exact version of \textit{Python} and the corresponding modules with which \textit{PyCorrFit} is currently running.
+\paragraph*{About.}
Information of the participating developers, the license, and documentation writers.
-\section{4 Hacker's corner}
-\paragraph*{New internal model functions}
-Additionally, new file formats can be implemented by programming of the readfiles module of \textit{PyCorrFit}. First, edit the code for \texttt{\_\_init\_\_.py} and then add the script \texttt{read\_FileFormat.py}.
+\section{Hacker's corner}
+\label{sec:hacke}
+\subsection{External model functions}
+\label{sec:hacke.extmod}
+\textit{PyCorrFit} supports the import of your own model functions. If your model function is not implemented, i.e. not available in the \textit{Models} menu, writing a short text file containing a model description is the easiest way to make \textit{PyCorrFit} work.
+Some examples can be found at GitHub in the \textit{PyCorrFit} repository, e.g. circular scanning FCS \cite{Petrasek2008} (\hyref{Figure}{fig:csfcs}) or a combination of diffusion and directed flow \cite{Brinkmeier1999}. Model functions are imported as text files (*.txt) that must follow a certain format and syntax:
+\begin{itemize}
+\item \textbf{Encoding}: \textit{PyCorrFit} can interpret the standard Unicode character set. The model files have to be encoded in \textit{UTF-8}.
+\item \textbf{Comments}: Lines starting with a hash (\texttt{\#}), empty lines, or lines containing only white space characters are ignored. The only exception is the first line starting with a hash followed by a white space and a short name of the model. This line is evaluated to complement the list of models in the dialogue\textit{ Choose }\textit{model}, when loading the data. Imported models are available from the menu \textit{Models/User}.
+\item \textbf{Units}: \textit{PyCorrFit} works with internal units for:
+\begin{itemize}
+\item Time: \SI{1}{ms}
+\item Distance: \SI{100}{nm}
+\item Diffusion coefficient: \SI{10}{\mu m^2s^{-1}}
+\item Inverse time: \SI{1000}{s^{-1}}
+\item Inverse area: \SI{100}{\mu m^{-2}}
+\item Inverse volume: \SI{1000}{\mu m^{-3}}
+\end{itemize}
+\item \textbf{Parameters:} To define a new model function, new parameters can be introduced. Parameters are defined by a sequence of strings separated by white spaces containing name, the dimension in angular brackets, the equal sign, and a starting value which appears in the main window for fitting. For example: \texttt{D [\SI{10}{\mu m^ 2 s^{-1}}] = 5.0}. User defined dimensions are only for display; thus mathematical expressions must correctly account for their conversion from interna [...]
+\item \textbf{Placeholder:} When defining composite mathematical expressions for correlation functions, one can use place-holders. Place-holders start with a lower-case ‘g’. For example, the standard, Gaussian 3D diffusion in free solution may be written as
+
+\begin{itemize}
+\item \texttt{gTrp = 1+ T/(1-T)*exp(-tau/tautrip)}
+\item \texttt{gTwoD = 1/(1+tau/taudiff)}
+\item \texttt{gThrD = 1/sqrt(1+tau/(taudiff*S**2))}
+\end{itemize}
+\end{itemize}
+The individual parts are then combined in the last line of the *.txt file, where the correlation function is defined starting with upper-case ’G’:
+
+\begin{equation}
+\texttt{G = 1/n * gTrp * gTwoD * gThrD} \notag
+\end{equation}
+For reference of mathematical operators, check for example \href{http://www.tutorialspoint.com/python/python_basic_operators.htm}{www.tutorialspoint.com / python / python\_basic\_operators.htm}. To illustrate a more complex example, a model function for circular scanning FCS is shown in \hyref{Figure}{fig:csfcs}.
+External models will be imported with internal model function IDs starting at $7000$. Models are checked upon import by the Python module sympy. If the import fails, there is most likely syntax error in the model file.
+\begin{figure}
+% for case sensitiver Verbatim, we need the package fancyvrb
+\begin{Verbatim}[frame = single]
+# CS-FCS T+2D+2D+S (Confocal)
+
+# Circular Scanning FCS model function for two 2D-diffusing species
+# including triplet component.
+
+## Definition of parameters:
+# First, the parameters and their starting values for the model function
+# need to be defined. If the parameter has a unit of measurement, then it
+# may be added separated by a white space before the "=" sign. The starting
+# value should be a floating point number. Floating point abbreviations
+# like "1e-3" instead of "0.001" may be used.
+
+# Diffusion coefficient of first component
+D1 [10µm²/s] = 200.0
+# Diffusion coefficient of second component
+D2 [10µm²/s] = 20.0
+# Fraction of species one
+F1 = 1.0
+# Half waist of the lateral detection area (w0 = 2*a)
+a [100nm] = 1.0
+# Particle number
+n = 5.0
+# Scan radius
+R [100nm] = 3.850
+# Frequency
+f [kHz] = .2
+# Triplet fraction
+T = 0.1
+# Triplet time
+tautrip [ms] = 0.001
+offset = 0.00001
+
+# The user may wish to substitute certain parts of the correlation function
+# with other values to keep the formula simple. This can be done by using
+# the prefix "g". All common mathematical functions, such as "sqrt()" or
+# "exp()" may be used. For convenience, "pi" and "e" are available as well.
+
+gTriplet = 1. + T/(1-T)*exp(-tau/tautrip)
+gScan1 = exp(-(R*sin(pi*f*tau))**2/(a**2+D1*tau))
+gScan2 = exp(-(R*sin(pi*f*tau))**2/(a**2+D2*tau))
+gTwoD1 = F1/(1.+D1*tau/a**2)
+gTwoD2 = (1-F1)/(1.+D2*tau/a**2)
+
+# The final line with the correlation function should start with a "G"
+# before the "=" sign.
+
+G = offset + 1./n * (gTwoD1 * gScan1 + gTwoD2 * gScan2) * gTriplet
+\end{Verbatim}
+\mycaption{user defined model function for PyCorrFit}{The working example shows a model function for circular scanning FCS (see also its appearance in the \textit{Main window} \hyref{Figure}{fig:csfcsplot} \label{fig:csfcs}}
+\end{figure}
+
+\subsection{Internal model functions}
+Alternatively, new models can be implemented by programming of the models module of \textit{PyCorrFit}. First, edit the code for \texttt{\_\_init\_\_.py} and then add the script containing the model function. There is no Tutorial yet, but the implemented model files are self-explanatory. If you need help creating a new internal model function and/or want to publish it with \textit{PyCorrFit}, do not hesitate to contact an active developer by creating a new issue on GitHub.
+
+\subsection{Correlation curve file format}
+\label{sec:hacke.csv}
+PyCorrFit can read correlation data from many file formats.
+If a file format is not yet listed, the correlation data could be converted into a compatible text-file (*.csv) or bundles of *.csv files within a compressed *.zip archive. For reformatting the following requirements must be fulfilled:
+
+\begin{itemize}
+\item \textbf{Encoding}: \textit{PyCorrFit} uses the standard Unicode character set (UTF-8). However, since no special characters are needed to save experimental data, other encodings may also work. New line characters are \texttt{{\textbackslash}r{\textbackslash}n} (Windows).
+\item \textbf{Comments}: Lines starting with a hash (\texttt{\#}), empty lines, or lines containing only white space characters are ignored. Exceptions are the keywords listed below.
+\item \textbf{Units}: PyCorrFit works with units/values for:
+
+\begin{itemize}
+\item Time: \SI{1}{ms}
+\item Intensity: \SI{1}{kHz}
+\item Amplitude offset: $G(0) = 0$ (not 1)
+\end{itemize}
+\item \textbf{Keywords:}\footnote{Keywords are case-insensitive.} \textit{PyCorrFit} reads the first two columns containing numerical values. The first table (non-hashed) is recognized as the correlation data containing the lag times in the first and the correlation data in the second column. (In case the *.csv file has been generated with \textit{PyCorrFit} up to three additional columns containing the fit function are ignored). The table ends, when the keyword \texttt{\# BEGIN TRACE} a [...]
+\item \textbf{Tags:}\footnote{Tags are case-insensitive.} Channel information can be entered using defined syntax in a header. The keyword
+\begin{center}
+\vspace{-1em}
+ \texttt{\# Type AC/CC Autocorrelation}
+\vspace{-1em}
+\end{center}
+ assigns the tag \texttt{AC} and the keyword
+\begin{center}
+\vspace{-1em}
+ {\texttt{\# Type AC/CC Crosscorrelation}}
+\vspace{-1em}
+\end{center}
+ assigns the tag \texttt{CC} to the correlation curve. These strings are consistently displayed in the user interface of the respective data page in \textit{PyCorrFit}. If no data type is specified, autocorrelation is assumed. Tags may be specified with additional information like channel numbers, e.g.
+\begin{center}
+\vspace{-1em}
+ \texttt{\# Type AC/CC Autocorrelation \_01}.
+\vspace{-1em}
+\end{center}
+In this case the tag \texttt{AC\_01} is generated. This feature is useful to keep track of the type of curve during the fitting and when post-processing the numerical fit results.
+\end{itemize}
-External models will be imported with internal model function IDs starting at $7000$. Models are checked upon import by the Python module sympy. If the import fails it might be a syntax error or just an error of sympy, since this module is still under development.
+\subsection{New file format}
+Alternatively, new file formats can be implemented by programming of the readfiles module of \textit{PyCorrFit}. First, edit the code for \texttt{\_\_init\_\_.py} and then add the script \texttt{read\_FileFormat.py}.
+There is no Tutorial yet, but the implemented scripts are self-explanatory. If you need help implementing a new file format and/or want to publish it with \textit{PyCorrFit}, do not hesitate to contact an active developer by creating a new issue on GitHub.
\section{Theoretical background}
-\subsection{Derivation of FCS model functions}
-This section introduces the calculation of FCS model functions. It supplies some background information and points out general properties of correlation functions.
-
- \subsubsection{General Autocorrelation function for a single species}
- FCS model functions describe how the signal $F(t)$, emitted from a certain observation volume, is temporally dependent on its own past (autocorrelation) or on some other signal (cross-correlation). The autocorrelation $G(\tau)$ of a signal $F(t)$ is computed as follows:
- \newline
- \newline
- %\fbox{ {
- \begin{minipage}{\textwidth}
- %\textbf{Mathematical foundation - Autocorrelation function:}
+\label{sec:theor}
+In the first place, \textit{PyCorrFit} was designed to evaluate FCS data, therefore we focus on fluorescence. However, the correlation theory could be applied to any other stochastic signal.
+
+\subsection{How FCS works}
+\label{sec:theor.howfc}
+
+FCS is a method to determine molecular properties of stochastically moving fluorescent molecules in solutions \cite{Elson1974,Magde1974,Magde1978}. The solution may be a liquid volume (3D) or a lipid membrane (2D) \cite{Widengren1998,Korlach1999,Schwille1999}. The diffusion may be free or anomalous due to barriers or obstacles \cite{Wachsmuth2000,Weiss2003}. The size of the diffusing particles range from synthetic dyes (\SI{800}{Da}) to large complexes or aggregates of labelled macromole [...]
+
+The measurement principle is to illuminate a small open volume within solutions of fluorescent molecules and to detect their molecular transits with a sub-microsecond time resolution by sensitive optics. The stochastic movements and other processes affecting fluorescence emission generate a fluctuating signal. The typical time pattern of these fluctuations can be revealed by a correlation analysis. The shape and time range of the decaying correlation function is defined by the exact geom [...]
