Tool: Download DICOM

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Download DICOM allows browsing and fetching publicly available medical image data into ChimeraX. See also: open, DICOM Browser, DICOM Metadata, ChimeraX DICOM Reference, Fetch by ID

Currently, Download DICOM interfaces with one database, The Cancer Imaging Archive (TCIA):

The Cancer Imaging Archive (TCIA): maintaining and operating a public information repository. Clark K, Vendt B, Smith K, Freymann J, Kirby J, Koppel P, Moore S, Phillips S, Maffitt D, Pringle M, Tarbox L, Prior F. J Digit Imaging. 2013 Dec;26(6):1045-57.

Data hierarchy:

• The top level of dataset organization in TCIA is a collection, typically corresponding to a research project involving multiple patients, with potentially multiple studies per patient.
• Each study may contain multiple series.
• An individual series is a 3D image (stack of 2D images) that can be opened as volume data in ChimeraX.

Download DICOM allows traversing the hierachy from collections → studies → series, then choosing series to fetch and open. It can be started from the Medical Imaging section of the Tools menu and manipulated like other panels (more...).

**The dialog is initially empty, and loading the data may take a few minutes – progress is reported in the ChimeraX window status line.**

One or more rows in the dialog can be chosen (highlighted) by clicking and dragging with the left mouse button; Ctrl-click (or command-click if using a Mac) toggles whether a row is chosen.

• Clicking Load Webpage or using the context menu entry to Load Webpage for Chosen Entries will open the TCIA webpage describing each chosen collection.
• Clicking Drill down to Studies will switch the dialog to listing the studies within each chosen collection.

When the dialog is listing studies, one or more studies can be chosen, and clicking Drill Down to Series will list the series they contain.

When the dialog is listing series, one or more can be chosen to Download and Open. Buttons for navigating back up the hierarchy (Back to Studies, Back to Collections) are provided at the lower levels.

The data are stored locally in ~/Downloads/ChimeraX/tciaDownload/.