Provided by: libopenslide-dev_3.4.0-1build1_amd64 
NAME
openslide-formats - Reference supported formats
DESCRIPTION
LIST OF KNOWN PROPERTIES
Properties generated by OpenSlide
openslide.background-color
The background color of the slide, given as an RGB hex triplet. This property is not always present.
openslide.bounds-height
The height of the rectangle bounding the non-empty region of the slide. This property is not always
present.
openslide.bounds-width
The width of the rectangle bounding the non-empty region of the slide. This property is not always
present.
openslide.bounds-x
The X coordinate of the rectangle bounding the non-empty region of the slide. This property is not
always present.
openslide.bounds-y
The Y coordinate of the rectangle bounding the non-empty region of the slide. This property is not
always present.
openslide.comment
A free-form text comment.
openslide.mpp-x
Microns per pixel in the X dimension of level 0. May not be present or accurate.
openslide.mpp-y
Microns per pixel in the Y dimension of level 0. May not be present or accurate.
openslide.objective-power
Magnification power of the objective. Often inaccurate; sometimes missing.
openslide.quickhash-1
A non-cryptographic hash of a subset of the slide data. It can be used to uniquely identify a
particular virtual slide, but cannot be used to detect file corruption or modification.
openslide.vendor
The name of the vendor backend.
Properties for TIFF-based formats
tiff.Artist
The contents of the TIFF Artist tag.
tiff.Copyright
The contents of the TIFF Copyright tag.
tiff.DateTime
The contents of the TIFF DateTime tag.
tiff.DocumentName
The contents of the TIFF DocumentName tag.
tiff.HostComputer
The contents of the TIFF HostComputer tag.
tiff.ImageDescription
The contents of the TIFF ImageDescripton tag.
tiff.Make
The contents of the TIFF Make tag.
tiff.Model
The contents of the TIFF Model tag.
tiff.ResolutionUnit
The contents of the TIFF ResolutionUnit tag.
tiff.Software
The contents of the TIFF Software tag.
tiff.XPosition
The contents of the TIFF XPosition tag.
tiff.XResolution
The contents of the TIFF XResolution tag.
tiff.YPosition
The contents of the TIFF YPosition tag.
tiff.YResolution
The contents of the TIFF YResolution tag.
Vendor-specific properties
A list of vendor-specific properties can be found on the pages for each vendor format, linked from
Supported Virtual Slide Formats[1].
TRESTLE FORMAT
Format
single-file pyramidal tiled TIFF, with non-standard metadata and overlaps; additional files contain
more metadata and detailed overlap info
File extensions
.tif
OpenSlide vendor backend
trestle
Detection
Trestle slides are stored in single-file TIFF format. OpenSlide will detect a file as Trestle if:
1. The file is TIFF.
2. The TIFF Software tag starts with MedScan.
3. The ImageDescription tag is present.
4. All images are tiled.
Relevant TIFF tags
┌──────────────────────────┬───────────────────────────────────────┐
│ Tag │ Description │
├──────────────────────────┼───────────────────────────────────────┤
│ ImageDescription │ Stores some important key-value │
│ │ pairs, see below │
├──────────────────────────┼───────────────────────────────────────┤
│ Software │ Starts with ”MedScan” │
├──────────────────────────┼───────────────────────────────────────┤
│ XResolution, YResolution │ 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. │
└──────────────────────────┴───────────────────────────────────────┘
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 ”trestle.”.
┌──────────────────┬─────────────────────────────────────┐
│ Key │ Description │
├──────────────────┼─────────────────────────────────────┤
│ 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. │
└──────────────────┴─────────────────────────────────────┘
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.
Overlaps
The OverlapsXY pseudo-field encodes a list of tile overlap values as ASCII.
Example: ”64 64 32 32 16 16” (note the initial space).
These values represent the standard overlaps between adjacent tiles in X and Y, in pixels. This example
encodes 3 levels worth of overlaps. Further overlaps are assumed to have the value 0.
