ARGOS format

Format

single-file pyramidal tiled BigTIFF with non-standard metadata

File extensions

.avs

OpenSlide vendor backend

argos

Vendor Documentation

Documentation PDF

Detection

ARGOS slides are stored in single-file BigTIFF format. OpenSlide will detect a file as ARGOS if:

1. The file is TIFF.
2. The initial image is tiled.
3. Tag 65000 contains valid XML whose root element is Argos.Scan.Metadata.

Relevant TIFF tags

Tag	Description
65000	Metadata XML

Metadata XML

The first TIFF directory includes metadata XML in TIFF tag 65000. The field type is ASCII, but in our samples the value is not NUL-terminated as required by TIFF, causing libtiff to warn about it.

Value	Description
MaxZ	Integer identifier for highest focal plane
MinZ	Integer identifier for lowest focal plane
ScanArea	Coordinates of scanned portion of the slide (cm)
ZRange	Distance between outermost focal planes (μm)

TIFF Image Directory Organization

The TIFF file contains the image pyramid of the lowest focal plane, followed by each higher plane in succession. Images are sparse, with missing tiles represented by a zero TileOffset and a zero TileByteCount.

The last two TIFF directories are the thumbnail and macro images, which are both stripped.

Associated Images

thumbnail

second-to-last image in the file, non-tiled

macro

last image in the file, non-tiled

Known Properties

All simple key-value data encoded in the metadata XML is represented as properties prefixed with “argos.”.

openslide.barcode

argos.Barcode

openslide.mpp-x

calculated as 10000/tiff.XResolution, if tiff.ResolutionUnit is centimeter

openslide.mpp-y

calculated as 10000/tiff.YResolution, if tiff.ResolutionUnit is centimeter

openslide.objective-power

normalized argos.ObjectiveMagnification

Test Data

https://openslide.cs.cmu.edu/download/openslide-testdata/Argos/