Migration to QuPath 0.6.x

First version compatible with QuPath 0.6.x

• Upgrade build tools from groovy to kotlin
• Update gradle version
• Remove deprecated methods from QuPath 0.5.x

v0.10.2-code

This is not a new release ; just to update the Soucre code package that wasn't pushed yet.

Last QuPath-0.5.x compatible version

This is the last version of the extension which is compatible with QuPath 0.5.x. Next versions will only be compatible with QuPath 0.6.x

• fix #61 by adding a new field for cellpose-sam
• fix #62 by initializing with empty strings instead of null

Add an option to skip testDir

• Fixes #58
• Update Javadoc

Add an option to not resave the training images

Fixes #56

Improved label image reading and code linting

From several forum posts, it was clear that for large tiles and large fields of view, the extension was having issues.

This caused tiles to be empty and the detections being incomplete.

It seems like it was caused by the way we used to read objects in using JTS.

This new update changes the way label images are converted to QuPath objects by using the same strategy as LaRoMe's Labels2Rois
https://github.com/BIOP/ijp-LaRoMe/blob/master/src/main/java/ch/epfl/biop/ij2command/Labels2Rois.java

Fundamentally, this should not change the way cells are detected now vs before, though no testing has been done. One thing to note is that if Cellpose ever allows for objects with holes to be detected, then the current strategy will need to be changed again.

What's Changed

• Refactor 092024 by @lacan in #52

Full Changelog: v0.9.5...v0.9.6

Bugfix

As per https://forum.image.sc/t/a-bug-in-cellpose-for-qupath-extension-0-9-4/100641/5

This reverts the touching object handling that was broken in the previous version.

this is the information from the previous version

This new update adresses some issues linked to cellpose failing on large tiles, most likely linked to there being overly small tiles being created in some cases.

This was adressed for now by either ignoring images that are too small (which should be included in the overlap between tiles anyway) and by adding a check in case reading a label image has an error, which initially caused the extension to simply crash.

A new builder parameter setOutputModelName(String outputName) allows you to rename the resulting cellpose model after training.

Since Cellpose 3.0, cellpose models can have arbitrary names, so the extension renames the model to a *.cpm (Cellpose Model) with the timestamp of creation.

Feedback welcome

Small updates and error catching

This new update adresses some issues linked to cellpose failing on large tiles, most likely linked to there being overly small tiles being created in some cases.

This was adressed for now by either ignoring images that are too small (which should be included in the overlap between tiles anyway) and by adding a check in case reading a label image has an error, which initially caused the extension to simply crash.

A new builder parameter setOutputModelName(String outputName) allows you to rename the resulting cellpose model after training.

Parallel object reader, normalization bugfix gpu disable option and more

Welcome to a new release with the following important changes

• Adds useGPU( boolean ) to the builder to disable GPU (Enabled by default)
• Fixes a bug found and corrected by @tfehlmann where ops were being re-created per image, which caused an error during image saving
• Adds better error handling when no candidate files are present
• Adds readResultsAsynchronously() to the builder, which allows the extension to read the resulting labeled images for each tile as cellpose processes them, potentially making the extension faster
• Changes the logic for the VirtualEnvironmentRunner when using CONDA (Not available as such within the extension) as per a suggestion by @loicsauteur
• Allows pixelSize() to accept values smaller than the original pixel size in case you want to upsample your data before sending it to cellpose
• Uses a new log parser in order to parlse omnipose and cellpose v3 logs when training

What's Changed

• Ensure that operations are the same when processing multiple images by @tfehlmann in #44
• Bugfixes and update to Cellpose 3 logging by @lacan in #46

New Contributors

• @tfehlmann made their first contribution in #44

Full Changelog: v0.9.2...v0.9.3

Release for first publication in Zenodo

This is not a release per se, but will trigger Zenodo to generate a DOI for the software.