HALO Integration

[addon] [on-prem]

The bi-directional integration between PathcoreFlow and the HALO image analysis software from Indica Labs provides capabilities for:

• Using the HALO desktop application to perform image analysis on the images contained in the PathcoreFlow file repository (without downloading images to your PC)
• Automatic recognition of analysis results generated in the HALO application in PathcoreFlow
• Ability to view and share analysis results with colleagues from the PathcoreFlow environment

Integration Overview

In order to leverage the integration, image(s) must be launched from the PathcoreFlow environment using the Open in Halo context menu option. Doing so causes a SIS file to be downloaded. The SIS file is associated with the HALO application and when clicked will cause HALO — which is required to be installed on the user's PC — to launch with the selected image(s). At this stage in the workflow, PathcoreFlow only communicates metadata via the SIS file about the images that were selected for use in HALO.

Once the HALO app has launched, the user follows the normal workflow in that application and can proceed to interact with the HALO database and to perform analysis as they would normally.

Analysis results need not be exported since PathcoreFlow will query HALO’s GraphQL server for available results, as required, when users work with images in the PathcoreFlow environment. At present, PathcoreFlow can retrieve segmentation results, and any quantitative results (key-value pairs) an app may have generated. It’s important to note that these results will be automatically associated with the image(s) they were created from. These associations are made since PathcoreFlow and HALO are accessing the same underlying storage system and because the HALO application uses the file paths to identify images in its database.

Finally, users are able to view images via any web browser, overlaid with any segmentation results that may have been found by PathcoreFlow. Thus the results and images are accessible from the PathcoreFlow environment and there is no duplication of data, since HALO and PathcoreFlow share the same underlying storage system.

Open in HALO From PathcoreFlow

From the PathcoreFlow environment, one or more images and/or folders can be opened in HALO from the Repository page. Images can also be launched from within the Viewer, though this workflow is limited to the current image in the Viewer.

Viewing Results in PathcoreFlow

PathcoreFlow will automatically query HALO’s GraphQL server for the latest analysis results, as needed, when an image is opened in the Viewer or selected in the Repository page. If there is a need to refresh the results, simply refresh the browser by pressing the F5 key or via the refresh button in PathcoreFlow.

Viewing Segmentation Results

Segmentation results retrieved from HALO are automatically associated with the correct image. As a result, entries are created for each result in the Overlays Panel of the Viewer and these results are automatically overlaid and rendered on top of the image.

The results behave similar to other overlays and their properties (e.g. opacity, render mode, and pseudocolor) can be manipulated. See Overlays for more details.

Viewing Quantitative Results

Any quantitative results exported to PathcoreFlow can be seen in multiple locations for convenience. When receiving these results, PathcoreFlow automatically creates a String custom field for each key-value pair that is exported.