+
+\subsection{Framework for a single type of fluorescent dye}
+\label{sec:theor.frame}
+The following equations are described in many papers in different ways. Here we follow the notation of one of us \cite{Weidemann2009}. Fluorescence signals are a result of absorption and emission of photons by a fluorophore. Under experimental conditions, the signal depends on the time dependent distribution of fluorescent particles in the sample volume $c(\vec{r},t)$ and the normalized instrumental detection efficiency $W(\vec{r})$. The total intensity, signal $S(t)$, is the sum of all [...]
+ \begin{equation}
+ \label{eq1}
+ S(t) = q \int W(\vec{r}) c(\vec{r},t) \,dV
+ \end{equation}
+The factor $q$ combines all the photo-physical quantities associated with fluorescence emission like absorption cross section, quantum yield, and the peak intensity of excitation (laser power). In the following, time averages of observables are indicated by angular brackets. We apply the ergodic theorem (see below).
+ \begin{equation}
+ \label{eq2}
+ \langle S(t) \rangle = \lim_{t\to\ \infty} \int S(t) \,dt = q \int W(\vec{r}) c \,dV = qn
+ \end{equation}
+\hyref{Equation}{eq2} reveals that $q$ is the instrument dependent molecular brightness (kHz/particle), i.e. the average signal divided by the average number of particles $n$ observed within the effective detection volume $V_{\rm eff} = \int W(\vec{r}) \,dV$. During FCS measurements the detected signal is correlated by computing a normalized autocorrelation function:
+ \begin{equation}
+ \label{eq3}
+ G(\tau) = \frac{\langle S(t) \cdot S(t+\tau)\rangle}{\langle S(t) \rangle^2}-1 = \frac{\langle \delta S(t) \cdot \delta S(t+\tau)\rangle}{\langle S(t) \rangle^2} = \frac{g(\tau)}{\langle S(t) \rangle^2}
+ \end{equation}
+Here, $\tau$ denotes the lag time used for correlation and $\delta S(t) = S(t)-\langle S \rangle$ the amplitude of the signal fluctuation for a given time point. \hyref{Equation}{eq3} defines a function with a finite intercept decaying to zero, whereas $g(\tau)$, the non-normalized correlation function, decays to a finite value $\langle S \rangle^{-2}$. To visualize correlation times, the functions $G(\tau)$ are typically plotted against $\log(\tau)$ (\hyref{Figure}{fig:mainwin}).
+
+A general way to derive theoretical model functions is to evaluate \hyref{Equation}{eq3} with explicit expressions describing the instrumental detection efficiency $W(\vec{r})$ and the molecular dynamics governing the local fluorophore concentrations $c(\vec{r},t)$. For example, free diffusion of the molecules can be described by the so-called diffusion propagator.
\begin{equation}
- G(\tau) = \frac{\langle \delta F(t) \delta F(t+\tau) \rangle}{\langle F(t) \rangle^2} = \frac{g(\tau)}{\langle F(t) \rangle^2}.
+ \label{eq4}
+ P_\mathrm{d} \left( \vec{r} \,' | \vec{r},\tau \right) = \frac{1}{\left( 4 \pi D_t \tau \right) ^{3/2}} \exp \left[ - \frac{\left| \vec{r} \,' -\vec{r} \, \right|} {4D_t \tau} \right]
\end{equation}
- \begin{itemize} \small
- \item[$G(\tau)$] normalized autocorrelation curve
- \item[$\tau$] lag time
- \item[$\langle F \rangle$] the expectation value of $F(t)$. Applying the ergodic theorem, this can be rewritten as the time average \[ \langle F(t) \rangle = \lim_{T \rightarrow \inf }\frac{1}{T} \int_0^T F(t) \mathrm{d}t. \]
- \item[$\delta F(t)$] $= F(t) - \langle F(t) \rangle$ fluctuation of the fluorescence signal
- \item[$g(\tau)$] non normalized autocorrelation curve
- \end{itemize}
- \end{minipage}
- %}
- %}
- \newline
- \newline
- \newline
- The fluorescence signal is dependent on the size and shape of the detection volume (e.g. Gaussian shaped for confocal setups or exponential decaying for TIRF setups), on the propagator of the diffusing dye (free diffusion, diffusion with flow, etc.), and the brightness and concentration of the dye under observation\cite{Burkhardt2010}. \\
- \newline
- %\fbox{ {
- \begin{minipage}{\textwidth}
- %\textbf{General Correlation function for a single species:}
+The propagator $P_\mathrm{d} \left( \vec{r} \,' | \vec{r},\tau \right)$ is the conditional probability of a particle with diffusion coefficient $D_t$ to move from $\vec{r}$ to $\vec{r \,'}$ within a time period $\tau$.
+The probability to find a particle inside the volume $d^3r$ is simply the ratio of volumes $d^3r/V$.
+ Such a diffusion propagator leads to a Gaussian shaped probability distribution spreading in time when the molecules successively roam the sample volume $V$.
+Assuming that the time average and the ensemble average are equivalent (ergodic theorem), the average signal of a single particle is its molecular brightness $q$ normalized to its contribution to the entire volume, because the integral over the detection efficiency function is exactly the effective measurement volume $V_\mathrm{eff}$.
\begin{equation}
- G(\tau) = \frac{ q^2 C \int \! \mathrm{d}^3 r \int \! \mathrm{d}^3 r' \, \Omega(\mathbf{r})\Phi(\mathbf{r}, \mathbf{r'}, \tau) \Omega(\mathbf{r'}) }{\langle F(t) \rangle^2}
+ \label{eq5}
+ \langle s(t) \rangle = q \frac{\int W(\vec{r}) \,dV}{V} = \frac{V_\mathrm{eff}}{V} q
\end{equation}
- \begin{itemize} \small
- \item[$q$] molecular brightness, dependent on excitation intensity, quantum yield, i.e. emission properties and absorption cross sections of the dye, and the detection efficiency of the instrument.
- \item[$\Omega$] 3D molecule detection function, dependent on the shape of the pinholes used for detection and the excitation laser profile, i.e. the point spread function (PSF).
- \item[$\Phi$] diffusion propagator. The distribution of dyes in a liquid follows Fick's laws of diffusion. For free diffusion, this is a simple Gaussian distribution.
- \item[$F$] fluorescence signal of the sample. It is defined as
- \[ F(t) = q \int \! \mathrm{d}^3 r \, \Omega(\mathbf{r}) c(\mathbf{r}, t) \] with $c(\mathbf{r}, t)$ being dye distribution (particle concentration) inside the detection volume.
- \item[$C$] average concentration of the dye following the dynamics of the propagator $\Phi$. Using the ergodic hypothesis and assuming a normalized molecule detection function (${V_\mathrm{eff} = \int \!\! d^3r \, \Omega(\mathbf{r}) = 1}$), the concentration computes to $ C = \langle F(t) \rangle / q$.
- \end{itemize}
- \end{minipage}
- %}
- %}
-
-
-\subsubsection{General Autocorrelation function for multiple species}
-%Most experiments do not only include a single species of fluorescent dye. When considering a three dimensional detection volume with a freely diffusing dye, adding a lipid bilayer with a different fluorescent dye (diffusing in two dimensions inside the bilayer) will result in two distinct contributions to the fluorescence signal, namely 2D diffusion and 3D diffusion. For $n$ different species inside the detection volume, the autocorrelation function becomes:
-Most experiments include particles with more than one dynamic property. Labeled particles may have different size or the temporal dynamics may include a triplet term. For $n$ different species inside the detection volume, the autocorrelation function becomes:
- \newline
- \newline
- %\fbox{ {
- \begin{minipage}{\textwidth}
- %\textbf{General Correlation function for n species:}
+Accordingly, we can express the average product of two signals separated by $\tau$ as
\begin{equation}
- G(\tau) = \frac{g(\tau)}{\langle F(t) \rangle^2} = \frac{\sum_{i=1}^n \sum_{j=1}^n g_{ij}(\tau)}{\langle F(t) \rangle^2}
+ \label{eq6}
+ \langle s(t) \cdot s(t + \tau) \rangle = \frac{q^2}{V}\iint W(\vec{r}) P_\mathrm{d} \left( \vec{r} \,' | \vec{r},\tau \right) W(\vec{r} \,') dVdV'
\end{equation}
+With the definition of the signal $S(t)$ and its average $\langle S(t) \rangle$
+\begin{align}
+S(t) &= \Sigma_{k=1}^n s_k(t) \\
+\langle S(t) \rangle &= \Sigma_{k=1}^n \langle s_k(t) \rangle := N \langle s(t) \rangle
+\end{align}
+- where $N$ is the total number of particles in the sample volume $V$ - we can reduce $G(\tau)$ to the sum of individual molecular contributions
+ \begin{align}
+ G(\tau) = \frac{\langle S(t) \cdot S(t+\tau)\rangle}{\langle S(t) \rangle^2}-1
+ =& \frac{\overbrace{N \langle s(t) \cdot s(t+\tau)\rangle}^{\mbox{\small same particles}} +\overbrace{N(N-1) \langle s(t) \rangle^2}^{\mbox{\small different particles}}}{N^2 \langle s(t) \rangle^2}-1 \notag \\
+ \approx & \frac{\langle s(t) \cdot s(t+\tau)\rangle}{N \langle s(t) \rangle^2} \label{eq7}
+ \end{align}
+Inserting \hyref{Equation}{eq5} and \hyref{Equation}{eq6} yields
\begin{equation}
- g_{ij}(\tau) = q_i q_j \int \! \mathrm{d}^3 r \int \! \mathrm{d}^3 r' \, \Omega(\mathbf{r})\Phi_{ij}(\mathbf{r}, \mathbf{r'}, \tau) \Omega(\mathbf{r'})
+ \label{eq8}
+ G(\tau) = \frac{V}{N} \frac{\iint W(\vec{r}) P_\mathrm{d} \left( \vec{r} \,' | \vec{r},\tau \right) W(\vec{r} \,') dVdV'}{\left( \int W(\vec{r}) \,dV \right)^2}
\end{equation}
- \begin{itemize} \small
- \item[$g(\tau)$] non normalized correlation function
- \item[$g_{ij}(\tau)$] non normalized cross correlation between two species $i$ and $j$. For $n$ species, $i,j \in [1,...,n]$.
- \item[$q_i$] molecular brightness of species $i$
- \item[$\Omega$] 3D molecule detection function
- \item[$\Phi_{ij}$] diffusion propagator computed from species $i$ with species $j$. If species $i$ and $j$ are independently diffusing, then $\Phi_{ij}$ is zero.
- $ C_{ij} \Phi_{ij}(\mathbf{r}, \mathbf{r'}, \tau) = \, \langle \delta c_i(\mathbf{r},0) \delta c_j(\mathbf{r'}, \tau) \rangle $
- \item[$C_{ij}$] average concentration of objects following the dynamics of $\Phi_{ij}$. If $i=j$, $C_{ii}=C_i$ is the concentration of the dye $i$.
- \end{itemize}
- \end{minipage}
- %}
- %}
- \newline
- \newline
- If the propagators $\Phi_{ij}(x,y,z; x',y',z'; \tau)$ and the molecule detection function $\Omega(x,y,z)$ factorize into an axial ($z$) and a lateral ($x,y$) part, so will $g_{ij}(\tau)$:
+Note that the molecular brightness $q$ cancels; when considering multiple species with different $q$, this is no longer the case.
