[med-svn] [Git][med-team/openslide][master] 4 commits: d/openslide-formats.3: refresh the manual page.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Sep 6 11:37:23 BST 2026
Étienne Mollier pushed to branch master at Debian Med / openslide
Commits:
f6fe9526 by Étienne Mollier at 2026-09-06T12:27:29+02:00
d/openslide-formats.3: refresh the manual page.
Closes: #1146814
- - - - -
0960055f by Étienne Mollier at 2026-09-06T12:28:02+02:00
d/rules: ensure openslide-format(3) version consistency.
This change implements a check at an early stage of the package
construction, in order to make sure that there is no delta between the
new upstream version and its shipped documentation.
- - - - -
f760fb6b by Étienne Mollier at 2026-09-06T12:31:01+02:00
d/control: update file formats support list.
The change includes a subtle wording change in order to make the delta
between the package description and the exhaustive list of supported
format less problematic.
- - - - -
83fc5f46 by Étienne Mollier at 2026-09-06T12:33:32+02:00
d/changelog: initialize the changelog.
Note: upload is postponed until 4.0.1+dfsg-1 migrates to testing.
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/openslide-formats.3
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+openslide (4.0.1+dfsg-2) UNRELEASED; urgency=medium
+
+ * d/openslide-formats.3: refresh the manual page. (Closes: #1146814)
+ * d/rules: ensure openslide-format(3) version consistency.
+ This change implements a check at an early stage of the package
+ construction, in order to make sure that there is no delta between the
+ new upstream version and its shipped documentation.
+ * d/control: update file formats support list.
+ The change includes a subtle wording change in order to make the delta
+ between the package description and the exhaustive list of supported
+ format less problematic.
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 06 Sep 2026 12:32:30 +0200
+
openslide (4.0.1+dfsg-1) unstable; urgency=medium
* Migrate openslide 4.0.1 to unstable for auto-openslide transition.
=====================================
debian/control
=====================================
@@ -36,13 +36,19 @@ Description: library for reading whole slide image files
multi-resolution, and only a small amount of image data might be needed at a
particular resolution.
.
- This library currently supports:
+ This library supports notably:
- Aperio (.svs, .tif)
+ - ARGOS (.avs)
+ - DICOM (.dcm)
- Hamamatsu (.vms, .vmu, .ndpi)
+ - Huron (.tif)
- Leica (.scn)
- MIRAX (.mrxs)
+ - Philips (.tiff)
- Sakura (.svslide)
- Trestle (.tif)
+ - Ventana (.bif, .tif)
+ - Zeiss (.czi)
- Generic tiled TIFF (.tif)
.
This package contains the libraries needed to run OpenSlide applications.
@@ -67,13 +73,19 @@ Description: Development files for the OpenSlide library
multi-resolution, and only a small amount of image data might be needed at a
particular resolution.
.
- This library currently supports:
+ This library supports notably:
- Aperio (.svs, .tif)
+ - ARGOS (.avs)
+ - DICOM (.dcm)
- Hamamatsu (.vms, .vmu, .ndpi)
+ - Huron (.tif)
- Leica (.scn)
- MIRAX (.mrxs)
+ - Philips (.tiff)
- Sakura (.svslide)
- Trestle (.tif)
+ - Ventana (.bif, .tif)
+ - Zeiss (.czi)
- Generic tiled TIFF (.tif)
.
This package contains development files needed to build OpenSlide applications.
@@ -96,13 +108,19 @@ Description: Manipulation and conversion tools for OpenSlide
multi-resolution, and only a small amount of image data might be needed at a
particular resolution.
.
- This library currently supports:
+ This library supports notably:
- Aperio (.svs, .tif)
+ - ARGOS (.avs)
+ - DICOM (.dcm)
- Hamamatsu (.vms, .vmu, .ndpi)
+ - Huron (.tif)
- Leica (.scn)
- MIRAX (.mrxs)
+ - Philips (.tiff)
- Sakura (.svslide)
- Trestle (.tif)
+ - Ventana (.bif, .tif)
+ - Zeiss (.czi)
- Generic tiled TIFF (.tif)
.
