https://github.com/biop/qupath-extension-spotiflow - Migration to QuPath 0.6.x

This release make the extension compatible with QuPath 0.6.x and fixes a bunch of bugs / features

Bug fix

• Enable to use MAC GPU option (thanks to @AlbertDominguez in #8)
• When running spotiflow on multiple channels, all the points for all the channels are now correctly displayed - fix #11
• Forcing minDistance parameter to be an integer number - fix #12
• Correctly handle waitFor() process on Mac systems - fix #15
• Try to separate UI code in a separate JavaFX thread - fix #15
• Remove points ouside parent shape - fix #14
• Fix compatibility with spotiflow 0.5.7 and 0.5.8 - fix #13
• Fix warning on null PathClass by using .resetPathClass() instead

New feature

• Saving temp images as OME-Zarr files (only from spotiflow 0.5.8) - fix #9 and #2
• Set options to clear child object or not
• Set option to save the builder

Refactor

• Add a supplementary folder layer in the temp dir to separate shapes between images
• Run spotiflow command only once, even if multiple channels/parents are selected
• Refactor savePredictionImages to cleanTempDir
• Update github actions

- Java
Published by Rdornier 11 months ago

https://github.com/biop/qupath-extension-spotiflow - v0.1.0

First version release

WARN: This version is NOT compatible with spotiflow > 0.5.7

This is the first stable version of the qupath spotiflow extension. Spotiflow prediction is fully supported, but spotiflow training is not supported at the moment. Some of the spotiflow parameters are handled in the builder ; the others can be added via the function addParameter(). An example of how to use this example is available under Extension -> Spotiflow -> Spotiflow detection script template

Full changelog available on 0.1.0-rc2 and 0.1.0-rc1

Java doc available here.

User documentation available in the README

• Fix #7 to be used on Linux and Mac (tested on Linux & Windows, no yet tested on Mac => feedback welcome)

- Java
Published by Rdornier about 1 year ago

https://github.com/biop/qupath-extension-spotiflow - v0.1.0-rc2

• Handle 3D dataset, run spotiflow model in 3D => fix #4
• Adding device, subpixel, min distance and probability threshold to builder arguments => fix #3
• Adding classification to points => fix #1
• Saving image as ome-tiff, instead of tiff => partially fix #2
• Create sub folders by image and for 3D to save image patches

- Java
Published by Rdornier about 1 year ago

https://github.com/biop/qupath-extension-spotiflow - v0.1.0-rc1

This is the first release candidate for qupath-spotiflow. At this time, it only works on windows machines, beacuse the way spotiflow is managed in the python environment is not exactly the same as for cellpose.

• Spotiflow prediction is fully supported, with pre-trained model and custom models
• Spotiflow training is not supported yet
• Only one channel is processed at a time, even if multiple channels are passed in arguments
• You have an option to not resave prediction images if they are already saved
• a help is available by calling spotiflow.helpPredict() after the builder creation

The source code has to be cleaned from all qupath-cellpose methods that are not used anymore.

- Java
Published by Rdornier about 1 year ago