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PathcoreFlow User Manual

Visiopharm Integration

[add-on]

The bi-directional integration between PathcoreFlow and Visiopharm’s image analysis software provides capabilities for:

  • Using the Visiopharm desktop application to perform image analysis on the images contained in the PathcoreFlow Repository (without downloading images to your PC)
  • One click export of analysis results generated in the Visiopharm application to the PathcoreFlow Repository
  • Ability to view and share analysis results with colleagues from the PathcoreFlow environment
  • Ability to export annotations generated in PathcoreFlow to Visiopharm
This integration requires the Visiopharm desktop application to be installed on the PC from which the integration is used as well as the Bi-directional integration for Visiopharm add-on.

Integration Overview

In order to leverage the integration, image(s) must be launched from the PathcoreFlow environment using the Open in VIS context menu option. Doing so will launch the Visiopharm application — which is required to be installed on the user's PC — with the selected image(s). At this stage in the workflow, PathcoreFlow only communicates metadata about the images that were selected, enough for the Visiopharm application to locate these images.

The integration is coordinated via PathcoreFlow’s API and is therefore very efficient, transferring the least data possible and only as needed.

Once the Visiopharm app has launched, the user follows the normal workflow in that application and can proceed to interact with the Visiopharm database and to perform analysis as they would normally. Other than the occasional prompt for your PathcoreFlow credentials, it will be largely transparent to the user that the images being processed in Visiopharm actually reside in the PathcoreFlow database securely over the network, rather than their own local storage.

As necessary, analysis results can be exported to the PathcoreFlow Repository via a dedicated export button in the Visiopharm application. At present, Visiopharm exports an MLD file which may contain segmentation results, overlays and/or heatmaps, as well as 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 can be made because the Open in VIS option was used to trigger the process in the first place.

Finally, users are able to view images overlaid along with any MLD results that may have been exported in the PathcoreFlow environment via any web browser. Thus the results and images live in a single database and can be shared and retained easily via the PathcoreFlow Repository.

Open in Visiopharm From PathcoreFlow

One or more images, or a single folder, can be opened with Visiopharm from the PathcoreFlow Repository page. Images can also be launched from within the Viewer, though this workflow is limited to the current image in the Viewer.

To launch Visiopharm with a selection of images from the Repository

  1. Navigate to any folder in the Repository (click on the Folder Repository button from the Navigation Menu then navigate to a folder)

  2. Select one or more images by holding the Ctrl key (on Windows) or ⌘ / Command key (on macOS) key and clicking on them

  3. Bring up the context menu for the item (or items)

  4. Click Open in VIS

  5. (Optional) In the popup menu, select Include annotations as ROI to send PathcoreFlow annotations to Visiopharm

  6. (Optional) In the popup menu, select Map annotation colors to different ROI types to to map the PathcoreFlow annotation colors to Visiopharm ROIs (this step may be needed for Visiopharm apps that rely on specified ROI labels)

  7. Click on the Open button to launch Visiopharm

To launch Visiopharm with all files in the current folder

  1. Click on the Down Arrow button next to the current folder's breadcrumb

  2. Click Open in VIS

  3. (Optional) In the popup menu, select Include annotations as ROI to send PathcoreFlow annotations to Visiopharm

  4. (Optional) In the popup menu, select Map annotation colors to different ROI types to to map the PathcoreFlow annotation colors to Visiopharm ROIs (this step may be needed for Visiopharm apps that rely on specified ROI labels)

  5. Click on the Open button to launch Visiopharm

Your browser may warn that PathcoreFlow is opening an application. If so, you must allow this to happen in order for Visiopharm to launch. You may also make this preference permanent to avoid the extra step in the future.

Exporting Results to PathcoreFlow

Use the Upload to PACS/IMS button from the Visiopharm application to export the results that have been generated back to PathcoreFlow. This option may only be available for images that have been launched via the integration (i.e using the Open in VIS button) AND if your Visiopharm Default Application preference in PathcoreFlow is set to “VIS” (as opposed to “VIS Basic”). See My Account to change preferences.

To export results for an image to PathcoreFlow from Visiopharm

  1. Click on File to open File menu

  2. Under File menu, choose Export from the left-hand sidebar

  3. Click on the Upload to PACS/IMS button

If there are no errors in the Visiopharm application, export has happened successfully and the results should be visible in PathcoreFlow after several minutes. If multiple results are exported for the same image, PathcoreFlow will retain all of these results as well as the date/time they were exported.

Newly received MLD files are immediately visible in the Overlays Panel but they must be processed before their content becomes visible in the PathcoreFlow image Viewer. Refresh the page if you suspect a recent export from Visiopharm is not listed in the Overlays Panel.

Viewing Results in PathcoreFlow

Visiopharm may export an MLD file, if available, and any quantitative results that have been generated by the app in the form of key-value pairs.

Viewing MLD Results

MLD files exported from Visiopharm are automatically associated with the correct image. These results are recorded as entries in the Overlays Panel and the contents of the MLD files are automatically treated as an overlay and rendered on top of the image.

To see the MLD results

  1. Open the image in the PathcoreFlow Viewer

  2. If the left sidebar is not displayed, toggle it by clicking on the Menu > button at the bottom left of the Viewer

  3. Hover or click on the Overlays button in the left sidebar

  4. Look for entries ending in .mld in the list of overlays

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

Heatmap results have an additional Apply Color Lookup Table option in the overlays panel, which allows a user to change how the data is visualized.

There may be multiple result sets exported from Visiopharm. Review the timestamp to differentiate these.

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.

To view quantitative results from the Repository

  1. Navigate to any folder in the Repository (click on the Folder Repository button from the Navigation Menu then navigate to a folder)

  2. Select an image that has been processed with Visiopharm

  3. Click on the Analysis Results tab of the right-hand panel. You may need to click on the Expand button if the panel is collapsed

  4. Look for the Visiopharm icon next to the fields listed to identify results exported from Visiopharm

To view quantitative results from within the Viewer

  1. Open the image in the PathcoreFlow Viewer

  2. If the left sidebar is not displayed, toggle it by clicking on the Menu > button at the bottom left of the Viewer

  3. Hover or click on the Overlays button in the left sidebar

  4. Look for an entry named “LayerData.mld” in the list of overlays

  5. Click on the Plus button to expand the quantitative results section

Analysis results are also added to an image's custom metadata fields and can be viewed from the information panel.