[med-svn] r8090 - trunk/packages/openslide/trunk/debian

Thu Oct 6 09:48:27 UTC 2011

Author: malat-guest
Date: 2011-10-06 09:48:27 +0000 (Thu, 06 Oct 2011)
New Revision: 8090

Modified:
   trunk/packages/openslide/trunk/debian/openslide-show-properties.1
Log:
fix up layout for trestle

Modified: trunk/packages/openslide/trunk/debian/openslide-show-properties.1
===================================================================

--- trunk/packages/openslide/trunk/debian/openslide-show-properties.1	2011-10-06 08:16:17 UTC (rev 8089)
+++ trunk/packages/openslide/trunk/debian/openslide-show-properties.1	2011-10-06 09:48:27 UTC (rev 8090)
@@ -58,9 +58,294 @@
 .fi
 .PP
 .SH Vendor-specific properties
-.SS Aperio format
+.SH Trestle format
+
+.IP Format 0.4i
+single-file pyramidal tiled TIFF, with non-standard metadata and overlaps; additional files can contain more metadata and detailed overlap info
+.IP File extensions
+\&.tif
+.IP OpenSlide vendor backend
+trestle
+.IP OpenSlide ops backend
+tiff
+
+.SS Detection
+
+.nr step 1 1
+Trestle slides are stored in single-file TIFF format. OpenSlide will detect a file as Trestle if:
+.IP \n[step] 3
+The file is TIFF.
+.IP \n+[step]
+The TIFF Software tag starts with \*(lqMedScan\*(rq.
+.IP \n+[step]
+The ImageDescription tag is present.
+
+.SS Relevant TIFF tags
+
+.TS
+allbox, tab(^); ll.
+ \fBTag\fR^\fBDescription\fR
+ ImageDescription^Stores some important key-value pairs, see below
+ Software^Starts with "MedScan"
+ XResolution, YResolution^T{
+Seems to store microns-per-pixel (MPP), which may or may not take into account
+the correct objective power. Note that this is inverted from standard TIFF,
+which stores pixels-per-unit, not units-per-pixel.
+T}
+.TE
+
+.SS Extra data stored in ImageDescription
+
+The ImageDescription tag contains semicolon-delimited key-value pairs. A key-value pair is equals-delimited. We use the OverlapsXY and Background Color keys from the ImageDescription, and ignore the rest. All of these values are stored as properties starting with \*(lqtrestle.\*(rq.
+
+.TS
+allbox, tab(^); ll.
+ \fBKey\fR^\fBDescription\fR
+ Background Color^Hex-encoded background color info, assumed to be in the format RRGGBB.
+ White Balance^Hex-encoded white balance
+ Objective Power^Reported objective power, often incorrect.
+ JPEG Quality^The JPEG quality value.
+ OverlapsXY^Overlaps, see below.
+.TE
+
+.SS TIFF Image Directory Organization
+
+The first image in the TIFF file is the full-resolution image. The subsequent images are assumed to be decreasingly sized reduced-resolution images.
+
+.SS Overlaps
+
+The OverlapsXY pseudo-field encodes a list of tile overlap values as ASCII.
+
+Example: \*(lq 64 64 32 32 16 16\*(rq (note the initial space).
+
+These values are assumed to represent the amount of overlap between adjacent tiles in pixels, in both X and Y. This example encodes 3 levels worth of overlaps. Further overlaps are assumed to have the value 0.
+
+.SS Associated Images
+
+None.
+
+.SS Known Properties
+
+All data encoded in the ImageDescription TIFF field is represented as properties prefixed with "trestle.".
+
+.SH Hamamatsu format
 .nf
 Format
+  multi-file JPEG/NGR with proprietary metadata and index file formats
+File extensions
+  .vms, .vmu
+OpenSlide vendor backend
+  hamamatsu
+OpenSlide ops backend
+  jpeg for .vms, ngr for .vmu
+.SS Detection
+
+OpenSlide will detect a file as Hamamatsu if:
+
+.AL
+.LI
+The file given is a INI-style text file.
+.LI
+It has a [Virtual Microscope Specimen] (VMS) or [Uncompressed Virtual Microscope Specimen] (VMU) group.
+.LI
+The file specifies a positive number of layer (NoLayers>=1). Currently, only one of these focal plane layers is read.
+.LI
+If VMS, there are at least 1 row and 1 column of JPEG images (NoJpegColumns and NoJpegRows).
+.LI
+The mapfile given by MapFile is a valid readable file in the same directory as the VMS file.
+.LI
+The files given by the various ImageFile lines do not exceed the number of rows and columns as specified above.
+.LI
+The mapfile and image files are all valid JPEG files or all valid NGR files.
+.LI
+The restart interval in each JPEG file is zero, or evenly divides into the number of MCUs per row.
+.LI
+The image files (except the map file) all have the same "tile" sizes (see below).
+.LE
+
+.SS Overview
+
+The Hamamatsu format consists of an index file (VMS or VMU), 2 or more image files, and (in the case of VMS) an "optimisation" file.
+
+Multiple focal planes are ignored, only focal plane 0 is read.
+
+Because JPEG does not allow for large files, multiple JPEG files are needed to encode large images. To avoid having many files, the Hamamatsu format uses close to maximum size (65K by 65K) JPEG files.
+