This package contains command line tools for file manipulation.
=====================================
debian/openslide-formats.3
=====================================
@@ -1,13 +1,13 @@
'\" t
.\" Title: OPENSLIDE-FORMATS
.\" Author: [see the "AUTHORS" section]
-.\" Generator: DocBook XSL Stylesheets v1.79.1 <http://docbook.sf.net/>
-.\" Date: 07/29/2016
+.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
+.\" Date: 09/06/2026
.\" Manual: File Formats
-.\" Source: OpenSlide 3.4.1+dfsg
+.\" Source: OpenSlide 4.0.1+dfsg
.\" Language: English
.\"
-.TH "OPENSLIDE\-FORMATS" "3" "07/29/2016" "OpenSlide 3\&.4\&.1+dfsg" "File Formats"
+.TH "OPENSLIDE\-FORMATS" "3" "09/06/2026" "OpenSlide 4\&.0\&.1+dfsg" "File Formats"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
@@ -38,6 +38,11 @@ openslide\&.background\-color
The background color of the slide, given as an RGB hex triplet\&. This property is not always present\&.
.RE
.PP
+openslide\&.barcode
+.RS 4
+The contents of the slide\(cqs barcode\&. This property is not always present\&.
+.RE
+.PP
openslide\&.bounds\-height
.RS 4
The height of the rectangle bounding the non\-empty region of the slide\&. This property is not always present\&.
@@ -60,7 +65,12 @@ The Y coordinate of the rectangle bounding the non\-empty region of the slide\&.
.PP
openslide\&.comment
.RS 4
-A free\-form text comment\&.
+A free\-form text comment\&. This property is not always present\&.
+.RE
+.PP
+openslide\&.icc\-size
+.RS 4
+The size of the slide\(cqs ICC profile, if any\&.
.RE
.PP
openslide\&.mpp\-x
@@ -171,8 +181,7 @@ single\-file pyramidal tiled TIFF, with non\-standard metadata and compression
.PP
File extensions
.RS 4
-\&.svs,
-\&.tif
+\&.svs
.RE
.PP
OpenSlide vendor backend
@@ -181,7 +190,7 @@ aperio
.RE
.SS "Vendor Documentation"
.PP
-\m[blue]\fBhttp://www\&.aperio\&.com/documents/api/Aperio_Digital_Slides_and_Third\-party_data_interchange\&.pdf\fR\m[]
+\m[blue]\fBDocumentation PDF\fR\m[]\&\s-2\u[2]\d\s+2
.SS "Detection"
.PP
Aperio slides are stored in single\-file TIFF format\&. OpenSlide will detect a file as Aperio if:
@@ -232,6 +241,7 @@ Description
T}
.T&
l l
+l l
l l.
T{
ImageDescription
@@ -243,6 +253,11 @@ Compression
T}:T{
May be 33003 or 33005, which represent specific kinds of JPEG 2000 compression, see below
T}
+T{
+NewSubfileType
+T}:T{
+1 for the label associated image, 9 for the macro associated image
+T}
.TE
.sp 1
.SS "Extra data stored in ImageDescription"
@@ -250,13 +265,9 @@ T}
For tiled images, the
ImageDescription
tag contains some dimensional downsample 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 \(lqaperio\&.\(rq\&. Currently, OpenSlide does not use any of the information present in these key\-value fields\&.
-.PP
-For stripped images, the
-ImageDescription
-tag may contain a name, followed by a carriage return\&. This is used for naming the associated images\&. The second image in the file does not have a name, though it is an associated image\&.
.SS "TIFF Image Directory Organization"
.PP
-\m[blue]\fBhttp://www\&.aperio\&.com/documents/api/Aperio_Digital_Slides_and_Third\-party_data_interchange\&.pdf\fR\m[]
+\m[blue]\fBDigital Slides and Third\-Party Data Interchange\fR\m[]\&\s-2\u[2]\d\s+2
page 14:
.PP
The first image in an SVS file is always the baseline image (full resolution)\&. 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 \(lqpyramid\(rq 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\&.
