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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. We gratefully acknowledge support from the NIAID for ChimeraX development related to medical image analysis.

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 Browser, DICOM Metadata, 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 files also contain associated information (metadata). This information is not shown automatically when the files are opened, but can be displayed with the DICOM Browser and DICOM Metadata tools.

DICOM Model Hierarchy

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

  1. DICOM folder (if multiple patients)
  2. patient (ID)
  3. study (date)
  4. series (description), each corresponding to a volume model, typically 3D imaging (e.g. CT, MRI) and derivations thereof (e.g., segmentations)

The DICOM Browser also shows the hierarchy.

DICOM Initial Display Settings

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


UCSF Resource for Biocomputing, Visualization, and Informatics / November 2022