Individual tile overlaps may differ from the standard overlaps. These individual overlaps are recorded in
.tif-Nb files adjacent to the .tif file, where N is the level number. OpenSlide does not read these
files, though they have been partially decoded; see issue 21[2] for details.
Associated Images
macro
the image with a filename extension of ”.Full” (optional)
Known Properties
All data encoded in the ImageDescription TIFF field is represented as properties prefixed with
”trestle.”.
openslide.mpp-x
copy of tiff.XResolution (note that this is a totally non-standard use of this TIFF tag)
openslide.mpp-y
copy of tiff.YResolution (note that this is a totally non-standard use of this TIFF tag)
openslide.objective-power
normalized trestle.Objective Power
Test Data
http://openslide.cs.cmu.edu/download/openslide-testdata/Trestle/
HAMAMATSU FORMAT
Format
multi-file JPEG/NGR with proprietary metadata and index file formats, and single-file TIFF-like
format with proprietary metadata
File extensions
.vms, .vmu, .ndpi
OpenSlide vendor backend
hamamatsu
Detection
OpenSlide will detect a file as Hamamatsu if:
1. The file given is a INI-style text file.
2. It has a [Virtual Microscope Specimen] (VMS) or [Uncompressed Virtual Microscope Specimen] (VMU)
group.
3. If VMS, there are at least 1 row and 1 column of JPEG images (NoJpegColumns and NoJpegRows).
or if:
1. The file has a TIFF directory structure.
2. The Software tag starts with NDP.scan.
Overview
The Hamamatsu format has three variants. VMS and VMU consist of an index file, 2 or more image files, and
(in the case of VMS) an “optimisation” file. NDPI consists of a single TIFF-like file with some custom
TIFF tags. VMS and NDPI contain JPEG images; VMU contains NGR images (a custom uncompressed format).
Multiple focal planes are ignored, only focal plane 0 is read.
JPEG does not allow for files larger than 65535 pixels on a side. In VMS, multiple JPEG files are used to
encode large images. To avoid having many files, VMS uses close to maximum size (65K by 65K) JPEG files.
NDPI, instead, stuffs large levels into a single JPEG and sets the overflowed width/height fields to 0.
Unfortunately, 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 (in VMS) or in a TIFF tag (in NDPI). 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 4096x8, for example.)
Unfortunately, the VMS 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 VMS 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 │ Apparently 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 │
└────────────────────────┴───────────────────────────────────────┘
NDPI File
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.
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.
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. libjpeg will refuse to read the header
of such a file, so the JPEG data stream must be altered when fed into libjpeg.
Here are the observed TIFF tags:
┌─────────────────┬───────────────────────────────────────┐
│ 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 │ SourceLens, correctly downsampled for │
│ │ each entry. -1 for macro image, -2 │
│ │ for a map of non-empty regions. │
├─────────────────┼───────────────────────────────────────┤
│ 65422 │ XOffsetFromSlideCentre │
├─────────────────┼───────────────────────────────────────┤
│ 65423 │ YOffsetFromSlideCentre │
├─────────────────┼───────────────────────────────────────┤
│ 65424 │ Seemingly the Z offset from the │
│ │ center focal plane, in some unit │
├─────────────────┼───────────────────────────────────────┤
│ 65425 │ Unknown, always 0? │
├─────────────────┼───────────────────────────────────────┤
│ 65426 │ Optimisation entries, as above │
├─────────────────┼───────────────────────────────────────┤
│ 65427 │ Reference │
├─────────────────┼───────────────────────────────────────┤
│ 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 │ Scanner serial number │
├─────────────────┼───────────────────────────────────────┤
│ 65443 │ Unknown, have seen 0 or 16 │
├─────────────────┼───────────────────────────────────────┤
│ 65444 │ Unknown, always 80? │
├─────────────────┼───────────────────────────────────────┤
│ 65445 │ Unknown, have seen 0, 2, 10 │
├─────────────────┼───────────────────────────────────────┤
│ 65446 │ Unknown, always 0? │
├─────────────────┼───────────────────────────────────────┤
│ 65449 │ ASCII metadata block, key=value │
│ │ pairs, not always present │
├─────────────────┼───────────────────────────────────────┤
│ 65455 │ Unknown, have seen 13 │
├─────────────────┼───────────────────────────────────────┤
│ 65456 │ Unknown, have seen 101 │
├─────────────────┼───────────────────────────────────────┤
│ 65457 │ Unknown, always 0? │
├─────────────────┼───────────────────────────────────────┤
│ 65458 │ Unknown, always 0? │
└─────────────────┴───────────────────────────────────────┘
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 (only for VMS/VMU)
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 (only for VMS/VMU)
These files are given by the VMS/VMU 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, or SourceLens of -1 in NDPI
Known Properties
All key-value data stored in the VMS/VMU file, and known tags from the NDPI file, are encoded as
properties prefixed with ”hamamatsu.”.
