Segmentation and Markup Formats

Research Formats may be preferable for current Groundwork activities. The applications may already be installed and the researchers familiar with their use, allowing groundwork to proceed immediately. Managing the files manually is tractable at the scale of groundwork studies.

DICOM Formats may be preferable in the Profiles themselves. DICOM addresses a number of issues that will be faced when we try to roll this out in a clinical environment: where do the segmentations get stored, how do we move them over the network, how do we exchange them on portable media, how do we associate them with the patient record, how do we find/retrieve them later for comparison, how do we identify the images from which they were derived, how do we identify the space in which they exist for later registration, how do we de-identify them for research purposes, etc.

Research Segmentation Formats

<<Include details of 3D Doctor and PLY formats here>>

DICOM Segmentation Formats

DICOM provides several ways to encode segmentations.

NOTE: Both Supplement documents and the DICOM Standard are referenced below. Supplement documents are no longer maintained after they have been made Final Text and incorporated into the DICOM Standard. They are convenient to review since they contain only the materials related to a specific topic, but be aware that implementations should use the DICOM Standard since it may contain fixes and updates not in the original supplement.

Contours - Supp 65

Polyline contours in the plane of an image define a boundary enclosing a segmentation. Contours may be drawn on multiple images in a set to segment a volume.

The contours are embedded into a DICOM Structured Report object as a list of polyline vertices. This supplement was written to address the needs of storing the results of Chest CAD based on X-ray or CT images. The approach could be adapted to other applications and appropriate extensions made to DICOM.

Document: Supplement 65 (See Pg 4-5, 15-18, 22-24 for a cursory overview; See Pgs 30-42 for the basic details and various code tables and code definitions on Pgs 55-105 e.g. RECIST Repsonse Criteria codes on Pg 77)

Specification: DICOM 2008 (Supp 65 is Final Text)

Masks - Supp 111

Pixel/voxel masks in the plane of an image define images pixels that are part of a segmentation. Masks may be drawn on multiple images in a set to segment a volume. The mask values may be binary or fractional. Fraction may be used to represent either the fraction of the voxel which is a part of the segmentation (partial volumes), or the fractional probability that the voxel belongs to the segmentation.

The masks are stored in objects that look very much like DICOM images, except instead of image pixels they contain mask pixels.

Document: Supplement 111 (See Pg 4 for a cursory overview; See Pgs 15-19, 28-31, 34 for the basic details)

Specification: DICOM 2008 (Supp 111 is Final Text)

Surfaces - Supp 132

A Surface Mesh (i.e. polygons/triangles) connecting points in space, which may or may not be in the plane of an image, define the volume which is part of a segmentation.

The surfaces are stored in a DICOM object which can be managed similarly to other DICOM files, but contains lists of points and vectors instead of an array of pixels.

Document: Supplement 132 (See Pgs 4, 38-40 for a cursory overview; See Pgs 9, 15-25 for the basic details)

Specification: (Supp 132 was approved for Final Text in late 2008 - will be incorporated shortly)