@@ -264,28 +275,33 @@ The first image in an SVS file is always the baseline image (full resolution)\&.
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\(cqs 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\&.
.SS "JPEG 2000 (compression types 33003 or 33005)"
.PP
-Some Aperio files use compression type 33003 or 33005\&. Images using this compression need to be decoded as a JPEG 2000 codestream\&. For 33003: YCbCr format, possibly with a chroma subsampling of 4:2:2\&. For 33005: RGB format\&. Note that the TIFF file may not encode the colorspace or subsampling parameters in the
+Some Aperio files use compression type 33003 or 33005\&. Images using this compression need to be decoded as a JPEG 2000 codestream\&. For 33003: YCbCr format with no MCT, possibly with a chroma subsampling of 4:2:2\&. For 33005: MCT, which OpenJPEG decodes into RGB\&. Note that the TIFF file may not encode the colorspace or subsampling parameters in the
PhotometricInterpretation
field, nor the
YCbCrSubsampling
field, even though the TIFF standard seems to require this\&. The correct subsampling can be found in the JPEG 2000 codestream\&.
+.SS "ICC Profiles"
+.PP
+The slide ICC profile is taken from the
+ICC Profile
+tag of the first image\&.
.SS "Associated Images"
.PP
-thumbnail
-.RS 4
-the second image in the file
-.RE
+There are up to three stripped images: a thumbnail image, which is always the second image in the file; and label and macro images at the end of the file, with subfile types 1 and 9 respectively\&.
.PP
label
.RS 4
-optional, the name \(lqlabel\(rq is given in
-ImageDescription
+optional, non\-tiled image with subfile type 1
.RE
.PP
macro
.RS 4
-optional, the name \(lqmacro\(rq is given in
-ImageDescription
+optional, non\-tiled image with subfile type 9
+.RE
+.PP
+thumbnail
+.RS 4
+the second image in the file
.RE
.SS "Known Properties"
.PP
@@ -312,7 +328,7 @@ aperio\&.AppMag
.RE
.SS "Test Data"
.PP
-\m[blue]\fBhttp://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Aperio/\fR\m[]
+\m[blue]\fBhttps://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Aperio/\fR\m[]\&\s-2\u[3]\d\s+2
.SH "HAMAMATSU FORMAT"
.PP
Format
@@ -924,7 +940,7 @@ T}
.PP
NDPI uses a TIFF\-like structure, but libtiff cannot read the headers of an NDPI file\&. This is 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\&.
+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, and ASCII values are always stored out\-of\-line even when TIFF would store them inline\&.
.PP
NDPI stores an image pyramid in TIFF directory entries\&. In some files, the lower\-resolution pyramid levels contain no restart markers\&. The macro image, and sometimes an active\-region map, seems to come last\&.
.PP
@@ -934,14 +950,16 @@ or
ImageHeight
exceeds the JPEG limit of 65535, then the width or height as stored in the JPEG file is 0\&. libjpeg will refuse to read the header of such a file, so the JPEG data stream must be altered when fed into libjpeg\&.
.PP
-NDPI is based on the classic TIFF format, which does not support files larger than 4 GB\&. However, NDPI files can be larger than 4 GB\&. NDPI generally handles this by overflowing the corresponding TIFF fields, requiring the reader to guess the high\-order bits\&. This affects TIFF Value Offsets with pointers to out\-of\-line values, as well as the value of the
-StripOffsets
-field\&. Some TIFF fields (e\&.g\&.
-Software) have the same Value Offset in every directory; for these, no concatenation of high\-order bits is necessary\&. For the others (primarily field 65426) it seems reasonable to select high\-order bits which place the value at the largest offset below the directory itself, since the TIFF directory is positioned after the data it points to\&. NDPI always stores next\-directory offsets (in the TIFF header and at the end of each directory) as 64\-bit quantities, even though TIFF specifies them as 32 bits; this is possible because the TIFF standard places them at the end of their parent data structures\&.
