Visualizing images
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IDC integrates two different viewers, which will be used depending on the type of images being opened. Visualization of radiology images uses the open-source v3. The is used for visualization of pathology and slide microscopy images. We customized both of those viewers slightly to add features specific to IDC. You can find all of those modifications in the respective forks under the IDC GitHub organization for OHIF and SliM viewers: and . IDC Viewer is opened every time you click the "eye" icon in the study or series table of the IDC Portal.
The OHIF and SliM viewers do not support 32 bit browsers.
IDC Viewer is a "zero-footprint" client-side viewer: before you can see the image in the viewer, it has to be downloaded to your browser from the IDC DICOM stores. IDC Viewer communicates the data it receives through a proxy via the interface implemented in GCP .
The main functions of the viewer are available via the toolbar controls shown below.
The functionality supported by those tools should be self-explanatory, or can be discovered via quick experimentation.
IDC Viewer supports visualization of DICOM Segmentation objects (SEG) and DICOM Radiotherapy Structure Sets (RTSTRUCT). When available in a given study, you will see those modalities labeled as such in the left-hand panel of the viewer, as shown below. To see a specific SEG or RTSTRUCT, double-click on the corresponding thumbnail. After that you can open the RTSTRUCT/SEG panel in the upper right corner to jump to the locations of the specific structure sets or segments, and to control their individual visibility.
Note that certain modalities, such as Segmentation (SEG) and Real World Value Mapping (RWVM) objects, cannot be selected for visualization from the IDC Portal. SEG can only be viewed in the context of the image series segmented, and RWVM series are not viewable and will not show up in the left panel of the viewer.
Below is an example of series objects that are not viewable at the series level.
The IDC pathology viewer allows for interactive visualization of digital slide microscopy (SM) images.
Here are some specific examples, taken from the IDC Portal dashboard:
You can share the viewer URLs if you want to refer to visualizations of the specific items from IDC. You can also use this functionality if you want to visualize specific items from your notebook or a custom dashboard (e.g., a Google DataStudio dashboard).
If you want to visualize your own images, or if you would like to combine IDC images with the analysis results or annotations you generated, you do have several options:
If you want to report a problem related to visualization of a specific study in the IDC Viewer, please use the "Debug Info" tool to collect debugging information. Please report the issue on the , including the entire content of the debugging information to help us investigate the issue.
You can use IDC Viewer to visualize any of the suitable data in IDC. To configure the IDC Viewer URL, simply append StudyInstanceUID of a study available in IDC to the following prefix: (for the radiology viewer) and/ (for the digital pathology viewer). This will open the entire study in the viewer. You can also configure the URL to open specific series of the study, as defined by the list of SeriesInstanceUID items. When you open the IDC Viewer from the IDC Portal, the URLs of the pages will be populated following those conventions.
open entire study with the StudyInstanceUID1.3.6.1.4.1.14519.5.2.1.6279.6001.224985459390356936417021464571: .
open the specified subset of series from the study above:
Digital pathology viewer uses a slightly different convention, as should be evident from this example URL:
You can use Google FireCloud to deploy v2 radiology or microscopy viewers as web applications, without having to use virtual machines or docker, and for free!
If you want to visualize images inside a Colab/Jupyter notebook - you can use - details in
You can use open source zero-footprint viewer to visualize and volume render any image series by simply pointing it to the cloud bucket with the files - see details in