+Unfortunately, (unlike TIFF) JPEG provides very poor support for random-access decoding of parts of a file. To get around this, JPEG restart markers are placed at regular intervals, and these offsets are specified in the optimisation file. With restart markers identified, OpenSlide can treat JPEG as a tiled format, where the height is the height of an MCU row, and the width is the number of MCUs per row divided by the restart marker interval times the width of an MCU. (This often leads to oddly-shaped and inefficient tiles of 8x2048, for example.)
+
+Unfortunately, the optimisation file does not give the location of every restart marker, only the ones found at the beginning of an MCU row. It also seems that the file ends early, and does not give the location of the restart marker at the last MCU row of the last image file.
+
+Thus, the optimisation file can only be taken as a hint, and cannot be trusted. The entire set of JPEG files must be scanned for restart markers in order to facilitate random access. OpenSlide does this lazily as needed, and also in a background thread that runs only when OpenSlide is otherwise idle.
+
+The map file is a lower-resolution version of the other images, and can be used to make a 2-level JPEG pyramid. JPEG also allows for lower-resolution decoding, so further pyramid levels are synthesized from each JPEG file.
+
+VMS File
+
+The .vms file is the main index file for the VMS format. It is a Windows INI-style key-value pair file, with sections. Only keys in the Virtual Microscope Specimen group are read by OpenSlide.
+
+Here are known keys from the file:
+
+Key	Description
+NoLayers	Number of layers, currently must be 1 to be accepted
+NoJpegColumns	Number of JPEG files across, given in ImageFile attributes
+NoJpegRows	Number of JPEG files down, given in ImageFile attributes
+ImageFile	Semantically equivalent to ImageFile(0,0,0), though not specified that way. The image in position (0,0,0) of the set of images
+ImageFile(x,y)	Semantically equivalent to ImageFile(0,x,y), though not specified that way. The image in position (0,x,y) of the set of images
+ImageFile(z,x,y)	Where x and y are non-negative integers. Both x and y cannot be 0. z is a positive integer. These are the images that make up the virtual slide, as a concatenation of JPEG images. x and y specify the location of each JPEG, z specifies the focal plane
+MapFile	A lower-resolution version of all the ImageFiles
+OptimisationFile	File specifying some of the restart marker offsets in each ImageFile
+AuthCode	Unknown
+SourceLens	Possibly the magnification
+PhysicalWidth	Width of the slide in some unit?
+PhysicalHeight	Height of the slide in some unit?
+LayerSpacing	Unknown
+MacroImage	Image file for the "macro" associated image
+PhysicalMacroWidth	Unknown
+PhysicalMacroHeight	Unknown
+XOffsetFromSlideCentre	Unknown
+YOffsetFromSlideCentre	Unknown
+VMU File
+
+The .vmu file is the main index file for the VMU format. Only keys in the Uncompressed Virtual Microscope Specimen group are read by OpenSlide.
+
+Here are known keys from the file:
+
+Key	Description
+NoLayers	(see VMS above)
+ImageFile	(see VMS above)
+ImageFile(x,y)	(see VMS above)
+ImageFile(z,x,y)	(see VMS above)
+MapFile	(see VMS above)
+MapScale	Seems to be the downsample factor of the map
+AuthCode	(see VMS above)
+SourceLens	(see VMS above)
+PixelWidth	Width of the image in pixels
+PixelHeight	Height of the image in pixels
+PhysicalWidth	(see VMS above)
+PhysicalHeight	(see VMS above)
+LayerSpacing	(see VMS above)
+LayerOffset	Unknown
+MacroImage	(see VMS above)
+PhysicalMacroWidth	(see VMS above)
+PhysicalMacroHeight	(see VMS above)
+XOffsetFromSlideCentre	(see VMS above)
+YOffsetFromSlideCentre	(see VMS above)
+Reference	Unknown
+BitsPerPixel	Bits per pixel, currently expected to be 36
+PixelOrder	Currently expected to be RGB
+Creator	String describing the software creating this image
+IlluminationMode	Unknown
+ExposureMultiplier	Unknown, possibly the multiplier used to scale to 15 bits?
+GainRed	Unknown
+GainGreen	Unknown
+GainBlue	Unknown
+FocalPlaneTolerance	Unknown
+NMP	Unknown
+MacroIllumination	Unknown
+FocusOffset	Unknown
+RefocusInterval	Unknown
+CubeName	Unknown
+HardwareModel	Name of the hardware
+HardwareSerial	Serial number of the hardware
+NoFocusPoints	Unknown
+FocusPoint0X	Unknown
+FocusPoint0Y	Unknown
+FocusPoint0Z	Unknown
+FocusPoint1X	Unknown
+FocusPoint1Y	Unknown
+FocusPoint1Z	Unknown
+FocusPoint2X	Unknown
+FocusPoint2Y	Unknown
+FocusPoint2Z	Unknown
+FocusPoint3X	Unknown
+FocusPoint3Y	Unknown
+FocusPoint3Z	Unknown
+NoBlobPoints	Unknown
+BlobPoint0Blob	Unknown
+BlobPoint0FocusPoint	Unknown
+BlobPoint1Blob	Unknown
+BlobPoint1FocusPoint	Unknown
+BlobPoint2Blob	Unknown
+BlobPoint2FocusPoint	Unknown
+BlobPoint3Blob	Unknown
+BlobPoint3FocusPoint	Unknown
+BlobMapWidth	Unknown
+BlobMapHeight	Unknown
+Optimisation File (only for VMS)
+
