Update to qupath-extension-biop-omero-1.0.x

Breaking change

• The omero folder under your HRM-share has to be cleaned before using this new release (both under raw and deconvolved folder). This is due to changes in the way of downloading images (coming from omero-gateway update).
• You need to have the version 1.0.1 of the qupath-extension-biop-omero to make this extension working.

Update dependencies

• simple-omero-client 5.18.0
• omero-gateway 5.9.1
• qupath-extension-biop-omero 1.0.1
• upgrade to QuPath 0.5.1

Warning

You need to upgrade your OMERO-Java dependencies to the latest version. Please, download and replace your existing

• omero-ij plugin by the version 5.8.4 omero_ij-5.8.4-all.jar
• omero java dependencies (i.e. libs folder) by the version 5.6.11 OMERO.java-5.6.11-ice36.zip

Improvements

• Fix Transfer tags from raw to deconvolved images #3
• Fix Add images to new QuPath project #4
• Pre fill the username ans server host and select the right textField.
• Adding MAC support
• Use simple-omero-client as the main omero-client and refactor the code accordingly
• Add a threshold on the name similarity
• Update logger

Update to QuPath 0.5.x

• Update build.gradle file
• Move to gradle 8.5
• Replace deprecated methods
• Make the code compatible with QuPath 0.5.x

Update dependencies

• Update qupath-extension-biop-omero dependency to the latest version (0.4.4) that fixes the bug on the OMERO server

• Update the version of the omero dependencies to the latest ones

• Close the imageServers objects when necessary, to release these objects from the RAM.

Update server address

Update the HRMShare folder address due to internal server changes.

Adding Jsoup dependency

Jsoup dependency is now shipped with the jar to make things working properly.

First release

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.

2. 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.