+Solving these integrals for the confocal detection scheme yields a relatively simple equation containing the diffusion coefficient $D_t$ (molecular property) and the $1/e^2$ decay lengths $w_0$ and $z_0$ capturing the dimension of the Gaussian detection volume transversal and parallel to the optical axis, respectively (instrumental properties).
\begin{equation}
- g_{ij}(\tau) = q_i q_j \cdot g_{ij,z}(\tau) \cdot g_{ij,xy}(\tau)
+ \label{eq9}
+ G(\tau) = \frac{1}{n} \left(1+\frac{4 D_t \tau}{w_0^2} \right) ^{-1} \left(1+\frac{4D_t \tau}{z_0^2} \right)^{-1/2}
\end{equation}
- Following the example with a freely diffusing species $A$ and a laterally diffusing species $B$ inside a membrane at $z = z_0$, it can be concluded:
- \begin{eqnarray*}
- g_{AA}(\tau) = && q_A^2 \cdot g_{AA,z}(\tau) \cdot g_{AA,xy}(\tau) \\
- g_{BB}(\tau) = && q_B^2 \cdot g_{BB,z_0}(\tau) \cdot g_{BB,xy}(\tau) \\
- g_{AB}(\tau) = g_{BA} (\tau) = && q_A q_B \cdot g_{AB,z}(\tau) \cdot g_{AB,xy}(\tau) \\
- g(\tau) = && g_{AA}(\tau) + 2 g_{AB}(\tau) + g_{BB}(\tau)
- \end{eqnarray*}
- To obtain the normalized autocorrelation function, the average $\langle F(t) \rangle$ has to be calculated:
- \begin{eqnarray*}
- F(t) = && \sum_{i=1}^n F_i(t) \\
- F_A(t) = && q_A \int \! \mathrm{d}^3 r \, \Omega(\mathbf{r}) C_A(\mathbf{r}, t) \\
- F_B(t) = && q_B \int \! \mathrm{d}x \! \int \! \mathrm{d}y \, \Omega(x,y,z=z_0) C_B(x,y, t) \\
- \langle F(t) \rangle = && \langle F_A(t) \rangle + \langle F_B(t) \rangle
- \end{eqnarray*}
- It is noticeable, that $C_B$ is a 2D concentration, whereas $C_A$ is a 3D concentration. Since there is no correlation between the two freely diffusing species $A$ and $B$, $g_{AB}(\tau)$ is zero. The normalized autocorrelation curve may now be calculated like this:
- \begin{eqnarray*}
- G(\tau) = && \frac{g(\tau)}{\langle F(t) \rangle^2} \\
- G(\tau) = && \frac{g_{AA}(\tau) + g_{BB}(\tau)}{(\langle F_A(t) \rangle + \langle F_B(t) \rangle)^2} \\
- \end{eqnarray*}
-
- \subsubsection{Cross-correlation}
- Cross-correlation is a generalization of autocorrelation. Cross-correlation functions are derived in the same manner as autocorrelation functions. Here, signals recorded in two detection channels are cross-correlated to obtain the correlation function.
+The inverse intercept $(G(0))^{-1}$ is proportional to the total concentration of oberved particles $C = N/V = n/V_{\rm eff} = n/ (\pi^{3/2}w_0^2z_0)$. It is common to define the diffusion time $\tau_{\rm diff} = {w_0}^2/4D_t$ and the structural parameter $\textit{SP}=z_0^2/w_0^2$ as a measure of the elongated detection volume. Replacement finally yields the well known autocorrelation function for 3D diffusion in a confocal setup (Model ID 6012)
\begin{equation}
- G_{XY}(\tau) = \frac{\langle \delta F_X(t) \delta F_Y(t+\tau) \rangle}{\langle F_X(t) \rangle \langle F_Y(t) \rangle}
+ \label{eq10}
+ G(\tau) \stackrel{\rm def}{=} G^{\rm D}(\tau) = \frac{1}{n} \overbrace{ \left(1+\frac{\tau}{\tau_{\rm {diff}}} \right) ^{-1}}^{\rm 2D} \overbrace{ \left(1+\frac{\tau}{\textit{SP}^2 \, \tau_{\rm {diff}}} \right)^{-1/2}}^{\rm 3D}
\end{equation}
-A cross-correlation analysis of two species labeled by two types of dyes observed in two corresponding detection channels can be used for binding assays. Only complexes giving simultaneous signal in both channels contribute to the cross-correlation amplitude. Thus a finite cross-correlation indicates co-diffusion.
-
- \subsubsection{Extension of the theory}
- By modifying the propagator $\Phi$ and the detection volume $\Omega$, other effects, like triplet blinking or binding reactions can be quantified. In many cases, analytical solutions to the above integrals are not straightforward and approximations have to be made. For example, the Gaussian shaped detection profile in confocal FCS is already an approximation. However, deviations from the true results are considered to be small \cite{Zhang2007}. \hyref{Section}{sec:mdls} introduces sever [...]
+For confocal FCS, both the detection volume $W(\vec{r})$ and the propagator for free diffusion $P_\mathrm{d}$ are described by exponentials (Gaussian functions). Therefore, spatial relationships can be factorized for each dimension $xyz$. As a result, \hyref{Equation}{eq10} can be written as a combination of transversal (2D) and longitudinal (3D) diffusion.
+
+\subsection{Autocorrelation of multiple species}
+\label{sec:theor.autoc}
+Very often in FCS, one observes more than one dynamic property. Besides diffusion driven number fluctuations, a fluorophore usually shows some kind of inherent blinking, due to triplet state transitions (organic dyes) or protonation dependent quenching (GFPs) \cite{Widengren1995}.
+ \begin{equation}
+ \label{eq11}
+ G(\tau) \stackrel{\rm def}{=} G^{\rm T}(\tau) G^{\rm D}(\tau) = \left( 1+ \frac{T}{1-T} \exp\left[-\frac{\tau}{\tau_{\rm trp}} \right] \right)G^{\rm D}(\tau)
+ \end{equation}
+Blinking increases the correlation amplitude $G(0)$ by the triplet fraction $1/(1-T)$. Accordingly, the average number of observed particles is decreased $n = (1-T)/G(0)$. In case of GFP blinking, two different blinking times have been described and the rate equations can get quite complicated.
+Besides photo-physics, the solution may contain mixtures of fluorescent particles with different dynamic properties, e.g. different mobility states or potential for transient binding. Such mixtures show several correlation times in the correlation curve. \hyref{Equation}{eq11} can be derived by considering the correlation functions of an ensemble, which can be built up by the contribution of $n$ single molecules in the sample volume:
+ \begin{equation}
+ \label{eq12}
+ G(\tau) = \frac{g(\tau)}{\langle S(t) \rangle^2} = \frac{\sum_{i=1}^n \sum_{j=1}^n g_{ij}(\tau)}{\langle S(t) \rangle^2}
+ \end{equation}
+with $g_{ij}(\tau)$ as the pairwise correlation function of identical ($i = j$) or distinguishable ($i \not= j$) particles
+ \begin{equation}
+ \label{eq13}
+ g_{ij}(\tau) = \langle s(t) \cdot s(t + \tau) \rangle = \frac{q_iq_j}{V} \int \int W(\vec{r}) P_{\mathrm{d},ij} \left( \vec{r} \,' | \vec{r},\tau \right) W(\vec{r}\,') dVdV'
+ \end{equation}
+Note that the diffusion propagator $P_{\mathrm{d},ij}$ is now indexed, since the movement of some particle pairs may depend on each other and therefore show correlations. If particle $i$ and particle $j$ move independently, the mixed terms cancel $g_{ij}(\tau) = 0$.
+Due to the sums in \hyref{Equation}{eq12}, adding up individual contributions of sub-ensembles is allowed. A frequently used expression to cover free diffusion of similarly labelled, differently sized particles is simply the sum of correlation functions, weighted with their relative fractions $F_k = nk/n$ to the overall amplitude $G(0) = 1/n$:
+ \begin{equation}
+ \label{eq14}
+ G^{\rm D}(\tau) = \sum_{k=1}^m F_k G^{\rm D}(\tau) = \frac{1}{n} \sum_{k=1}^m F_k \left(1+\frac{\tau}{\tau_{{\rm diff},k}} \right) ^{-1} \left(1+\frac{\tau}{\textit{SP}^2 \, \tau_{{\rm diff},k}} \right)
+ \end{equation}
+Up to three diffusion times can usually be discriminated ($m = 3$) \cite{Meseth1999}. Note that this assumes homogenous molecular brightness of the different diffusion species. One of the molecular brightness values $q_k$ is usually taken as a reference ($\alpha_k = q_k/q_1$). Brighter particles are over-represented \cite{Thompson1991}
+ \begin{equation}
+ \label{eq15}
+ G^{\rm D}(\tau) = \frac{1}{n \left( \sum_k F_k \alpha_k \right)^2} \sum_k F_k \alpha_k^2 G_k^D(\tau)
+ \end{equation}
+Inhomogeneity in molecular brightness affects both the total concentration of observed particles as well as the real molar fractions $F_k^{\rm cor}$ \cite{Thompson1991}
+ \begin{equation}
+ \label{eq16}
+ n = \frac{1}{G^{\rm D}(0)} \frac{\sum_k F_k^{\rm {cor}} \alpha_k^2}{\left( \sum_k F_k^{\rm {cor}} \alpha_k \right)^2} \quad\mbox {with} \quad F_k^{\rm {cor}} = \frac{F_k/\alpha_k^2}{\sum_k F_k/\alpha_k}
+ \end{equation}
+
+\subsection{Correcting non-correlated background signal}
+\label{sec:theor.correc}
+In FCS, the total signal is composed of the fluorescence and the non-correlated background: $S = F + B$. Non-correlated background signal like shot noise of the detectors or stray light decreases the relative fluctuation amplitude and must be corrected to derive true particle concentrations \cite{Koppel1974,Thompson1991}. In \textit{PyCorrFit}, the background value [kHz] can be manually set for each channel (B1, B2) (\hyref{Figure}{fig:mainwin}). For autocorrelation measurements ($B1 = B [...]
+ \begin{equation}
+ \label{eq17}
+ n = \frac{1}{G^{\rm D}(0)} \left( \frac{S-B}{S} \right)^2 = \frac{1}{(1-T)G(0)} \left( \frac{S-B}{S} \right)^2.
+ \end{equation}
+For dual-channel applications with cross-correlation (next section) the amplitudes must be corrected by contributions from each channel \cite{Weidemann2013}
+ \begin{equation}
+ \label{eq18}
+ G_{\times,\rm {cor}}(0) = G_{\times, \rm meas}(0) \left( \frac{S_1}{S_1-B_1} \right) \left( \frac{S_2}{S_2-B_2} \right)
+ \end{equation}
+
+\subsection{Cross-correlation}
+\label{sec:theor.cross}
+Cross-correlation is an elegant way to measure molecular interactions. The principle is to implement a dual-channel setup (e.g. channels 1 and 2), where two, interacting populations of molecules can be discriminated \cite{Foo2012,Ries2010,Schwille1997,Weidemann2002}. In a dual-channel setup, complexes containing particles with both properties will evoke simultaneous signals in both channels. Such coincidence events can be extracted by cross-correlation between the two channels. A promine [...]