openslide.mpp-x
for NDPI, calculated as 10000/tiff.XResolution, if tiff.ResolutionUnit is centimeter
openslide.mpp-y
for NDPI, calculated as 10000/tiff.YResolution, if tiff.ResolutionUnit is centimeter
openslide.objective-power
normalized hamamatsu.SourceLens
Test Data
NDPI format
http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu/
VMS format
http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu-vms/
APERIO FORMAT
Format
single-file pyramidal tiled TIFF, with non-standard metadata and compression
File extensions
.svs, .tif
OpenSlide vendor backend
aperio
Vendor Documentation
http://www.aperio.com/documents/api/Aperio_Digital_Slides_and_Third-party_data_interchange.pdf
Detection
Aperio slides are stored in single-file TIFF format. OpenSlide will detect a file as Aperio if:
1. The file is TIFF.
2. The initial image is tiled.
3. The ImageDescription tag starts with Aperio.
Relevant TIFF tags
┌──────────────────┬───────────────────────────────────────┐
│ Tag │ Description │
├──────────────────┼───────────────────────────────────────┤
│ ImageDescription │ Stores some important key-value pairs │
│ │ and other information, see below │
├──────────────────┼───────────────────────────────────────┤
│ Compression │ May be 33003 or 33005, which │
│ │ represent specific kinds of JPEG 2000 │
│ │ compression, see below │
└──────────────────┴───────────────────────────────────────┘
Extra data stored in ImageDescription
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 ”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 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.
TIFF Image Directory Organization
http://www.aperio.com/documents/api/Aperio_Digital_Slides_and_Third-party_data_interchange.pdf page 14:
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 “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 image, which is a low resolution picture taken of the
entire slide. The label and macro images are always stripped.
JPEG 2000 (compression types 33003 or 33005)
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
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.
Associated Images
thumbnail
the second image in the file
label
optional, the name “label” is given in ImageDescription
macro
optional, the name “macro” is given in ImageDescription
Known Properties
All key-value data encoded in the ImageDescription TIFF field is represented as properties prefixed with
”aperio.”.
openslide.mpp-x
normalized aperio.MPP
openslide.mpp-y
normalized aperio.MPP
openslide.objective-power
normalized aperio.AppMag
Test Data
http://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/
MIRAX FORMAT
Format
multi-file with very complicated proprietary metadata and indexes
File extensions
.mrxs
OpenSlide vendor backend
mirax
Detection
OpenSlide will detect a file as MIRAX if:
1. The file is not a TIFF.
2. The filename ends with .mrxs.
3. A directory exists in the same location as the file, with the same name as the file minus the
extension.
4. A file named Slidedat.ini exists in the directory.
Overview
MIRAX can store slides in JPEG, PNG, or BMP formats. Because JPEG does not allow for large images, and
JPEG and PNG provide very poor support for random-access decoding of part of an image, multiple images
are needed to encode a slide. To avoid having many individual files, MIRAX packs these images into a
small number of data files. The index file provides offsets into the data files for each required piece
of data.