+Conversely, on some pyramid levels without restart markers, the TIFF
+ImageWidth
+and
+ImageHeight
+may not match the JPEG dimensions due to inconsistent rounding\&.
.PP
-It is not clear whether NDPI can support individual directories larger than 4 GB\&. Such files would require additional inferences for the
-StripByteCounts
-field, for Value Offsets that are identical across directories, and for the optimisation entries\&.
+NDPI is based on the classic TIFF format, which does not support files larger than 4 GB\&. However, NDPI files can be larger than 4 GB\&. NDPI handles this by storing the high\-order bits of file offsets beyond the ends of standard TIFF structures\&. TIFF puts next\-directory offsets (in the TIFF header and at the end of each directory) at the ends of their parent data structures, so NDPI simply extends these values to 64\-bit quantities\&. The high\-order bits of directory entry Value Offsets are stored in an array immediately after the end of each TIFF directory, 4 bytes per directory entry\&. Values that would normally be stored inline in the Value Offset (not ASCII, as mentioned above) are still stored inline, even if the high 32 bits are non\-zero (e\&.g\&.
+StripOffsets
+and
+StripByteCounts, which always have a Count of 1 in NDPI), and other values are still stored out\-of\-line\&.
.PP
Here are the observed TIFF tags:
.TS
@@ -986,6 +1004,8 @@ l l
l l
l l
l l
+l l
+l l
l l.
T{
ImageWidth
@@ -1040,7 +1060,7 @@ T}
T{
65420
T}:T{
-Always exists, always 1\&. File format version?
+Always exists, always 1\&. File format version?
T}
T{
65421
@@ -1070,7 +1090,7 @@ T}
T{
65426
T}:T{
-Optimisation entries, as above
+Low 32 bits of optimisation entries, as above
T}
T{
65427
@@ -1088,6 +1108,11 @@ T}:T{
Unknown, have seen 0\&.0
T}
T{
+65432
+T}:T{
+High 32 bits of optimisation entries
+T}
+T{
65433
T}:T{
Unknown, I have seen 1500 in this tag
@@ -1157,6 +1182,11 @@ T{
T}:T{
Unknown, always 0?
T}
+T{
+65459
+T}:T{
+Unknown, have seen ASCII \(lqJPEG\(rq, \(lqNative RGB\(rq, and \(lqRGB\(rq
+T}
.TE
.sp 1
.SS "Optimisation File (only for VMS)"
@@ -1221,14 +1251,18 @@ hamamatsu\&.SourceLens
.PP
NDPI format
.RS 4
-\m[blue]\fBhttp://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Hamamatsu/\fR\m[]
+\m[blue]\fBhttps://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Hamamatsu/\fR\m[]\&\s-2\u[4]\d\s+2
.RE
.PP
VMS format
.RS 4
-\m[blue]\fBhttp://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Hamamatsu\-vms/\fR\m[]
+\m[blue]\fBhttps://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Hamamatsu\-vms/\fR\m[]\&\s-2\u[5]\d\s+2
.RE
-.SH "LEICA FORMAT"
+.SS "ImHex Patterns"
+<listitem>\m[blue]\fBVMS optimisation file\fR\m[]\&\s-2\u[6]\d\s+2
+</listitem><listitem>\m[blue]\fBVMU NGR file\fR\m[]\&\s-2\u[7]\d\s+2
+</listitem><listitem>\m[blue]\fBNDPI file\fR\m[]\&\s-2\u[8]\d\s+2
+</listitem>.SH "LEICA FORMAT"
.PP
Format
.RS 4
@@ -1280,12 +1314,8 @@ The initial image is tiled\&.
.\}
The
ImageDescription
-tag contains valid XML in either of these namespaces:
-<listitem>http://www\&.leica\-microsystems\&.com/scn/2010/03/10 </listitem>
-<listitem>http://www\&.leica\-microsystems\&.com/scn/2010/10/01 </listitem>
+tag contains valid XML in either of these namespaces:<listitem>http://www\&.leica\-microsystems\&.com/scn/2010/03/10 </listitem><listitem>http://www\&.leica\-microsystems\&.com/scn/2010/10/01 </listitem>
.RE
-.PP
-To open Leica files, OpenSlide must be built with libtiff 4 or above\&.
