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Published May 16, 2024 | Version v0.9.3
Software Open

BIOP/qupath-extension-cellpose: Parallel object reader, normalization bugfix gpu disable option and more

  • 1. EPFL - SV - PTECH - BIOP
  • 2. @TheJacksonLaboratory

Description

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 3 logs when training

What's Changed

  • Ensure that operations are the same when processing multiple images by @tfehlmann in https://github.com/BIOP/qupath-extension-cellpose/pull/44
  • Bugfixes and update to Cellpose 3 logging by @lacan in https://github.com/BIOP/qupath-extension-cellpose/pull/46

New Contributors

  • @tfehlmann made their first contribution in https://github.com/BIOP/qupath-extension-cellpose/pull/44

Full Changelog: https://github.com/BIOP/qupath-extension-cellpose/compare/v0.9.2...v0.9.3

Files

BIOP/qupath-extension-cellpose-v0.9.3.zip

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