DICOM format

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

Format Documentation

DICOM Whole Slide Imaging

Detection

OpenSlide will detect a file as DICOM if:

  1. The file can be parsed as a DICOM Part 10 file.
  2. 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
thumbnail ORIGINAL\PRIMARY\THUMBNAIL\RESAMPLED
DERIVED\PRIMARY\THUMBNAIL\RESAMPLED
label ORIGINAL\PRIMARY\LABEL\NONE
DERIVED\PRIMARY\LABEL\NONE
macro ORIGINAL\PRIMARY\OVERVIEW\NONE
DERIVED\PRIMARY\OVERVIEW\NONE

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/