The camera on MIRAX scanners takes overlapping photos and records the position of each one. Each photo is
then split into multiple images which do not overlap. Overlaps only occur between images that come from
different photos.
To generate level n + 1, each image from level n is downsampled by 2 and then concatenated into a new
image, 4 old images per new image (2 x 2). This process is repeated for each level, irrespective of image
overlaps. Therefore, at sufficiently high levels, a single image can contain one or more embedded
overlaps of non-integral width.
Index File
The index file starts with a five-character ASCII version string, followed by the SLIDE_ID from the
slidedat file. The rest of the file consists of 32-bit little-endian integers (unaligned), which can be
data values or pointers to byte offsets within the index file.
The first two integers point to offset tables for the hierarchical and nonhierarchical roots,
respectively. These tables contain one record for each VAL in the HIERARCHICAL slidedat section. For
example, the record for NONHIER_1_VAL_2 would be stored at nonhier_root + 4 * (NONHIER_0_COUNT + 2).
Each record is a pointer to a linked list of data pages. The first two values in a data page are the
number of data items in the page and a pointer to the next page. The first page always has 0 data items,
and the last page has a 0 next pointer.
There is one hierarchical record for each zoom level. The record contains data items consisting of an
image index, offset and length within a file, and a file number. The file number can be converted to a
data file name via the 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’s downsample
factor are omitted.
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.
Data Files
A data file begins with a header containing a five-character ASCII version string, the SLIDE_ID from the
slidedat file, the file number encoded into three ASCII characters, and 256 bytes of padding. The
remainder of the file contains packed data referenced by the index file.
Slide Position File
The slide position file is referenced by the VIMSLIDE_POSITION_BUFFER.default nonhierarchical section. It
contains one entry for each camera position (not each image position) in row-major order. Each entry is
nine bytes: a flag byte, the X pixel coordinate of the photo (4 bytes, little-endian, may be negative),
and the Y coordinate (4 bytes, little-endian, may be negative). In slides with CURRENT_SLIDE_VERSION ≥
1.9, the flag byte is 1 if the slide file contains images for this camera position, 0 otherwise. In older
slides, the flag byte is always 0.
In slides with CURRENT_SLIDE_VERSION ≥ 2.2, the slide position file is compressed with DEFLATE and
referenced by the StitchingIntensityLayer.StitchingIntensityLevel nonhierarchical section.
Associated Images
thumbnail
the image named ”ScanDataLayer_SlidePreview” in Slidedat.ini (optional)
label
the image named ”ScanDataLayer_SlideBarcode” in Slidedat.ini (optional)
macro
the image named ”ScanDataLayer_SlideThumbnail” in Slidedat.ini (optional)
Known Properties
All key-value data stored in the Slidedat.ini file are encoded as properties prefixed with ”mirax.”.
openslide.mpp-x
normalized MICROMETER_PER_PIXEL_X from the Slidedat section corresponding to level 0 (typically
mirax.LAYER_0_LEVEL_0_SECTION.MICROMETER_PER_PIXEL_X)
openslide.mpp-y
normalized MICROMETER_PER_PIXEL_Y from the Slidedat section corresponding to level 0 (typically
mirax.LAYER_0_LEVEL_0_SECTION.MICROMETER_PER_PIXEL_Y)
openslide.objective-power
normalized mirax.GENERAL.OBJECTIVE_MAGNIFICATION
See Also
Introduction to MIRAX/MRXS[3]. Note that our terminology has changed since that document was written;
where it says “tile”, substitute “image”, and where it says “subtile”, substitute “tile”.
Test Data
http://openslide.cs.cmu.edu/download/openslide-testdata/Mirax/
SAKURA FORMAT
Format
SQLite database containing pyramid tiles and metadata
File extensions
.svslide
OpenSlide vendor backend
sakura
Detection
OpenSlide will detect a file as Sakura if:
1. The file is a SQLite database.
2. The DataManagerSQLiteConfigXPO table contains exactly one row, and its TableName field refers to a
unique table.