+The optimisation file contains a list of 32- (or 64- or 320- ?) bit little endian values, giving the file offset into an MCU row, each offset starts at a 40-byte alignment, and the last row (of the entire file, not each image) seems to be missing. The offsets are all packed into 1 file, even with multiple images. The order of images is left-to-right, top-to-bottom.
+
+Map File
+
+The VMS map file is a standard JPEG file. Its restart markers (if any) are not included in the optimisation file. The VMU map file is in NGR format. This file can be used to provide a lower-resolution view of the slide.
+
+Image Files
+
+These files are given by the various ImageFile keys. They are assumed to have a height which is a multiple of the MCU height. They are assumed to have a width which is a multiple of MCUs per row divided by the restart interval.
+
+For VMS, these files are in JPEG, for VMU they are in NGR format.
+
+NGR Format
+
+The NGR file contains uncompressed 16-bit RGB data, with a small header. The files we have encountered start with GN, two more bytes, and then width, height, and column width in little endian 32-bit format. The column width must divide evenly into the width. Column width is important, since NGR files are generated in columns, where the first column comes first in the file, followed by subsequent files. Columns are painted left-to-right.
+
+At offset 24 is another 32-bit integer which gives the offset in the file to the start of the image data. The image data we have encountered is in 16-bit little endian format.
+
+Associated Images
+
+macro
+the image file given by the MacroImage value in the VMS/VMU file
+Known Properties
+
+All key-value data stored in the VMS/VMU file are encoded as properties prefixed with "hamamatsu.".
+
+Test Data
+
+http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu/ (ndpi format, wrapped vms format, currently not readable by OpenSlide)
+
+http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu-vms/ (vms format)
+
+Preliminary NDPI Notes
+
+NDPI is basically VMS stuffed into a broken TIFF file. libtiff cannot read the headers of a TIFF file, because NDPI specifies the RowsPerStrip as the height of the file, and after doing out the multiplication, this typically overflows libtiff and it refuses to open the file. Also, the TIFF tags are not stored in sorted order (sometimes, they may have fixed this in later versions).
+
+Unlike the VMS format, the NDPI is stored in a pyramid format as TIFF directory entries. The macro image seems to come last.
+
+If one just reads the TIFF tags directly, perhaps using tiffdump, one will find:
+
+Tag	Description
+ImageWidth	Width of the image
+ImageHeight	Height of the image
+Make	"Hamamatsu"
+Model	"NanoZoomer" or "C9600-12", etc
+XResolution	Seemingly correct X resolution, when interpreted with ResolutionUnit
+YResolution	Seemingly correct Y resolution, when interpreted with ResolutionUnit
+ResolutionUnit	Seemingly correct resolution unit
+Software	"NDP.scan", sometimes with a version number
+StripOffsets	The offset of the JPEG file for this layer
+StripByteCounts	The length of the JPEG file for this layer
+65420	Unknown, always 1?
+65421	Magnification? SourceLens from VMS? Seems correctly downsampled for each entry. (-1 for macro image, -2 for some sort of mask?)
+65422	XOffsetFromSlideCentre
+65423	YOffsetFromSlideCentre
+65424	Unknown, always 0?
+65425	Unknown, always 0?
+65426	Optimisation entries, as above
+65428	Unknown, AuthCode?
+65433	Unknown, I have seen 1500 in this tag
+65439	Unknown, perhaps some polygon ROI?
+65440	Unknown, I have seen this: <0 0 0 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 1 9 1 10 1 11 1 12 1 13 1 14 1 15 1 16 1 17>
+65441	Unknown, always 0?
+65442	Seems to be Model
+65443	Unknown, always 0?
+65444	Unknown, always 80?
+65445	Unknown, always 2?
+65446	Unknown, always 0?
+Unlike in VMS, JPEG files in NDPI are not necessarily valid. If ImageWidth or ImageHeight exceeds the JPEG limit of 65535, then the width or height as stored in the JPEG file is 0. JPEG files are not split into validly-sized files like in VMS. libjpeg will refuse to read the header of such a file, so the JPEG data stream must be altered when fed into libjpeg. Since a random access source manager is already required to read VMS JPEG files, this change is not too bad.
+
+.SH Aperio format
+.nf
+Format
   single-file pyramidal tiled TIFF, with non-standard metadata and compression
 File extensions
   .svs, .tif
@@ -82,7 +367,7 @@
 information as well as what look like offsets. Additionally, vertical
 line-delimited key-value pairs are stored, in at least the full-resolution
 image. A key-value pair is equals-delimited. These key-values are stored as
-properties starting with ”aperio.”. Currently, OpenSlide does not use any of
+properties starting with "aperio.". Currently, OpenSlide does not use any of
 the information present in these key-value fields.
 