.SS "Relevant TIFF tags"
.TS
allbox tab(:);
@@ -1345,7 +1375,7 @@ namespace, OpenSlide 3\&.4\&.0 and earlier report this property as a Base64\-enc
namespace, OpenSlide reports the barcode as it is stored in the XML, since we do not know whether those barcodes are Base64\-encoded\&. If you have a
2010/03/10
slide with a bar code, please comment in
-\m[blue]\fBthis bug\fR\m[]\&\s-2\u[2]\d\s+2
+\m[blue]\fBthis bug\fR\m[]\&\s-2\u[9]\d\s+2
or contact the OpenSlide mailing list\&.)
.RE
.PP
@@ -1386,6 +1416,11 @@ objective
of the main image
.RE
.PP
+openslide\&.barcode
+.RS 4
+leica\&.barcode
+.RE
+.PP
openslide\&.mpp\-x
.RS 4
calculated as
@@ -1411,7 +1446,7 @@ leica\&.objective
.RE
.SS "Test Data"
.PP
-\m[blue]\fBhttp://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Leica/\fR\m[]
+\m[blue]\fBhttps://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Leica/\fR\m[]\&\s-2\u[10]\d\s+2
.SH "MIRAX FORMAT"
.PP
Format
@@ -1510,7 +1545,7 @@ DATAFILE
slidedat section\&. The image index is equal to
image_y * GENERAL\&.IMAGENUMBER_X + image_x\&. Image coordinates which are not multiples of the zoom level\(cqs downsample factor are omitted\&.
.PP
-Nonhierarchical records refer to associated images and additional metadata\&. Nonhierarchical data items consist of three zero values followed by an offset, length, and file number as in hierarchical records\&.
+Nonhierarchical records refer to associated images and additional metadata\&. Nonhierarchical data items consist of two values which are usually zero, followed by an offset, length, and file number as in hierarchical records\&.
.SS "Data Files"
.PP
A data file begins with a header containing a five\-character ASCII version string, the
@@ -1534,26 +1569,26 @@ In slides with
CURRENT_SLIDE_VERSION
≥ 2\&.2, the slide position file is compressed with DEFLATE and referenced by the
StitchingIntensityLayer\&.StitchingIntensityLevel
-nonhierarchical section\&.
+nonhierarchical section\&. In some such slides, the nonhierarchical record has a second data item which points to a DEFLATE\-compressed blob with four bytes of additional metadata per camera position\&.
.SS "Associated Images"
.PP
-thumbnail
+label
.RS 4
-the image named \(lqScanDataLayer_SlidePreview\(rq in
+the image named \(lqScanDataLayer_SlideBarcode\(rq in
Slidedat\&.ini
(optional)
.RE
.PP
-label
+macro
.RS 4
-the image named \(lqScanDataLayer_SlideBarcode\(rq in
+the image named \(lqScanDataLayer_SlideThumbnail\(rq in
Slidedat\&.ini
(optional)
.RE
.PP
-macro
+thumbnail
.RS 4
-the image named \(lqScanDataLayer_SlideThumbnail\(rq in
+the image named \(lqScanDataLayer_SlidePreview\(rq in
Slidedat\&.ini
(optional)
.RE
@@ -1586,11 +1621,14 @@ mirax\&.GENERAL\&.OBJECTIVE_MAGNIFICATION
.RE
.SS "See Also"
.PP
-\m[blue]\fBIntroduction to MIRAX/MRXS\fR\m[]\&\s-2\u[3]\d\s+2\&. Note that our terminology has changed since that document was written; where it says \(lqtile\(rq, substitute \(lqimage\(rq, and where it says \(lqsubtile\(rq, substitute \(lqtile\(rq\&.
