StarDist 0.9.1

Bugfix release to address issues with arm64 wheels for macOS.

(If you've cloned the repository, also note that the master branch has been renamed to main.)

Full Changelog: 0.9.0...0.9.1

StarDist 0.9.0

Changes

• Add support for Keras 3 in #266
  • TensorFlow 2.16+ has Keras 3.x as a dependency (although it is possible to use legacy Keras 2.x if need-be)
• Enable training with sparse label masks in 7a68fa7 (inspired by @ksugar)
• Add support for Python 3.12
• Various bug fixes and improvements, including
  • Resolve integer overflow when running on a large 3D image by @ximion in #249
  • Fix and improve the export function for Bioimage.IO by @qin-yu in #254

Breaking changes

• Exporting to TensorFlow's "SavedModel" format is no longer supported when using Keras 3

Full Changelog: 0.8.5...0.9.0

StarDist 0.8.5

Bugfix release (problem with source distribution stardist-0.8.4.tar.gz).

This only affects (presumably very few) people who can't install from wheels.
Everybody else should be fine with the 0.8.4 release.
(You're not affected if you already installed version 0.8.4 without problems.)

See StarDist 0.8.4 for release notes.

StarDist 0.8.4

This is a maintenance release with the following changes:

• Support Python 3.11
• Fix issue when using TensorFlow 2.13.0
• Fix various deprecation warnings
• Fix issue when using 'None' as class labels
• Suppress some outputs from Keras/TensorFlow (cf. forum post)
• Require CSBDeep 0.7.4

Not part of the Python package, but important:

• Update documentation (with contributions from @psobolewskiPhD and @ajinkya-kulkarni)
• Update Dockerfile
• Fix matplotlib configuration issue in example notebooks
• Fix a bioimage.io test issue (@FynnBe)
• Update GitHub issue templates
• Fix various GitHub action issues

StarDist 0.8.3

This is a minor release with the following (non-breaking) changes:

• Add command line prediction scripts
• Update documentation regarding installation on Apple silicon
• Internal changes needed for stardist-napari (cf. stardist/stardist-napari#20)

We thank @romainGuiet and @psobolewskiPhD for contributing to this release.

StarDist 0.8.2

• Build wheels for macOS with Clang (thanks to @jaimergp), enabling support for Apple Silicon
• Deprecate Python 3.6
• Support Python 3.10

StarDist 0.8.1

Minor changes to bioimage.io model import (#187)

StarDist 0.8.0

• Enable model export for bioimage.io model zoo (#171); see new example notebook how to use
• Add optional scale parameter to model.predict_instances (#181)
• Various new features, improvements, and bug fixes

StarDist 0.7.3

Maintenance release to support TensorFlow >= 2.6.0, requiring CSBDeep >= 0.6.3 (see release notes).

Please note the new installation instructions:

• Unchanged when using TensorFlow 2.x: pip install stardist
• Updated when using TensorFlow 1.x: pip install "stardist[tf1]"

StarDist 0.7.2

This is a minor release that fixes a few issues (cf. #57, #154, #156).