 For stripped images, the ImageDescription tag may contain a name, followed by a
@@ -97,12 +382,12 @@
 This image is always tiled, usually with a tile size of 240x240 pixels. The
 second image is always a thumbnail, typically with dimensions of about 1024x768
 pixels. Unlike the other slide images, the thumbnail image is always stripped.
-Following the thumbnail there may be one or more intermediate “pyramid” images.
+Following the thumbnail there may be one or more intermediate "pyramid" images.
 These are always compressed with the same type of compression as the baseline
 image, and have a tiled organization with the same tile size.
 
 Optionally at the end of an SVS file there may be a slide label image, which is
-a low resolution picture taken of the slide’s label, and/or a macro camera
+a low resolution picture taken of the slide's label, and/or a macro camera
 image, which is a low resolution picture taken of the entire slide. The label
 and macro images are always stripped.
 
@@ -122,13 +407,13 @@
 thumbnail
   the second image in the file
 label
-  optional, the name “label” is given in ImageDescription
+  optional, the name "label" is given in ImageDescription
 macro
-  optional, the name “macro” is given in ImageDescription
+  optional, the name "macro" is given in ImageDescription
 .fi
 .SS Known Properties
 
-All key-value data encoded in the ImageDescription TIFF field is represented as properties prefixed with ”aperio.”.
+All key-value data encoded in the ImageDescription TIFF field is represented as properties prefixed with "aperio.".
 
 .SH "SEE ALSO"
 openslide-write-png(1), openslide-quickhash1sum(1), tiffinfo(1), tiffdump(1)