+ \begin{equation}
+ \label{eq19}
+ G_\times (\tau) \stackrel{\rm def}{=} G_{12} (\tau) = \frac{\langle \delta S_1(t) \delta S_2(t+\tau)\rangle}{\langle S_1(t) \rangle \langle S_2(t) \rangle} \approx \frac{\langle \delta S_2(t) \delta S_1(t+\tau)\rangle}{\langle S_1(t) \rangle \langle S_2(t) \rangle} = G_{21} (\tau)
+ \end{equation}
+A finite cross-correlation amplitude $G_{12}(0)$ indicates co-diffusion of complexes containing both types of interaction partners. The increase of the cross-correlation amplitude is linear for heterotypic binding but non-linear for homotypic interactions or higher order oligomers. The absolute magnitude of the cross-correlation amplitude must be calibrated because the chromatic mismatch of the detection volumes (different wavelength, different size) and their spatial displacement ($d_\m [...]
+ \begin{equation}
+ \label{eq20}
+ G(\tau) = \frac{1}{n} \left(1+\frac{4 D_t \tau}{w_0^2} \right) ^{-1} \left(1+\frac{4D_t \tau}{z_0^2} \right)^{-1/2} \exp \left(- \frac{d_\mathrm{x}^2 + d_\mathrm{y}^2}{4 D_t \tau + w_{0,\rm eff}} + \frac{d_\mathrm{z}^2}{4 D_t \tau + z_{0,\rm eff}} \right)
+ \end{equation}
+The ratio between cross- and autocorrelation amplitude is used as a readout which can be linked to the degree of binding. Let us consider a heterodimerization, where channel $1$ is sensitive for green labelled particles ($g$) and channel $2$ is sensitive for red labelled particles ($r$), then the ratio of cross- and autocorrelation amplitudes is proportional to the fraction of ligand bound \cite{Weidemann2002}
+ \begin{eqnarray}
+ \label{eq21}
+ CC_1 \stackrel{\rm def}{=} \frac{G_\times(0)}{G_1(0)} & \propto & \frac{c_{gr}}{c_r} \nonumber \\ CC_2 \stackrel{\rm def}{=} \frac{G_\times(0)}{G_2(0)} &\propto & \frac{c_{gr}}{c_g}
+ \end{eqnarray}
+Recently, a correction for bleed-through of the signals between the two channels has been worked out \cite{Bacia2012}. The effect on binding curves measured with cross-correlation can be quite dramatic \cite{Weidemann2013}. To treat spectral cross-talk, the experimenter has to determine with single coloured probes how much of the signal (ratio in \%) is detected by the orthogonal, 'wrong' channel ($BT_{12}, BT_{12}$). Usually the bleed-through from the red into the green channel can be n [...]
+ \begin{eqnarray}
+ \label{eq22}
+ \langle F_1 \rangle & = & \langle \hat{F}_1 \rangle + \langle \hat{F}_2 \rangle BT_{21} \cong \langle \hat{F}_1 \rangle \nonumber \\ \langle F_2 \rangle & = & \langle \hat{F}_2 \rangle + \langle \hat{F}_1 \rangle BT_{12}
+ \end{eqnarray}
+Here, the dashed fluorescence signals are the true contributions from single labelled species. Thus, each set of simultaneously recorded auto and cross-correlation curves suffers from a specific fraction of wrong signal in the vulnerable red channel, $X_2 = BT_{12} \langle \hat{F}_1 \rangle/\hat{F}_2 \rangle$, which can be used to back-correct the cross-correlation amplitudes \cite{Bacia2012,Weidemann2013}
+\begin{subequations}
+\label{eq23}
+ \begin{align}
+ \frac{c_{gr}}{c_r} & \propto \frac{CC_1-X_2}{\left( 1-X_2 \right)} \label{eq23a} \\
+ \frac{c_{gr}}{c_g} & \propto \frac{CC_2-X_2 \left( 1-X_2 \right) \frac{G_1^{\rm D}(0)}{G_2^{\rm D}(0)}}{1+ X_2 \frac{G_1^{\rm D}(0)}{G_2^{\rm D}(0)} - 2 X_2 CC_2} \label{eq23b}
+ \end{align}
+\end{subequations}
+As apparent from \hyref{Equations}{eq23}, it is much simpler to use the autocorrelation amplitude measured in the green channel for normalization (\ref{eq23a}) and not the cross-talk affected red channel (\ref{eq23b}). Finally, the proportionality between the fraction ligand bound and the measured cross-correlation ratio depend solely on the effective detection volumes of all three channels (two auto- and the cross-correlation channels) and must be determined with appropriate positive c [...]
+
+\subsection{Extensions of the method}
+\label{sec:theor.exten}
+Using as confocal alignment for FCS measurements is very successful and widely applied. However, mainly in the context of membrane research, other excitation schemes have been explored. Once the excitation and detection geometry is changed one has to account for it in the model functions. This is usually done by modifying the expressions of the instrumental detection efficiency $W(\vec{r})$ in \hyref{Equation}{eq8}. However, in many cases analytical solutions to the above integrals are n [...]
+
+\subsubsection{Perpendicular scanning FCS (pSFCS)}
+\label{sec:theor.exten.perpe}
+Scanning FCS with a scan path perpendicular to the membrane plane was introduced to measure the lateral diffusion of fluorescent components of a fluid lipid membrane \cite{Ries2006}. Using the linear scan option of a confocal laser scanning microscope (CLSM), the focal spot is moved repeatedly on a straight line through a free standing membrane (typically the equatorial face of a giant vesicle). The fluorescence photons emitted from the detection volume are continuously recorded and stor [...]
+
+\subsubsection{Circular scanning FCS (cSFCS)}
+\label{sec:theor.exten.circu}
+The principle of circular scanning FCS is similar. Here, the laser focus is moved in small circles, several µm in diameter. While pSFCS requires relatively large free standing membranes, cSFCS can be performed in µm sized homogeneous fluorescent regions of supported bilayers, cell membranes, as well as the apical poles of giant vesicles. Once the radius of the circular scan path has been accurately determined (e.g. with a fluorescent grid), the diffusion coefficients can be determined fr [...]
+
+\begin{figure}[h]
+\centering
+\includegraphics[width=\linewidth]{PyCorrFit_Screenshot_CSFCS.png}
+ \mycaption{user interface with external model function}{cSFCS curve of DiO diffusing in a reconstituted lipid bilayer on glass support. Fitting yields a diffusion coefficient of \SI{0.28}{\mu m^2s^{-1}} ($F1=1$, so only one component is fitted). The source code of the external model function for this fit is shown in \hyref{Figure}{fig:csfcs}.\label{fig:csfcsplot}}
+\end{figure}
+
+\vspace{1em}
+\subsubsection{Total internal reflection FCS (TIR-FCS)}
+\label{sec:theor.exten.total}
+TIR-FCS was developed to measure transient ligand binding events to receptors in the membrane \cite{Thompson2007}. In contrast to scanning FCS, the detection volume is fixed. However, the geometry is confined to the surface showing an exponential decay of the evanescent field along $z$, whereas the lateral boundaries imposed in $xy$ by a pinhole in the detection path. The situation is notoriously difficult to model and different solutions have been proposed.
+
+\paragraph{TIR-FCS with Gaussian-shaped lateral detection volume.}
+The detection volume is axially confined by an evanescent field and has an effective size of
+\begin{align}
+V = \pi R_0^2 d_\mathrm{eva}
+\end{align}
+where $R_0$ is the lateral extent of the detection volume and $d_\mathrm{eva}$ is the evanescent field depth\footnote{Where the field has decayed to $1/e$}. From the concentration $C$, the effective number of particles is $n = CV$.
+The decay constant $\kappa$ is the inverse of the depth $d_\mathrm{eva}$ :
+\begin{align}
+d_\mathrm{eva} = \frac{1}{\kappa}
+\end{align}
+
+\paragraph{TIR-FCS with a square-shaped lateral detection volume.}
+The detection volume is axially confined by an evanescent field of depth $d_\mathrm{eva} = 1 / \kappa$.
+The lateral detection area is a convolution of the point spread function of the microscope of size $\sigma$,
+\begin{align}
+\sigma = \sigma_0 \frac{\lambda}{\mathit{NA}},
+\end{align}
+with a square of side length $a$.
\subsection{Non-linear least-squares fit}
-\label{cha:PyCorFit_leastsq}
-PyCorrFit uses the non-linear least-squares fitting capabilities from \texttt{scipy.optimize}. This package utilizes the Levenberg–Marquardt algorithm to minimize the sum of the squares. More information on this topic can be obtained from the online documentation of \texttt{leastsq}\footnote{\url{http://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.leastsq.html##scipy.optimize.leastsq}}.
+\label{sec:theor.nonle}
+\textit{PyCorrFit} uses the non-linear least-squares fitting capabilities from \texttt{scipy.optimize}. This package utilizes the Levenberg–Marquardt algorithm to minimize the sum of the squares. More information on this topic can be obtained from the online documentation of \texttt{leastsq}\footnote{\url{http://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.leastsq.html##scipy.optimize.leastsq}}.
One can define a distance $d(G,H)$ between two discrete functions $G$ and $H$ with the discrete domain of definition $\tau_1 \dots \tau_n$ as the sum of squares:
\begin{equation}
d(G,H) = \sum_{i=1}^n \left[ G(\tau_i) - H(\tau_i) \right]^2
@@ -609,11 +693,12 @@ The minimum distance $\chi^2$ is used to characterize the success of a fit. Note
\subsection{Weighted fitting}
-In certain cases, it is useful to implement weights (standard deviation) $\sigma_i$ for the calculation of $\chi^2$. For example, very noisy parts of a correlation curve can falsify the resulting fit. In PyCorrFit, weighting is implemented as follows:
+\label{sec:theor.weigh}
+In certain cases, it is useful to implement weights (standard deviation) $\sigma_i$ for the calculation of $\chi^2$. For example, very noisy parts of a correlation curve can falsify the resulting fit. In \textit{PyCorrFit}, weighting is implemented as follows:
\begin{equation}
\chi^2_\mathrm{weighted} = \min_{\alpha_1, \dots, \alpha_k} \sum_{i=1}^n \frac{\left[ G(\tau_i,\alpha_1, \dots, \alpha_k) - H(\tau_i) \right]^2}{\sigma_i^2}
\end{equation}
-PyCorrFit is able to calculate the weights $\sigma_i$ from the experimental data. The different approaches of this calculation of weights implemented in PyCorrFit are explained in \hyref{section}{cha_graphint}.
+\textit{PyCorrFit} is able to calculate the weights $\sigma_i$ from the experimental data. The different approaches of this calculation of weights implemented in \textit{PyCorrFit} are explained in \hyref{Section}{sec:intro.graph}.
\input{PyCorrFit_doc_models}
diff --git a/doc-src/PyCorrFit_doc_models.tex b/doc-src/PyCorrFit_doc_models.tex
index adece58..70b4bb7 100644
--- a/doc-src/PyCorrFit_doc_models.tex
+++ b/doc-src/PyCorrFit_doc_models.tex
@@ -1,28 +1,9 @@
-\subsection{Implemented model functions}
-\label{sec:mdls}
-This is an overview of all the model functions that are currently\footnote{\today} implemented in PyCorrFit. To each model a unique model ID is assigned by PyCorrFit. Most of the following information is also accessible from within PyCorrFit using the \textbf{Page info} tool.
