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 Type attribute of each matching file to determine the file’s role within the whole slide image:

Role	Allowed Image Type values
Slide level	`ORIGINAL\PRIMARY\VOLUME\NONE` `DERIVED\PRIMARY\VOLUME\NONE` `DERIVED\PRIMARY\VOLUME\RESAMPLED`
Associated image	`ORIGINAL\PRIMARY\LABEL\NONE` `ORIGINAL\PRIMARY\OVERVIEW\NONE` `ORIGINAL\PRIMARY\THUMBNAIL\RESAMPLED` `DERIVED\PRIMARY\LABEL\NONE` `DERIVED\PRIMARY\OVERVIEW\NONE` `DERIVED\PRIMARY\THUMBNAIL\RESAMPLED`
Ignored	All others

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`
JPEG 2000 lossless	`1.2.840.10008.1.2.4.90`	`RGB` `YBR_ICT`

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	Allowed Image Type values
`label`	`ORIGINAL\PRIMARY\LABEL\NONE` `DERIVED\PRIMARY\LABEL\NONE`
`macro`	`ORIGINAL\PRIMARY\OVERVIEW\NONE` `DERIVED\PRIMARY\OVERVIEW\NONE`
`thumbnail`	`ORIGINAL\PRIMARY\THUMBNAIL\RESAMPLED` `DERIVED\PRIMARY\THUMBNAIL\RESAMPLED`

Known Properties

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

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/