DICOM format

Format: international standard multi-file medical imaging format
File extensions: .dcm
OpenSlide vendor backend: dicom

Format Documentation

Detection

OpenSlide will detect a file as DICOM if:

The file can be parsed as a DICOM Part 10 file.
The file does not have a .tif or .tiff filename extension or cannot be parsed as a TIFF file.
The Media Storage SOP Class UID is VL Whole Slide Microscopy Image Storage (1.2.840.10008.5.1.4.1.1.77.1.6).

File Organization

OpenSlide uses libdicom to parse and load DICOM files.

OpenSlide non-recursively scans the containing directory for other DICOM files with the same Series Instance UID attribute value as the specified file. It uses the Image Flavor (value 3 of the Image Type attribute) of each matching file to determine the file’s role within the whole slide image:

Role	Image Flavor values
Slide level	`VOLUME`
Associated image	`LABEL` `OVERVIEW` `THUMBNAIL`
Ignored	All others

A slide level can be spread across multiple files that share a Concatenation UID.

If multiple files in the directory have the same SOP Instance UID, the extra copies are ignored.

A file’s Dimension Organization Type can be TILED_FULL, TILED_SPARSE, or 3D. These transfer syntaxes and photometric interpretations are supported:

Pixel encoding	Transfer Syntax UID	Allowed Photometric Interpretation values
Uncompressed little-endian	`1.2.840.10008.1.2.1`	`RGB`
JPEG baseline	`1.2.840.10008.1.2.4.50`	`RGB` `YBR_FULL_422`
JPEG 2000	`1.2.840.10008.1.2.4.91`	`RGB` `YBR_ICT` `YBR_RCT`
JPEG 2000 (lossless only)	`1.2.840.10008.1.2.4.90`	`RGB` `YBR_RCT`

ICC Profiles

The slide ICC profile is taken from the ICC Profile attribute of the highest-resolution image. Associated image ICC profiles are taken from the ICC Profile of the associated image.

Associated Images

Associated image	Image Flavor
`label`	`LABEL`
`macro`	`OVERVIEW`
`thumbnail`	`THUMBNAIL`

Known Properties

Many DICOM attributes are represented hierarchically as properties prefixed with “dicom.”.

openslide.barcode: Barcode Value from highest-resolution level
openslide.mpp-x: normalized X component of Pixel Spacing from highest-resolution level
openslide.mpp-y: normalized Y component of Pixel Spacing from highest-resolution level
openslide.objective-power: Objective Lens Power from highest-resolution level

Test Data

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