-
-\subsubsection{Confocal FCS}
-The confocal detection volume with the structural parameter
-\begin{align}
-\mathit{SP}= \frac{z_0}{r_0}
-\end{align}
-has an effective size of
-\begin{align}
-V = \pi^{3/2} r_0^2 z_0
-\end{align}
-where $r_0$ is its lateral and $z_0$ its axial (in case of 3D diffusion) extension. Thus, the effective number of particles is defined as
-\begin{align}
-N = C V
-\end{align}
-with the concentration $C$ given implicitly in the model functions.
-The diffusion coefficient is calculated from the diffusion time $\tau_\mathrm{diff}$ using
-\begin{align}
-D = \frac{1}{4 \tau_\mathrm{diff}} \left( \frac{z_0}{\mathit{SP}} \right)^2 = \frac{r_0^2}{4 \tau_\mathrm{diff}}.
-\end{align}
-The parameters in the equation above need to be calibrated to obtain the diffusion coefficient. Usually a reference dye with a known diffusion coefficient is used to determine the lateral extension of the detection volume $r_0$ with a fixed structural parameter of e.g. $\mathit{SP}=4$.\\
-\vspace{2em}
+\section{Implemented model functions}
+\label{sec:imple}
+This is an overview of all the model functions that are implemented in \textit{PyCorrFit}. To each model a unique model ID is assigned. Most of the following information is also accessible from within \textit{PyCorrFit} using the \textit{Page info} tool.
+\subsection{Confocal FCS}
+\label{sec:imple.confo}
% 2D diffusion
%\noindent \begin{tabular}{lp{.7\textwidth}}
@@ -72,12 +53,12 @@ ID & \textbf{6011} \\
Descr. & Three-dimensional free diffusion with a Gaussian laser profile (eliptical), including a triplet component\cite{Widengren1994, Widengren1995, Haupts1998}. \\
\end{tabular}
\begin{align}
-G(\tau) = A_0 + \frac{1}{N} \frac{1}{(1+\tau/\tau_\mathrm{diff})} \frac{1}{\sqrt{1+\tau/(\mathit{SP}^2 \tau_\mathrm{diff})}} \left(1 + \frac{T e^{-\tau/\tau_\mathrm{trip}}}{1-T} \right)
+G(\tau) = A_0 + \frac{1}{n} \frac{1}{(1+\tau/\tau_\mathrm{diff})} \frac{1}{\sqrt{1+\tau/(\mathit{SP}^2 \tau_\mathrm{ diff})}} \left(1 + \frac{T e^{-\tau/\tau_\mathrm{trip}}}{1-T} \right)
\end{align}
\begin{center}
\begin{tabular}{ll}
$A_0$ & Offset \\
-$N$ & Effective number of particles in confocal volume \\
+$n$ & Effective number of particles in confocal volume \\
$\tau_\mathrm{diff}$ & Characteristic residence time in confocal volume \\
$\mathit{SP}$ & Structural parameter, describes elongation of the confocal volume \\
$T$ & Fraction of particles in triplet (non-fluorescent) state\\
@@ -92,19 +73,19 @@ $\tau_\mathrm{trip}$ & Characteristic residence time in triplet \\
\noindent \begin{tabular}{lp{.7\textwidth}}
Name & \textbf{Confocal (Gaussian) T+3D+3D} \\
ID & \textbf{6030} \\
-Descr. & Two-component three-dimensional free diffusion with a Gaussian laser profile, including a triplet component\cite{Elson1974, Aragon1976, Palmer1987, Thomps:bookFCS2002}. \\
+Descr. & Two-component three-dimensional free diffusion with a Gaussian laser profile, including a triplet component\cite{Elson1974, Aragon1976, Palmer1987}. \\
\end{tabular}
\begin{align}
-G(\tau) &= A_0 + \frac{1}{N (F + \alpha (1-F))²} \left(1 + \frac{T e^{-\tau/\tau_\mathrm{trip}}}{1-T} \right) \times \\
+G(\tau) &= A_0 + \frac{1}{n (F + \alpha (1-F))²} \left(1 + \frac{T e^{-\tau/\tau_\mathrm{trip}}}{1-T} \right) \times \\
\notag &\times \left[ \frac{F}{(1+\tau/\tau_1)} \frac{1}{\sqrt{1+\tau/(\mathit{SP}^2 \tau_1)}} + \alpha^2 \frac{1-F}{ (1+\tau/\tau_2) } \frac{1}{\sqrt{1+\tau/(\mathit{SP}^2 \tau_2)}} \right]
\end{align}
\begin{center}
\begin{tabular}{ll}
$A_0$ & Offset \\
-$N$ & Effective number of particles in confocal volume ($N = N_1+N_2$) \\
+$n$ & Effective number of particles in confocal volume ($n = n_1+n_2$) \\
$\tau_1$ & Diffusion time of particle species 1 \\
$\tau_2$ & Diffusion time of particle species 2 \\
-$F$ & Fraction of molecules of species 1 ($N_1 = F N$) \\
+$F$ & Fraction of molecules of species 1 ($n_1 = F n$) \\
$\alpha$ & Relative molecular brightness of particles 1 and 2 ($ \alpha = q_2/q_1$) \\
$\mathit{SP}$ & Structural parameter, describes elongation of the confocal volume \\
$T$ & Fraction of particles in triplet (non-fluorescent) state\\
@@ -122,12 +103,12 @@ ID & \textbf{6002} \\
Descr. & Two-dimensional diffusion with a Gaussian laser profile, including a triplet component\cite{Aragon1976, Qian1991, Rigler1993,Widengren1994, Widengren1995, Haupts1998}. \\
\end{tabular}
\begin{align}
-G(\tau) = A_0 + \frac{1}{N} \frac{1}{(1+\tau/\tau_\mathrm{diff})} \left(1 + \frac{T e^{-\tau/\tau_\mathrm{trip}}}{1-T} \right)
+G(\tau) = A_0 + \frac{1}{n} \frac{1}{(1+\tau/\tau_\mathrm{diff})} \left(1 + \frac{T e^{-\tau/\tau_\mathrm{trip}}}{1-T} \right)
\end{align}
\begin{center}
\begin{tabular}{ll}
$A_0$ & Offset \\
-$N$ & Effective number of particles in confocal area \\
+$n$ & Effective number of particles in confocal area \\
$\tau_\mathrm{diff}$ & Characteristic residence time in confocal area \\
$T$ & Fraction of particles in triplet (non-fluorescent) state\\
$\tau_\mathrm{trip}$ & Characteristic residence time in triplet state \\
@@ -141,18 +122,18 @@ $\tau_\mathrm{trip}$ & Characteristic residence time in triplet state \\
\noindent \begin{tabular}{lp{.7\textwidth}}
Name & \textbf{Confocal (Gaussian) T+2D+2D} \\
ID & \textbf{6031} \\
-Descr. & Two-component, two-dimensional diffusion with a Gaussian laser profile, including a triplet component\cite{Elson1974, Aragon1976, Palmer1987, Thomps:bookFCS2002}. \\
+Descr. & Two-component, two-dimensional diffusion with a Gaussian laser profile, including a triplet component\cite{Elson1974, Aragon1976, Palmer1987}. \\
\end{tabular}
\begin{align}
-G(\tau) = A_0 + \frac{1}{N (F + \alpha (1-F))²} \left[ \frac{F}{1+\tau/\tau_1} + \alpha^2 \frac{1-F}{ 1+\tau/\tau_2 } \right] \left(1 + \frac{T e^{-\tau/\tau_\mathrm{trip}}}{1-T} \right)
+G(\tau) = A_0 + \frac{1}{n (F + \alpha (1-F))²} \left[ \frac{F}{1+\tau/\tau_1} + \alpha^2 \frac{1-F}{ 1+\tau/\tau_2 } \right] \left(1 + \frac{T e^{-\tau/\tau_\mathrm{trip}}}{1-T} \right)
\end{align}
\begin{center}
\begin{tabular}{ll}
$A_0$ & Offset \\
-$N$ & Effective number of particles in confocal area ($N = N_1+N_2$) \\
+$n$ & Effective number of particles in confocal area ($n = n_1+n_2$) \\
$\tau_1$ & Diffusion time of particle species 1 \\
$\tau_2$ & Diffusion time of particle species 2 \\
-$F$ & Fraction of molecules of species 1 ($N_1 = F N$) \\
+$F$ & Fraction of molecules of species 1 ($n_1 = F n$) \\
$\alpha$ & Relative molecular brightness of particles 1 and 2 ($ \alpha = q_2/q_1$) \\
$T$ & Fraction of particles in triplet (non-fluorescent) state\\
$\tau_\mathrm{trip}$ & Characteristic residence time in triplet state \\
@@ -166,18 +147,18 @@ $\tau_\mathrm{trip}$ & Characteristic residence time in triplet state \\
\noindent \begin{tabular}{lp{.7\textwidth}}
Name & \textbf{Confocal (Gaussian) T+3D+2D} \\
ID & \textbf{6032} \\
-Descr. & Two-component, two- and three-dimensional diffusion with a Gaussian laser profile, including a triplet component\cite{Elson1974, Aragon1976, Palmer1987, Thomps:bookFCS2002}. \\
+Descr. & Two-component, two- and three-dimensional diffusion with a Gaussian laser profile, including a triplet component\cite{Elson1974, Aragon1976, Palmer1987}. \\
\end{tabular}
\begin{align}
-G(\tau) = A_0 + \frac{1}{N (1 - F + \alpha F)²} \left[ \frac{1-F}{1+\tau/\tau_\mathrm{2D}} + \frac{ \alpha^2 F}{ (1+\tau/\tau_\mathrm{3D}) } \frac{1}{\sqrt{1+\tau/(\mathit{SP}^2 \tau_\mathrm{3D})}} \right] \left(1 + \frac{T e^{-\tau/\tau_\mathrm{trip}}}{1-T} \right)
+G(\tau) = A_0 + \frac{1}{n (1 - F + \alpha F)²} \left[ \frac{1-F}{1+\tau/\tau_\mathrm{2D}} + \frac{ \alpha^2 F}{ (1+\tau/\tau_\mathrm{3D}) } \frac{1}{\sqrt{1+\tau/(\mathit{SP}^2 \tau_\mathrm{3D})}} \right] \left(1 + \frac{T e^{-\tau/\tau_\mathrm{trip}}}{1-T} \right)
\end{align}
\begin{center}
\begin{tabular}{ll}
$A_0$ & Offset \\
-$N$ & Effective number of particles in confocal volume ($N = N_\mathrm{2D}+N_\mathrm{3D}$) \\
+$n$ & Effective number of particles in confocal volume ($n = n_\mathrm{2D}+n_\mathrm{3D}$) \\
$\tau_\mathrm{2D}$ & Diffusion time of surface bound particles \\
$\tau_\mathrm{3D}$ & Diffusion time of freely diffusing particles \\
-$F$ & Fraction of molecules of the freely diffusing species ($N_\mathrm{3D} = F N$) \\
+$F$ & Fraction of molecules of the freely diffusing species ($n_\mathrm{3D} = F n$) \\
$\alpha$ & Relative molecular brightness of particle species ($ \alpha = q_\mathrm{3D}/q_\mathrm{2D}$) \\
$\mathit{SP}$ & Structural parameter, describes elongation of the confocal volume \\
$T$ & Fraction of particles in triplet (non-fluorescent) state\\
@@ -186,24 +167,16 @@ $\tau_\mathrm{trip}$ & Characteristic residence time in triplet state \\
\end{center}
\vspace{2em}
-
-\subsubsection{Confocal TIR-FCS}
-The detection volume is axially confined by an evanescent field and has an effective size of
-\begin{align}
-V = \pi R_0^2 d_\mathrm{eva}
-\end{align}
-where $R_0$ is the lateral extent of the detection volume and $d_\mathrm{eva}$ is the evanescent field depth\footnote{Where the field has decayed to $1/e$}. From the concentration $C$, the effective number of particles is $N=CV$.
