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@Rdornier Rdornier released this 28 Feb 13:12
· 53 commits to main since this release
v0.1.0
5fb7c5d

This extension aims at linking our HRM server to QuPath. This extension depends on qupath-extension-biop-omero (v0.3.2 at the time of release => Earlier versions are not compatible).

The path to HRM folder is, for now, hard coded and cannot be changed.

Under Extension -> HRM, you will find 2 commands.

  1. Send to HRM

With an open project, you can select images you want to apply deconvolution on. Images can be stored either locally or on OMERO (using our qupath-extension-biop-omero). It will download, or copy, images in the user's Raw folder of HRM. Then, you can launch an HRM job from HRM server.

  1. Retrieve from HRM

When an HRM job is completed, you can click on this command to get back deconvolved images into your QuPath project. It will first, from HRM Deconvolved folder, upload deconvolved images on OMERO (with deconvolution parameters as key-values and log file as attachment) or copy all related files in a new folder at the raw image's parent. Then, it will import images in your QuPath project, with deconvolution parameters as QuPath metadata fields.

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