+\m[blue]\fBIntroduction to MIRAX/MRXS\fR\m[]\&\s-2\u[11]\d\s+2\&. Note that our terminology has changed since that document was written; where it says \(lqtile\(rq, substitute \(lqimage\(rq, and where it says \(lqsubtile\(rq, substitute \(lqtile\(rq\&.
.SS "Test Data"
.PP
-\m[blue]\fBhttp://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Mirax/\fR\m[]
-.SH "PHILIPS FORMAT"
+\m[blue]\fBhttps://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Mirax/\fR\m[]\&\s-2\u[12]\d\s+2
+.SS "ImHex Patterns"
+<listitem>\m[blue]\fBIndex file\fR\m[]\&\s-2\u[13]\d\s+2
+</listitem><listitem>\m[blue]\fBSlide position file\fR\m[]\&\s-2\u[14]\d\s+2
+</listitem>.SH "PHILIPS FORMAT"
.PP
Format
.RS 4
@@ -1663,8 +1701,6 @@ ObjectType
attribute with a value of
DPUfsImport\&.
.RE
-.PP
-To open BigTIFF files, OpenSlide must be built with libtiff 4 or above\&.
.SS "File Organization"
.PP
Philips TIFF is an export format\&. The native Philips format, iSyntax, is a custom multi\-file format not currently supported by OpenSlide\&.
@@ -1758,6 +1794,12 @@ WSI, and in that object\(cqs
PixelDataRepresentation
objects is represented as properties prefixed with \(lqphilips\&.\(rq\&.
.PP
+openslide\&.barcode
+.RS 4
+Base64\-decoded
+philips\&.PIM_DP_UFS_BARCODE
+.RE
+.PP
openslide\&.mpp\-x
.RS 4
calculated as
@@ -1771,9 +1813,7 @@ calculated as
.RE
.SS "Test Data"
.PP
-No public data available\&. Contact the
-\m[blue]\fBmailing list\fR\m[]\&\s-2\u[4]\d\s+2
-if you have some\&.
+\m[blue]\fBhttps://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Philips\-TIFF/\fR\m[]\&\s-2\u[15]\d\s+2
.SH "SAKURA FORMAT"
.PP
Format
@@ -2213,10 +2253,7 @@ T}:T{
T}
.TE
.sp 1
-
-
-Unique table
-.PP
+Unique table.PP
This is the table named by
DataManagerSQLiteConfigXPO\&.TableName\&. It contains named blobs including the JPEG tile data\&.
.TS
@@ -2291,7 +2328,7 @@ T}
T{
TOTAL_SIZE
T}:T{
-The data field is empty\&. The size field is the sum of all other size fields except ++MagicBytes and ++VersionBytes\&.
+The data field is empty\&. The size field is the sum of all other size fields except ++MagicBytes and ++VersionBytes\&.
T}
T{
T;2048|4096;4;2;0
@@ -2305,8 +2342,7 @@ MD5 hash of the T;2048|4096;4;2;0 image tile
T}
.TE
.sp 1
-Header blob
-.PP
+Header blob.PP
The
Header
blob is a small binary structure containing little\-endian integers as follows:
@@ -2527,7 +2563,7 @@ sakura\&.NominalLensMagnification
.SS "Test Data"
.PP
No public data available\&. Contact the
-\m[blue]\fBmailing list\fR\m[]\&\s-2\u[4]\d\s+2
+\m[blue]\fBmailing list\fR\m[]\&\s-2\u[16]\d\s+2
if you have some\&.
.SH "TRESTLE FORMAT"
.PP
@@ -2698,7 +2734,7 @@ files adjacent to the
file, where
N
is the level number\&. OpenSlide does not read these files, though they have been partially decoded; see
-\m[blue]\fBissue 21\fR\m[]\&\s-2\u[5]\d\s+2
+\m[blue]\fBissue 21\fR\m[]\&\s-2\u[17]\d\s+2
for details\&.