-The decay constant $\kappa$ is the inverse of the depth $d_\mathrm{eva}$ :
-\begin{align}
-d_\mathrm{eva} = \frac{1}{\kappa}
-\end{align}
-The model functions make use of the Faddeeva function (complex error function)\footnote{In user-defined model functions, the Faddeeva function is accessible through \texttt{wofz()}. For convenience, the function \texttt{wixi()} can be used which only takes $\xi$ as an argument and the imaginary $i$ can be omitted.}:
+\subsection{TIR-FCS}
+\label{sec:imple.tirfc}
+The model functions make use of the Faddeeva function (complex error function)\footnote{In user-defined model functions (\hyref{Section}{sec:hacke.extmod}), the Faddeeva function is accessible through \texttt{wofz()}. For convenience, the function \texttt{wixi()} can be used which only takes $\xi$ as an argument and the imaginary $i$ can be omitted.}:
\begin{align}
w\!(i\xi) &= e^{\xi^2} \mathrm{erfc}(\xi) \\
\notag &= e^{\xi^2} \cdot \frac{2}{\sqrt{\pi}} \int_\xi^\infty \mathrm{e}^{-\alpha^2} \mathrm{d\alpha} \label{eq:faddeeva}
\end{align}
-The lateral detection area has the same shape as in confocal FCS. Thus, correlation functions for two-dimensional diffusion of the confocal case apply and are not mentioned here. \\
-\vspace{2em}
+The lateral detection area has the same shape as in confocal FCS. Thus, correlation functions for two-dimensional diffusion of the confocal case apply and are not mentioned here.
+
+\subsubsection{TIR-FCS with Gaussian-shaped lateral detection volume}
% 3D diffusion (Gauß/exp)
@@ -231,10 +204,10 @@ $D$ & Diffusion coefficient \\
\noindent \begin{tabular}{lp{.7\textwidth}}
Name & \textbf{TIR (Gaussian/Exp.) T+3D+3D} \\
ID & \textbf{6034} \\
-Descr. & Two-component three-dimensional diffusion with a Gaussian lateral detection profile and an exponentially decaying profile in axial direction, including a triplet component\cite{Starr2001, Hassler2005, Ohsugi2006, Elson1974, Aragon1976, Palmer1987, Thomps:bookFCS2002}. \\
+Descr. & Two-component three-dimensional diffusion with a Gaussian lateral detection profile and an exponentially decaying profile in axial direction, including a triplet component\cite{Starr2001, Hassler2005, Ohsugi2006}. \\
\end{tabular}
\begin{align}
-G(\tau) = &A_0 + \frac{1}{N (1-F + \alpha F)^2} \left(1 + \frac{T e^{-\tau/\tau_\mathrm{trip}}}{1-T} \right) \times \\
+G(\tau) = &A_0 + \frac{1}{n (1-F + \alpha F)^2} \left(1 + \frac{T e^{-\tau/\tau_\mathrm{trip}}}{1-T} \right) \times \\
\notag \times \Bigg[ \,\, &
\frac{F \kappa}{1+ 4 D_1 \tau/R_0^2}
\left( \sqrt{\frac{D_1 \tau}{\pi}} + \frac{1 - 2 D_1 \tau \kappa^2}{2 \kappa} w\!\left(i \sqrt{D_1 \tau} \kappa\right) \right) + \\
@@ -245,10 +218,10 @@ G(\tau) = &A_0 + \frac{1}{N (1-F + \alpha F)^2} \left(1 + \frac{T e^{-\tau/\tau_
\begin{center}
\begin{tabular}{ll}
$A_0$ & Offset \\
-$N$ & Effective number of particles in confocal volume ($N = N_1+N_2$) \\
+$n$ & Effective number of particles in confocal volume ($n = n_1+n_2$) \\
$D_1$ & Diffusion coefficient of species 1 \\
$D_2$ & Diffusion coefficient of species 2 \\
-$F$ & Fraction of molecules of species 1 ($N_1 = F N$) \\
+$F$ & Fraction of molecules of species 1 ($n_1 = F n$) \\
$\alpha$ & Relative molecular brightness of particle species ($ \alpha = q_2/q_1$) \\
$R_0$ & Lateral extent of the detection volume \\
$\kappa$ & Evanescent decay constant ($\kappa = 1/d_\mathrm{eva}$)\\
@@ -265,10 +238,10 @@ $\tau_\mathrm{trip}$ & Characteristic residence time in triplet state \\
\noindent \begin{tabular}{lp{.7\textwidth}}
Name & \textbf{TIR (Gaussian/Exp.) T+3D+2D} \\
ID & \textbf{6033} \\
-Descr. & Two-component, two- and three-dimensional diffusion with a Gaussian lateral detection profile and an exponentially decaying profile in axial direction, including a triplet component\cite{Starr2001, Hassler2005, Ohsugi2006, Elson1974, Aragon1976, Palmer1987, Thomps:bookFCS2002}. \\
+Descr. & Two-component, two- and three-dimensional diffusion with a Gaussian lateral detection profile and an exponentially decaying profile in axial direction, including a triplet component\cite{Starr2001, Hassler2005, Ohsugi2006}. \\
\end{tabular}
\begin{align}
-G(\tau) &= A_0 + \frac{1}{N (1-F + \alpha F)^2} \left(1 + \frac{T e^{-\tau/\tau_\mathrm{trip}}}{1-T} \right) \times \\
+G(\tau) &= A_0 + \frac{1}{n (1-F + \alpha F)^2} \left(1 + \frac{T e^{-\tau/\tau_\mathrm{trip}}}{1-T} \right) \times \\
& \notag \times \left[
\frac{1-F}{1+ 4 D_\mathrm{2D} \tau/R_0^2} +
\frac{\alpha^2 F \kappa}{1+ 4 D_\mathrm{3D} \tau/R_0^2}
@@ -277,10 +250,10 @@ G(\tau) &= A_0 + \frac{1}{N (1-F + \alpha F)^2} \left(1 + \frac{T e^{-\tau/\tau_
\begin{center}
\begin{tabular}{ll}
$A_0$ & Offset \\
-$N$ & Effective number of particles in confocal volume ($N = N_\mathrm{2D}+N_\mathrm{3D}$) \\
+$n$ & Effective number of particles in confocal volume ($n = n_\mathrm{2D}+n_\mathrm{3D}$) \\
$D_\mathrm{2D}$ & Diffusion coefficient of surface bound particles \\
$D_\mathrm{3D}$ & Diffusion coefficient of freely diffusing particles \\
-$F$ & Fraction of molecules of the freely diffusing species ($N_\mathrm{3D} = F N$) \\
+$F$ & Fraction of molecules of the freely diffusing species ($n_\mathrm{3D} = F n$) \\
$\alpha$ & Relative molecular brightness of particle species ($ \alpha = q_\mathrm{3D}/q_\mathrm{2D}$) \\
$R_0$ & Lateral extent of the detection volume \\
$\kappa$ & Evanescent decay constant ($\kappa = 1/d_\mathrm{eva}$)\\
@@ -294,26 +267,13 @@ $\tau_\mathrm{trip}$ & Characteristic residence time in triplet state \\
\subsubsection{TIR-FCS with a square-shaped lateral detection volume}
-The detection volume is axially confined by an evanescent field of depth\footnote{Where the field has decayed to $1/e$} $d_\mathrm{eva} = 1 / \kappa$.
-The lateral detection area is a convolution of the point spread function of the microscope of size $\sigma$,
-\begin{align}
-\sigma = \sigma_0 \frac{\lambda}{\mathit{NA}},
-\end{align}
-with a square of side length $a$.
-The model functions make use of the Faddeeva function (complex error function)\footnote{In user-defined model functions, the Faddeeva function is accessible through \texttt{wofz()}. For convenience, the function \texttt{wixi()} can be used which only takes $\xi$ as an argument and the imaginary $i$ can be omitted.}:
-\begin{align}
-w\!(i\xi) &= e^{\xi^2} \mathrm{erfc}(\xi) \\
-\notag &= e^{\xi^2} \cdot \frac{2}{\sqrt{\pi}} \int_\xi^\infty \mathrm{e}^{-\alpha^2} \mathrm{d\alpha} \label{eq:faddeeva}
-\end{align}
-\vspace{2em}
-
% 3D TIRF diffusion (□xσ)
\noindent \begin{tabular}{lp{.7\textwidth}}
Name & \textbf{TIR (□x$\upsigma$/Exp.) 3D} \\
ID & \textbf{6010} \\
-Descr. & Three-dimensional diffusion with a square-shaped lateral detection area taking into account the size of the point spread function; and an exponential decaying profile in axial direction\cite{Ries2008390, Yordanov2011}. \\
+Descr. & Three-dimensional diffusion with a square-shaped lateral detection area taking into account the size of the point spread function; and an exponential decaying profile in axial direction\cite{Ries2008, Yordanov2011}. \\
\end{tabular}
\begin{align}
G(\tau) = \frac{\kappa^2}{C} &
@@ -339,7 +299,7 @@ $D$ & Diffusion coefficient \\
Name & \textbf{TIR (□x$\upsigma$/Exp.) 3D+3D} \\
ID & \textbf{6023} \\
Descr. & Two-component three-dimensional free diffusion with a square-shaped lateral detection area taking into account the size of the point spread function; and an exponential decaying profile in axial direction. \newline
-The correlation function is a superposition of three-dimensional model functions of the type \textbf{3D (□x$\upsigma$)} (6010)\cite{Ries2008390, Yordanov2011}. \\
+The correlation function is a superposition of three-dimensional model functions of the type \textbf{3D (□x$\upsigma$)} (6010)\cite{Ries2008, Yordanov2011}. \\
\end{tabular}
\vspace{2em}
@@ -348,7 +308,7 @@ The correlation function is a superposition of three-dimensional model functions
\noindent \begin{tabular}{lp{.7\textwidth}}
Name & \textbf{TIR (□x$\upsigma$) 2D} \\
ID & \textbf{6000} \\
-Descr. & Two-dimensional diffusion with a square-shaped lateral detection area taking into account the size of the point spread function\cite{Ries2008390, Yordanov2011}\footnote{The reader is made aware, that reference \cite{Ries2008390} contains several unfortunate misprints.}. \\
+Descr. & Two-dimensional diffusion with a square-shaped lateral detection area taking into account the size of the point spread function\cite{Ries2008, Yordanov2011}\footnote{The reader is made aware, that reference \cite{Ries2008} contains several unfortunate misprints.}. \\
\end{tabular}
\begin{align}
G(\tau) = \frac{1}{C} \left[
@@ -373,7 +333,7 @@ $D$ & Diffusion coefficient \\
Name & \textbf{TIR (□x$\upsigma$) 2D+2D} \\
ID & \textbf{6022} \\
Descr. & Two-component two-dimensional diffusion with a square-shaped lateral detection area taking into account the size of the point spread function. \newline
-The correlation function is a superposition of two-dimensional model functions of the type \textbf{2D (□x$\upsigma$)} (6000)\cite{Ries2008390, Yordanov2011}. \\
+The correlation function is a superposition of two-dimensional model functions of the type \textbf{2D (□x$\upsigma$)} (6000)\cite{Ries2008, Yordanov2011}. \\
\end{tabular}
\vspace{2em}
@@ -383,7 +343,7 @@ The correlation function is a superposition of two-dimensional model functions o
Name & \textbf{TIR (□x$\upsigma$/Exp.) 3D+2D} \\
ID & \textbf{6020} \\
Descr. & Two-component two- and three-dimensional diffusion with a square-shaped lateral detection area taking into account the size of the point spread function; and an exponential decaying profile in axial direction. \newline
-The correlation function is a superposition of the two-dimensional model function \textbf{2D (□x$\upsigma$)} (6000) and the three-dimensional model function \textbf{3D (□x$\upsigma$)} (6010)\cite{Ries2008390, Yordanov2011}.
