Aperio slides are stored in single-file TIFF format. OpenSlide will detect a file as Aperio if:
ImageDescriptiontag starts with
||Stores some important key-value pairs and other information, see below|
||May be 33003 or 33005, which represent specific kinds of JPEG 2000 compression, see below|
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
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.
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.
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
even though the TIFF standard seems to require this. The correct
subsampling can be found in the JPEG 2000 codestream.
All key-value data encoded in the
ImageDescription TIFF field is
represented as properties prefixed with “