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DICOM Files

DICOM (Digital Imaging and Communications in Medicine) refers to a broad and complex set of standards for medical images and related information. ChimeraX can read many but not all DICOM files. Errors may arise from trying to read types of data that are not yet handled properly, such as screen captures, non-axial series, and series encoded with 16-bit lossless jpeg.

See also: ChimeraX DICOM Reference, DICOM in VR tutorial, ChimeraX for Medical Image Analysis

In ChimeraX, DICOM format is indicated by the filename suffix .dcm or the format dicom option in the open command.

The open command verbose option shows detailed debugging information for DICOM input.

In general, 3D maps described as image series are read (DICOM modalities CT, MR, RTDOSE, etc.).

Some DICOM files contain 4D data or time series that can be played with the time slider shown automatically by ChimeraX or with the vseries command.

Some DICOM files contain SEG objects (segmentations as binary maps), and these are automatically associated with the corresponding image series to synchronize plane display. They can also be displayed as isosurfaces, for example: volume #1.1.1.1.5 show style surf level 1 region all

Radiotherapy structure set (RTSTRUCT) contours are also read and displayed.

DICOM Model Hierarchy

Models read from DICOM files are arranged in a hierarchy, as shown in the Model Panel:

  1. directory
  2. patient ID
  3. study date
  4. series description and number, if available, or body part and modality
  5. segmentations or other image series-dependent annotations (for example, segmentations of a particular CT scan)

DICOM Initial Display Settings

Each volume data model read from DICOM is initially displayed as a single Z plane in the “solid” style. DICOM-specific defaults for solid rendering correspond to the volume command options:


UCSF Resource for Biocomputing, Visualization, and Informatics / March 2019