3. The unique table contains a row with id = "++MagicBytes" and data = "SVGigaPixelImage".
File Organization
Sakura slides are SQLite 3 database files written by the eXpress Persistent Objects ORM. Tables contain
slide metadata, associated images, and JPEG tiles. Tiles are addressed as (downsample, level-0 X
coordinate, level-0 Y coordinate, color channel), with separate grayscale JPEGs for each color channel.
Despite the generality of the address format, tiles appear to be organized in a regular grid, with
power-of-two level downsamples and without overlapping tiles. The structure of the file allows scans to
be sparse, but it is not clear if this is actually done.
SQL Tables
Some irrelevant tables and columns have been omitted from the summary below.
DataManagerSQLiteConfigXPO.PP Useful only to get a reference to the unique table. OpenSlide requires this
table to contain exactly one row.
┌───────────┬──────┬───────────────────────────┐
│ Column │ Type │ Description │
├───────────┼──────┼───────────────────────────┤
│ TableName │ text │ Name of the unique table, │
│ │ │ described below │
└───────────┴──────┴───────────────────────────┘
SVSlideDataXPO.PP High-level metadata about a slide. OpenSlide assumes this table will contain exactly
one row.
┌────────────────────┬─────────┬──────────────────────────┐
│ Column │ Type │ Description │
├────────────────────┼─────────┼──────────────────────────┤
│ OID │ integer │ Primary key │
├────────────────────┼─────────┼──────────────────────────┤
│ m_labelScan │ integer │ Foreign key to label │
│ │ │ associated image in │
│ │ │ SVScannedImageDataXPO │
├────────────────────┼─────────┼──────────────────────────┤
│ m_overviewScan │ integer │ Foreign key to macro │
│ │ │ associated image in │
│ │ │ SVScannedImageDataXPO │
├────────────────────┼─────────┼──────────────────────────┤
│ SlideId │ text │ UUID │
├────────────────────┼─────────┼──────────────────────────┤
│ Date │ text │ File creation date? │
├────────────────────┼─────────┼──────────────────────────┤
│ Description │ text │ Descriptive text? │
├────────────────────┼─────────┼──────────────────────────┤
│ Creator │ text │ Author? │
├────────────────────┼─────────┼──────────────────────────┤
│ DiagnosisCode │ text │ Unknown, have seen “0” │
├────────────────────┼─────────┼──────────────────────────┤
│ HRScanCount │ integer │ Presumably the number of │
│ │ │ corresponding rows in │
│ │ │ SVHRScanDataXPO │
├────────────────────┼─────────┼──────────────────────────┤
│ Keywords │ text │ Descriptive text? │
├────────────────────┼─────────┼──────────────────────────┤
│ TotalDataSizeBytes │ integer │ Presumably the sum of │
│ │ │ TotalDataSizeBytes in │
│ │ │ corresponding │
│ │ │ SVHRScanDataXPO rows │
└────────────────────┴─────────┴──────────────────────────┘
SVHRScanDataXPO.PP A single high-resolution scan of a slide from SVSlideDataXPO. OpenSlide assumes this
table will contain exactly one row.