+The correlation function is a superposition of the two-dimensional model function \textbf{2D (□x$\upsigma$)} (6000) and the three-dimensional model function \textbf{3D (□x$\upsigma$)} (6010)\cite{Ries2008, Yordanov2011}.
\end{tabular}
\vspace{2em}
@@ -393,8 +353,7 @@ The correlation function is a superposition of the two-dimensional model functio
Name & \textbf{TIR (□x$\upsigma$/Exp.) 3D+2D+kin} \\
ID & \textbf{6021} \\
Descr. & Two-component two- and three-dimensional diffusion with a square-shaped lateral detection area taking into account the size of the point spread function; and an exponential decaying profile in axial direction. This model covers binding and unbinding kintetics. \newline
-The correlation function for this model was introduced in \cite{Ries2008390}. Because approximations are made in the derivation, please verify if this model is applicable to your problem before using it.
+The correlation function for this model was introduced in \cite{Ries2008}. Because approximations are made in the derivation, please verify if this model is applicable to your problem before using it.
\end{tabular}
-\vspace{2em}
diff --git a/sample_sessions/CSFCS_DiO-in-DOPC.fcsfit-session.zip b/sample_sessions/CSFCS_DiO-in-DOPC.fcsfit-session.zip
new file mode 100644
index 0000000..7d6c852
Binary files /dev/null and b/sample_sessions/CSFCS_DiO-in-DOPC.fcsfit-session.zip differ
diff --git a/sample_sessions/ConfocalFCS_Alexa488_xcorr.fcsfit-session.zip b/sample_sessions/ConfocalFCS_Alexa488_xcorr.fcsfit-session.zip
new file mode 100644
index 0000000..65194b0
Binary files /dev/null and b/sample_sessions/ConfocalFCS_Alexa488_xcorr.fcsfit-session.zip differ
diff --git a/setup.py b/setup.py
index e6fd5b6..843b7ac 100644
--- a/setup.py
+++ b/setup.py
@@ -1,4 +1,6 @@
#!/usr/bin/env python
+# To create a distribution package for pip or easy-install:
+# python setup.py sdist
from setuptools import setup, find_packages
from os.path import join, dirname, realpath
from warnings import warn
@@ -36,7 +38,8 @@ setup(
'pycorrfit.tools': 'src/tools'},
data_files=[('pycorrfit_doc', ['ChangeLog.txt', 'PyCorrFit_doc.pdf'])],
license="GPL v2",
- long_description=open(join(dirname(__file__), 'README.md')).read(),
+ description='Scientific tool for fitting correlation curves on a logarithmic plot.',
+ long_description=open(join(dirname(__file__), 'Readme.txt')).read(),
scripts=['bin/pycorrfit'],
include_package_data=True,
install_requires=[
diff --git a/src/frontend.py b/src/frontend.py
index b842d61..08399c3 100644
--- a/src/frontend.py
+++ b/src/frontend.py
@@ -412,6 +412,8 @@ class MyFrame(wx.Frame):
self.Bind(wx.EVT_MENU, self.OnSavePlotCorr, menuSavePlotCorr)
self.Bind(wx.EVT_MENU, self.OnSavePlotTrace, menuSavePlotTrace)
self.Bind(wx.EVT_MENU, self.OnDeletePage, menuClPa)
+ # Preferences
+ self.Bind(wx.EVT_MENU, self.OnLatexCheck, self.MenuUseLatex)
# Help
self.Bind(wx.EVT_MENU, self.OnSoftware, menuSoftw)
self.Bind(wx.EVT_MENU, self.OnAbout, menuAbout)
@@ -864,6 +866,44 @@ class MyFrame(wx.Frame):
self.OnFNBPageChanged()
+ def OnLatexCheck(self,e):
+ """ Checks if we can use latex. If not, create a pop-up window
+ stating so.
+ """
+ uselatex = self.MenuUseLatex.IsChecked()
+ if uselatex == False:
+ # do nothing
+ return
+ ## Check if we can use latex for plotting:
+ (r1, path) = misc.findprogram("latex")
+ (r2, path) = misc.findprogram("dvipng")
+ # Ghostscript
+ (r31, path) = misc.findprogram("gs")
+ (r32, path) = misc.findprogram("mgs") # from miktex
+ r3 = max(r31,r32)
+ if r1+r2+r3 < 3:
+ # Warn the user
+ if platform.system().lower() == 'windows':
+ text = ("Latex plotting features will not work.\n"+
+ "Please install MiKTeX.\n"+
+ "http://miktex.org/")
+ elif platform.system().lower() == 'darwin':
+ text = ("Latex plotting features will not work.\n"+
+ "Please install MacTeX.\n"+
+ "http://tug.org/mactex/")
+ else:
+ text = ("Latex plotting features will not work.\n"+
+ "Make sure you have these packages installed:\n"+
+ " - latex\n"+
+ " - dvipng\n"+
+ " - ghostscript\n"+
+ " - texlive-science\n"+
+ " - texlive-math-extra\n")
+ dlg = wx.MessageDialog(None, text, 'Latex not found',
+ wx.OK | wx.ICON_EXCLAMATION)
+ dlg.ShowModal()
+
+
def OnLoadBatch(self, e):
""" Open multiple data files and apply a single model to them
We will create a new window where the user may decide which
diff --git a/src/page.py b/src/page.py
index 7a4e3df..5bb9e7d 100644
--- a/src/page.py
+++ b/src/page.py
@@ -371,9 +371,8 @@ class FittingPanel(wx.Panel):
Topics in Fluorescence Spectroscopy,
Springer US, 2002, 1, 337-378
- and (for cross-correlation)
-
- Weidemann et al. ...?
+ The cross-correlation background correction can be derived in the
+ same manner.
"""
# Make a copy. Do not overwrite the original.
if dataexp is not None:
diff --git a/src/plotting.py b/src/plotting.py
index 27a5f1e..be9dc1c 100644
--- a/src/plotting.py
+++ b/src/plotting.py
@@ -181,7 +181,7 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
if Page.normparm is not None:
fitlabel += ur", normalized to "+Page.active_parms[0][Page.normparm]
- ## Check if we can use latex or plotting:
+ ## Check if we can use latex for plotting:
(r1, path) = findprogram("latex")
(r2, path) = findprogram("dvipng")
# Ghostscript
@@ -194,7 +194,9 @@ def savePlotCorrelation(parent, dirname, Page, uselatex=False,
rcParams['text.usetex']=True
rcParams['text.latex.unicode']=True
rcParams['font.family']='serif'
- rcParams['text.latex.preamble']=[r"\usepackage{amsmath}"]
+ rcParams['text.latex.preamble']=[r"""\usepackage{amsmath}
+ \usepackage[utf8x]{inputenc}
+ \usepackage{amssymb}"""]
fitlabel = ur"{\normalsize "+escapechars(fitlabel)+r"}"
tabtitle = ur"{\normalsize "+escapechars(tabtitle)+r"}"
labelweights = ur"{\normalsize "+escapechars(labelweights)+r"}"
@@ -353,7 +355,7 @@ def savePlotTrace(parent, dirname, Page, uselatex=False, verbose=False):
labels = [tabtitle+" A", tabtitle+" B"]
else:
return
- ## Check if we can use latex or plotting:
+ ## Check if we can use latex for plotting:
(r1, path) = findprogram("latex")
(r2, path) = findprogram("dvipng")
# Ghostscript
@@ -427,7 +429,7 @@ def savePlotSingle(name, x, dataexp, datafit, dirname = ".", uselatex=False):
plt.close()
except:
pass
- ## Check if we can use latex or plotting:
+ ## Check if we can use latex for plotting:
(r1, path) = findprogram("latex")
(r2, path) = findprogram("dvipng")
# Ghostscript
diff --git a/src/tools/statistics.py b/src/tools/statistics.py
index ee100fd..1f7e937 100644
--- a/src/tools/statistics.py
+++ b/src/tools/statistics.py
@@ -29,7 +29,7 @@
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
-
+import datetime
import wx
import wx.lib.plot as plot # Plotting in wxPython
import numpy as np
@@ -60,7 +60,8 @@ class Stat(wx.Frame):
pos = self.parent.GetPosition()
pos = (pos[0]+100, pos[1]+100)
wx.Frame.__init__(self, parent=self.parent, title="Statistics",
- pos=pos, style=wx.DEFAULT_FRAME_STYLE|wx.FRAME_FLOAT_ON_PARENT)
+ pos=pos,
+ style=wx.DEFAULT_FRAME_STYLE|wx.FRAME_FLOAT_ON_PARENT)
## MYID
# This ID is given by the parent for an instance of this class
self.MyID = None
@@ -93,33 +94,40 @@ class Stat(wx.Frame):
self.panel.Disable()
# A dropdown menu for the source Page:
text = wx.StaticText(self.panel,
- label="Create a table with all the selected\n"+
- "variables below from pages with the\n"+
- "same model as the current page.")
+ label="Create a table with all the selected\n"+
+ "variables below from pages with the\n"+
+ "same model as the current page.")
