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/