┌──────────────────────────┬─────────┬──────────────────────────────┐
│ Column │ Type │ Description │
├──────────────────────────┼─────────┼──────────────────────────────┤
│ OID │ integer │ Primary key │
├──────────────────────────┼─────────┼──────────────────────────────┤
│ ParentSlide │ integer │ Foreign key to │
│ │ │ SVSlideDataXPO │
├──────────────────────────┼─────────┼──────────────────────────────┤
│ ScanId │ text │ UUID │
├──────────────────────────┼─────────┼──────────────────────────────┤
│ Date │ text │ Scan date? │
├──────────────────────────┼─────────┼──────────────────────────────┤
│ Description │ text │ Descriptive text? │
├──────────────────────────┼─────────┼──────────────────────────────┤
│ Name │ text │ Scan name? │
├──────────────────────────┼─────────┼──────────────────────────────┤
│ PosOnSlideMm │ blob │ 16 bytes of binary │
├──────────────────────────┼─────────┼──────────────────────────────┤
│ ResolutionMmPerPix │ real │ Millimeters per pixel │
├──────────────────────────┼─────────┼──────────────────────────────┤
│ NominalLensMagnification │ real │ Objective power │
├──────────────────────────┼─────────┼──────────────────────────────┤
│ ThumbnailImage │ blob │ thumbnail associated image │
│ │ │ data │
├──────────────────────────┼─────────┼──────────────────────────────┤
│ TotalDataSizeBytes │ integer │ Same as TOTAL_SIZE blob in │
│ │ │ unique table │
├──────────────────────────┼─────────┼──────────────────────────────┤
│ FocussingMethod │ integer │ Unknown; have seen “1” │
├──────────────────────────┼─────────┼──────────────────────────────┤
│ FocusStack │ blob │ 8 bytes; have seen all zeros │
└──────────────────────────┴─────────┴──────────────────────────────┘
SVScannedImageDataXPO.PP Contains associated images other than the thumbnail.
┌────────────────────┬─────────┬───────────────────────┐
│ Column │ Type │ Description │
├────────────────────┼─────────┼───────────────────────┤
│ OID │ integer │ Primary key │
├────────────────────┼─────────┼───────────────────────┤
│ Id │ text │ UUID │
├────────────────────┼─────────┼───────────────────────┤
│ PosOnSlideMm │ blob │ 16 bytes of binary │
├────────────────────┼─────────┼───────────────────────┤
│ ScanCenterPosMm │ blob │ 16 bytes of binary │
├────────────────────┼─────────┼───────────────────────┤
│ ResolutionMmPerPix │ real │ Millimeters per pixel │
├────────────────────┼─────────┼───────────────────────┤
│ Image │ blob │ JPEG image data │
├────────────────────┼─────────┼───────────────────────┤
│ ThumbnailImage │ blob │ Low-resolution JPEG │
│ │ │ thumbnail │
└────────────────────┴─────────┴───────────────────────┘
tile.PP This table is most naturally used to map tile coordinates to tile IDs, but is not suitable for
individual lookups because it has no useful indexes.
┌──────────────┬─────────┬─────────────────────────────┐
│ Column │ Type │ Description │
├──────────────┼─────────┼─────────────────────────────┤
│ TILEID │ text │ Foreign key to unique table │
├──────────────┼─────────┼─────────────────────────────┤
│ PYRAMIDLEVEL │ integer │ Downsample of the pyramid │
│ │ │ level │
├──────────────┼─────────┼─────────────────────────────┤
│ COLUMNINDEX │ integer │ Level-0 X coordinate of the │
│ │ │ top-left corner of the tile │
├──────────────┼─────────┼─────────────────────────────┤
│ ROWINDEX │ integer │ Level-0 Y coordinate of the │
│ │ │ top-left corner of the tile │
├──────────────┼─────────┼─────────────────────────────┤
│ COLORINDEX │ integer │ 0 for red, 1 for green, 2 │
│ │ │ for blue │
└──────────────┴─────────┴─────────────────────────────┘
Unique table
This is the table named by DataManagerSQLiteConfigXPO.TableName. It contains named blobs including the
JPEG tile data.
┌────────┬─────────┬──────────────────────┐
│ Column │ Type │ Description │
├────────┼─────────┼──────────────────────┤
│ id │ text │ Primary key │
├────────┼─────────┼──────────────────────┤
│ size │ integer │ Length of data field │
├────────┼─────────┼──────────────────────┤
│ data │ blob │ Data item │
└────────┴─────────┴──────────────────────┘
This table stores a variety of blob types. IDs for image tiles appear to be mechanically generated from
the tile coordinates, but OpenSlide does not construct them directly. Instead, it uses the tile table to
obtain IDs for each tile.