.SS "Associated Images"
.PP
@@ -2733,7 +2769,7 @@ trestle\&.Objective Power
.RE
.SS "Test Data"
.PP
-\m[blue]\fBhttp://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Trestle/\fR\m[]
+\m[blue]\fBhttps://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Trestle/\fR\m[]\&\s-2\u[18]\d\s+2
.SH "VENTANA FORMAT"
.PP
Format
@@ -2793,8 +2829,11 @@ element, either as the root element or as a child of a
Metadata
root element\&.
.RE
+.SS "ICC Profiles"
.PP
-To open Ventana files, OpenSlide must be built with libtiff 4 or above\&.
+The slide ICC profile is taken from the
+ICC Profile
+tag of the highest\-resolution level\&.
.SS "Associated Images"
.PP
macro
@@ -2839,7 +2878,7 @@ ventana\&.Magnification
.RE
.SS "Test Data"
.PP
-\m[blue]\fBhttp://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Ventana/\fR\m[]
+\m[blue]\fBhttps://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Ventana/\fR\m[]\&\s-2\u[19]\d\s+2
.SH "GENERIC TILED TIFF FORMAT"
.PP
Format
@@ -2895,6 +2934,13 @@ The initial image is tiled\&.
.SS "TIFF Image Directory Organization"
.PP
The first image in the TIFF file is the full\-resolution image\&. Any other tiled images in the file with the \(lqreduced resolution\(rq bit set are assumed to be reduced\-resolution versions of the original\&.
+.PP
+Starting after OpenSlide 4\&.0\&.0, OpenSlide supports generic TIFF files with missing tiles, i\&.e\&. tiles with zero bytes of image data\&. These tiles are rendered as transparent pixels\&.
+.SS "ICC Profiles"
+.PP
+The slide ICC profile is taken from the
+ICC Profile
+tag of the highest\-resolution level\&.
.SS "Associated Images"
.PP
None\&.
@@ -2903,7 +2949,7 @@ None\&.
Many TIFF tags are encoded as properties starting with \(lqtiff\&.\(rq\&.
.SS "Test Data"
.PP
-\m[blue]\fBhttp://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Generic\-TIFF/\fR\m[]
+\m[blue]\fBhttps://openslide\&.cs\&.cmu\&.edu/download/openslide\-testdata/Generic\-TIFF/\fR\m[]\&\s-2\u[20]\d\s+2
.SH "AUTHORS"
.PP
The Carnegie Mellon School of Computer Science\&.
@@ -2916,22 +2962,97 @@ pages for each vendor format
\%http://openslide.org/formats/
.RE
.IP " 2." 4
+Documentation PDF
+.RS 4
+\%https://web.archive.org/web/20120420105738/http://www.aperio.com/documents/api/Aperio_Digital_Slides_and_Third-party_data_interchange.pdf
+.RE
+.IP " 3." 4
+https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/
+.RS 4
+\%http://openslide.orghttps://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/
+.RE
+.IP " 4." 4
+https://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu/
+.RS 4
+\%http://openslide.orghttps://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu/
+.RE
+.IP " 5." 4
+https://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu-vms/
+.RS 4
+\%http://openslide.orghttps://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu-vms/
+.RE
+.IP " 6." 4
+VMS optimisation file
+.RS 4
+\%http://openslide.orghttps://github.com/openslide/openslide/blob/main/misc/imhex/hamamatsu-vms-opt.hexpat
+.RE
+.IP " 7." 4
+VMU NGR file
+.RS 4
+\%http://openslide.orghttps://github.com/openslide/openslide/blob/main/misc/imhex/hamamatsu-vmu-ngr.hexpat
+.RE
+.IP " 8." 4
+NDPI file
+.RS 4
+\%http://openslide.orghttps://github.com/openslide/openslide/blob/main/misc/imhex/hamamatsu-ndpi.hexpat
+.RE
+.IP " 9." 4
this bug
.RS 4