## Page selection as in average tool
Pagetext = wx.StaticText(self.panel,
label="Curves ")
- Psize = text.GetSize()[0] - Pagetext.GetSize()[0]
+ Psize = text.GetSize()[0]/2
self.WXTextPages = wx.TextCtrl(self.panel, value="",
size=(Psize,-1))
# Set number of pages
pagenumlist = list()
for i in np.arange(self.parent.notebook.GetPageCount()):
Page = self.parent.notebook.GetPage(i)
- pagenumlist.append(int(filter(lambda x: x.isdigit(), Page.counter)))
+ pagenumlist.append(int(filter(lambda x: x.isdigit(),
+ Page.counter)))
valstring=misc.parsePagenum2String(pagenumlist)
self.WXTextPages.SetValue(valstring)
## Plot parameter dropdown box
self.PlotParms = self.GetListOfPlottableParms()
Parmlist = self.PlotParms
- DDtext = wx.StaticText(self.panel,
- label="Plot parameter ")
- DDsize = text.GetSize()[0] - DDtext.GetSize()[0]
- self.WXDropdown = wx.ComboBox(self.panel, -1, "", size=(DDsize,-1),
- choices=Parmlist, style=wx.CB_DROPDOWN|wx.CB_READONLY)
+ DDtext = wx.StaticText(self.panel, label="Plot parameter ")
+ self.WXDropdown = wx.ComboBox(self.panel, -1, "",
+ size=(Psize,-1), choices=Parmlist,
+ style=wx.CB_DROPDOWN|wx.CB_READONLY)
self.Bind(wx.EVT_COMBOBOX, self.OnDropDown, self.WXDropdown)
self.Bind(wx.EVT_TEXT, self.OnDropDown, self.WXTextPages)
self.WXDropdown.SetSelection(0)
+ ## Show Average and SD
+ textavg = wx.StaticText(self.panel, label="Average ")
+ textsd = wx.StaticText(self.panel, label="Standard deviation ")
+ self.WXavg = wx.TextCtrl(self.panel, size=(Psize,-1))
+ self.WXsd = wx.TextCtrl(self.panel, size=(Psize,-1))
+ self.WXavg.SetEditable(False)
+ self.WXsd.SetEditable(False)
# Create space for parameters
self.box = wx.StaticBox(self.panel, label="Export parameters")
self.masterboxsizer = wx.StaticBoxSizer(self.box, wx.VERTICAL)
@@ -134,15 +142,24 @@ class Stat(wx.Frame):
self.Bind(wx.EVT_BUTTON, self.OnSaveTable, self.btnSave)
# Add elements to sizer
self.topSizer = wx.BoxSizer(wx.VERTICAL)
- #self.topSizer.Add(text)
- Psizer = wx.BoxSizer(wx.HORIZONTAL)
- Psizer.Add(Pagetext)
- Psizer.Add(self.WXTextPages)
- DDsizer = wx.BoxSizer(wx.HORIZONTAL)
- DDsizer.Add(DDtext)
- DDsizer.Add(self.WXDropdown)
- self.topSizer.Add(Psizer)
- self.topSizer.Add(DDsizer)
+ GridAll = wx.FlexGridSizer(rows=4, cols=2, vgap=5, hgap=5)
+ GridAll.Add(Pagetext)
+ GridAll.Add(self.WXTextPages)
+ GridAll.Add(DDtext)
+ GridAll.Add(self.WXDropdown)
+ GridAll.Add(textavg)
+ GridAll.Add(self.WXavg)
+ GridAll.Add(textsd)
+ GridAll.Add(self.WXsd)
+ #Psizer = wx.BoxSizer(wx.HORIZONTAL)
+ #Psizer.Add(Pagetext)
+ #Psizer.Add(self.WXTextPages)
+ #DDsizer = wx.BoxSizer(wx.HORIZONTAL)
+ #DDsizer.Add(DDtext)
+ #DDsizer.Add(self.WXDropdown)
+ #self.topSizer.Add(Psizer)
+ #self.topSizer.Add(DDsizer)
+ self.topSizer.Add(GridAll)
self.topSizer.Add(self.masterboxsizer)
self.topSizer.Add(self.btnSave)
# Set size of window
@@ -159,7 +176,7 @@ class Stat(wx.Frame):
wx.Frame.SetIcon(self, parent.MainIcon)
self.Show(True)
self.OnDropDown()
-
+ self.OnDropDown()
def GetListOfAllParameters(self, e=None, return_std_checked=False):
""" Returns sorted list of parameters.
@@ -170,8 +187,8 @@ class Stat(wx.Frame):
# Now that we know our Page, we may change the available
# parameter options.
Infodict = self.InfoClass.GetCurInfo()
- # We want to sort the information and have some prechecked values
- # in the statistics window afterwards.
+ # We want to sort the information and have some prechecked
+ # values in the statistics window afterwards.
# new iteration
keys = Infodict.keys()
body = list()
@@ -191,23 +208,23 @@ class Stat(wx.Frame):
headparm = list()
bodyparm = list()
for parm in Infodict[key]:
- parminlist = False
+ #parminlist = False
try:
for fitp in Infodict["fitting"]:
parmname = parm[0]
errname = "Err "+parmname
if fitp[0] == errname:
headparm.append(parm)
- parminlist = True
+ #parminlist = True
headparm.append(fitp)
except:
# Maybe there was not fit...
pass
- if parminlist == False:
- bodyparm.append(parm)
+ #if parminlist == False:
+ headparm.append(parm)
elif key == "fitting":
for fitp in Infodict[key]:
- # We added the error data before in the parameter section
+ # We added the error data before in the parm section
if str(fitp[0])[0:4] != "Err ":
tail.append(fitp)
elif key == "supplement":
@@ -228,14 +245,21 @@ class Stat(wx.Frame):
# List of default checked parameters:
checked = np.zeros(len(Info), dtype=np.bool)
checked[:len(head)] = True
- # A list with additional strings that should be default checked if found
- # somewhere in the data.
- checklist = ["cpp", "duration", "bg rate"]
+ # A list with additional strings that should be default checked
+ # if found somewhere in the data.
+ checklist = ["cpp", "duration", "bg rate", "avg.", "Model name"]
for i in range(len(Info)):
item = Info[i]
for checkitem in checklist:
if item[0].count(checkitem):
checked[i] = True
+ # Alist with strings that should not be checked:
+ checklist = ["Err "]
+ for i in range(len(Info)):
+ item = Info[i]
+ for checkitem in checklist:
+ if item[0].count(checkitem):
+ checked[i] = False
if return_std_checked:
return Info, checked
@@ -263,7 +287,7 @@ class Stat(wx.Frame):
except:
pass
else:
- # save the key so we can find the parameter later
+ # save the key so we can find the parm later
parmlist.append(item[0])
parmvals.append(val)
else:
@@ -314,7 +338,8 @@ class Stat(wx.Frame):
# pageinfo.append(subitem)
#
# We want to replace the above iteration with an iteration that
- # covers missing values. This means checking for "label == subitem[0]"
+ # covers missing values. This means checking for
+ # "label == subitem[0]"
# and iteration over AllInfo with that consition.
for Info in pagekeys:
pageinfo = list()
@@ -335,11 +360,12 @@ class Stat(wx.Frame):
def OnCheckboxChecked(self, e="restore"):
"""
Write boolean data of checked checkboxes to Page variable
- *StatisticsCheckboxes*. If e=="restore", then we will attempt
- to get the info back from the page.
+ *StatisticsCheckboxes*. If e=="restore", then we will
+ attempt to get the info back from the page.
"""
# What happens if a checkbox has been checked?
- # We write the data to the Page (it will not be saved in the session).
+ # We write the data to the Page
+ # (it will not be saved in the session).
if e=="restore":
checklist = self.Page.StatisticsCheckboxes
if checklist is not None:
@@ -354,7 +380,8 @@ class Stat(wx.Frame):
def OnChooseValues(self, event=None):
- Info, checked = self.GetListOfAllParameters(return_std_checked=True)
+ Info, checked = self.GetListOfAllParameters(
+ return_std_checked=True)
#headcounter = 0
#headlen = len(head)
# We will sort the checkboxes in more than one column if there
@@ -408,7 +435,8 @@ class Stat(wx.Frame):
# Get valid pages
strFull = self.WXTextPages.GetValue()
try:
- PageNumbers = misc.parseString2Pagenum(self, strFull, nodialog=True)
+ PageNumbers = misc.parseString2Pagenum(self, strFull,
+ nodialog=True)
except:
PageNumbers = self.PageNumbers
else:
@@ -430,14 +458,16 @@ class Stat(wx.Frame):
plotcurve = list()
for page in pages:
self.Page = page
- pllabel, pldata = self.GetListOfPlottableParms(return_values=True)
+ pllabel, pldata = self.GetListOfPlottableParms(
+ return_values=True)
# Get the labels and make a plot of the parameters
if len(pllabel)-1 >= DDselid and pllabel[DDselid] == label:
x = int(page.counter.strip("#: "))
y = pldata[DDselid]
plotcurve.append([x,y])
else:
- # try to get the label by searching for the first instance
+ # try to get the label by searching for the first
+ # instance
for k in range(len(pllabel)):
if pllabel[k] == label:
x = int(page.counter.strip("#: "))
@@ -445,8 +475,8 @@ class Stat(wx.Frame):
plotcurve.append([x,y])
# Prepare plotting
self.canvas.Clear()
- linesig = plot.PolyMarker(plotcurve, size=1.5, fillstyle=wx.TRANSPARENT,
- marker='circle')
+ linesig = plot.PolyMarker(plotcurve, size=1.5,
+ fillstyle=wx.TRANSPARENT, marker='circle')
plotlist = [linesig]
# average line
@@ -455,24 +485,32 @@ class Stat(wx.Frame):
maxpage = np.max(np.array(plotcurve)[:,0])
except:
maxpage = 0
+ self.WXavg.SetValue("-")
+ self.WXsd.SetValue("-")
else:
- plotavg = [[0, avg], [maxpage, avg]]
+ # Plot data
+ plotavg = [[0.5, avg], [maxpage+.5, avg]]
lineclear = plot.PolyLine(plotavg, colour="black",
- style= wx.SHORT_DASH)
+ style= wx.SHORT_DASH)
plotlist.append(lineclear)
+ # Update Text control
+ self.WXavg.SetValue(str(avg))
+ self.WXsd.SetValue(str(np.std(np.array(plotcurve)[:,1])))
+
# Draw
self.canvas.Draw(plot.PlotGraphics(plotlist,
xLabel='page number',
yLabel=label))
-
+
# Correctly set x-axis
minticks = 2
self.canvas.SetXSpec(max(maxpage, minticks))
# Zoom out such that we can see the end of all curves
try:
+ # Something sometimes goes wrong here?
xcenter = np.average(np.array(plotcurve)[:,0])
ycenter = np.average(np.array(plotcurve)[:,1])
- scale = 1.1
+ scale = (maxpage+2.)/maxpage
self.canvas.Zoom((xcenter,ycenter), (scale, scale))
except:
pass
@@ -494,7 +532,8 @@ class Stat(wx.Frame):
pagenumlist = list()
for i in np.arange(self.parent.notebook.GetPageCount()):
Page = self.parent.notebook.GetPage(i)
- pagenumlist.append(int(filter(lambda x: x.isdigit(), Page.counter)))
+ pagenumlist.append(int(filter(lambda x: x.isdigit(),
+ Page.counter)))
valstring=misc.parsePagenum2String(pagenumlist)
self.WXTextPages.SetValue(valstring)
DDselection = self.WXDropdown.GetValue()
@@ -531,7 +570,8 @@ class Stat(wx.Frame):
(ax, ay) = self.GetSizeTuple()
(px, py) = self.topSizer.GetMinSizeTuple()
self.sp.SetSashPosition(px+5)
- self.SetSize((np.max([px+400,ax,oldsize[0]]), np.max([py,ay,oldsize[1]])))
+ self.SetSize((np.max([px+400,ax,oldsize[0]]),
+ np.max([py,ay,oldsize[1]])))
self.SetMinSize((px+400, py))
# Replot
self.OnDropDown()
@@ -539,9 +579,9 @@ class Stat(wx.Frame):
def OnSaveTable(self, event=None):
dirname = self.parent.dirname
- dlg = wx.FileDialog(self.parent, "Choose file to save", dirname, "",
- "Text file (*.txt)|*.txt;*.TXT",
- wx.SAVE|wx.FD_OVERWRITE_PROMPT)
+ dlg = wx.FileDialog(self.parent, "Choose file to save", dirname,
+ "", "Text file (*.txt)|*.txt;*.TXT",
+ wx.SAVE|wx.FD_OVERWRITE_PROMPT)
# user cannot do anything until he clicks "OK"
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetPath()
--
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