┌────────────────────┬──────────────────────────────────────┐
│ id │ Description │
├────────────────────┼──────────────────────────────────────┤
│ ++MagicBytes │ SVGigaPixelImage │
├────────────────────┼──────────────────────────────────────┤
│ ++VersionBytes │ Format version, e.g. 1.0.0 │
├────────────────────┼──────────────────────────────────────┤
│ Header │ A small binary structure. The first │
│ │ 12 bytes are little-endian 32-bit │
│ │ integers: tile size in pixels, image │
│ │ width in pixels, image height in │
│ │ pixels. │
├────────────────────┼──────────────────────────────────────┤
│ TOTAL_SIZE │ The data field is empty. The size │
│ │ field is the sum of all other size │
│ │ fields except ++MagicBytes and │
│ │ ++VersionBytes. │
├────────────────────┼──────────────────────────────────────┤
│ T;2048|4096;4;2;0 │ Image tile with downsample 4, X │
│ │ coordinate 2048, Y coordinate 4096, │
│ │ channel 2 (blue) │
├────────────────────┼──────────────────────────────────────┤
│ T;2048|4096;4;2;0# │ MD5 hash of the T;2048|4096;4;2;0 │
│ │ image tile │
└────────────────────┴──────────────────────────────────────┘
Associated Images
label
SVScannedImageDataXPO.Image corresponding to SVSlideDataXPO.m_labelScan
macro
SVScannedImageDataXPO.Image corresponding to SVSlideDataXPO.m_overviewScan
thumbnail
SVHRScanDataXPO.ThumbnailImage
Known Properties
sakura.Creator
SVSlideDataXPO.Creator
sakura.Date
SVSlideDataXPO.Date
sakura.Description
SVSlideDataXPO.Description
sakura.DiagnosisCode
SVSlideDataXPO.DiagnosisCode
sakura.FocussingMethod
SVHRScanDataXPO.FocussingMethod
sakura.Keywords
SVSlideDataXPO.Keywords
sakura.NominalLensMagnification
SVHRScanDataXPO.NominalLensMagnification
sakura.ResolutionMmPerPix
SVHRScanDataXPO.ResolutionMmPerPix
sakura.ScanId
SVHRScanDataXPO.ScanId
sakura.SlideId
SVSlideDataXPO.SlideId
openslide.mpp-x
calculated as 1000 * sakura.ResolutionMmPerPix
openslide.mpp-y
calculated as 1000 * sakura.ResolutionMmPerPix
openslide.objective-power
normalized sakura.NominalLensMagnification
Test Data
No public data available. Contact the mailing list[4] if you have some.
GENERIC TILED TIFF FORMAT
Format
single-file pyramidal tiled TIFF
File extensions
.tif
OpenSlide vendor backend
generic-tiff
Detection
OpenSlide will detect a file as generic TIFF if:
1. No other detections succeed.
2. The file is TIFF.
3. The initial image is tiled.
TIFF Image Directory Organization
The first image in the TIFF file is the full-resolution image. Any other tiled images in the file with
the “reduced resolution” bit set are assumed to be reduced-resolution versions of the original.
Associated Images
None.
Known Properties
Many TIFF tags are encoded as properties starting with ”tiff.”.
AUTHORS
The Carnegie Mellon School of Computer Science.
This manual page was written by Mathieu Malaterre <malat@debian.org> for the Debian GNU/Linux system (but
may be used by others).
NOTES
1. Supported Virtual Slide Formats
http://openslide.org/formats/
2. issue 21
http://openslide.orghttps://github.com/openslide/openslide/issues/21#issuecomment-23615583
3. Introduction to MIRAX/MRXS
http://lists.andrew.cmu.edu/pipermail/openslide-users/2012-July/000373.html
4. mailing list
http://lists.andrew.cmu.edu/mailman/listinfo/openslide-users/
OpenSlide 3.4.0 01/26/2014 OPENSLIDE-FORMATS(3)