\%http://openslide.orghttps://github.com/openslide/openslide/issues/155
.RE
-.IP " 3." 4
+.IP "10." 4
+https://openslide.cs.cmu.edu/download/openslide-testdata/Leica/
+.RS 4
+\%http://openslide.orghttps://openslide.cs.cmu.edu/download/openslide-testdata/Leica/
+.RE
+.IP "11." 4
Introduction to MIRAX/MRXS
.RS 4
\%http://openslide.orghttps://lists.andrew.cmu.edu/pipermail/openslide-users/2012-July/000373.html
.RE
-.IP " 4." 4
+.IP "12." 4
+https://openslide.cs.cmu.edu/download/openslide-testdata/Mirax/
+.RS 4
+\%http://openslide.orghttps://openslide.cs.cmu.edu/download/openslide-testdata/Mirax/
+.RE
+.IP "13." 4
+Index file
+.RS 4
+\%http://openslide.orghttps://github.com/openslide/openslide/blob/main/misc/imhex/mirax-index.hexpat
+.RE
+.IP "14." 4
+Slide position file
+.RS 4
+\%http://openslide.orghttps://github.com/openslide/openslide/blob/main/misc/imhex/mirax-position.hexpat
+.RE
+.IP "15." 4
+https://openslide.cs.cmu.edu/download/openslide-testdata/Philips-TIFF/
+.RS 4
+\%http://openslide.orghttps://openslide.cs.cmu.edu/download/openslide-testdata/Philips-TIFF/
+.RE
+.IP "16." 4
mailing list
.RS 4
\%http://openslide.orghttps://lists.andrew.cmu.edu/mailman/listinfo/openslide-users/
.RE
-.IP " 5." 4
+.IP "17." 4
issue 21
.RS 4
\%http://openslide.orghttps://github.com/openslide/openslide/issues/21#issuecomment-23615583
.RE
+.IP "18." 4
+https://openslide.cs.cmu.edu/download/openslide-testdata/Trestle/
+.RS 4
+\%http://openslide.orghttps://openslide.cs.cmu.edu/download/openslide-testdata/Trestle/
+.RE
+.IP "19." 4
+https://openslide.cs.cmu.edu/download/openslide-testdata/Ventana/
+.RS 4
+\%http://openslide.orghttps://openslide.cs.cmu.edu/download/openslide-testdata/Ventana/
+.RE
+.IP "20." 4
+https://openslide.cs.cmu.edu/download/openslide-testdata/Generic-TIFF/
+.RS 4
+\%http://openslide.orghttps://openslide.cs.cmu.edu/download/openslide-testdata/Generic-TIFF/
+.RE
=====================================
debian/rules
=====================================
@@ -41,6 +41,19 @@ debian/openslide-formats.3: properties.xml aperio.xml hamamatsu.xml leica.xml mi
(cd debian && sed -e 's at VER_FULL@$(VER_FULL)@g' openslide-formats.3.xml > openslide.tmp.xml)
(cd debian && xsltproc --xinclude openslide.tmp.xml)
+# Prevent inconsistencies between the manual page and the current
+# openslide version.
+MAN_VER = $(shell sed -n 's/.\\" Source: OpenSlide //p' debian/openslide-formats.3)
+execute_before_dh_update_autotools_config:
+ @ if [ "$(MAN_VER)" != "$(VER_FULL)" ] \
+ ; then echo 'E: debian/openslide-formats.3 documents openslide $(MAN_VER).' >&2 \
+ ; echo 'E: However, the current version shipped is $(VER_FULL).' >&2 \
+ ; echo 'E: Please run the following to refresh the manual:' >&2 \
+ ; echo 'E: $$ debian/rules debian/openslide-formats.3' >&2 \
+ ; echo 'E: Note it needs internet and a couple of XSL utilities.' >&2 \
+ ; exit 1 \
+ ; fi
+
override_dh_install:
dh_install
find debian/tmp -name lib*.la -delete
View it on GitLab: https://salsa.debian.org/med-team/openslide/-/compare/1f893629e8d876b8737f53e8aa0b7ea0055e71e2...83fc5f4646ce15fbc461d67b67725af6cd887d19
--
View it on GitLab: https://salsa.debian.org/med-team/openslide/-/compare/1f893629e8d876b8737f53e8aa0b7ea0055e71e2...83fc5f4646ce15fbc461d67b67725af6cd887d19
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