v1.3.0

Move classification to PyTorch

This release changes the dependency for classification to PyTorch (from TensorFlow). Users are advised to create a new environment before upgrading.

What's Changed

• Update caching by @adamltyson in #422
• Updating to Keras 3.0 and migrating to PyTorch by @IgorTatarnikov in #418
• Update init.py by @adamltyson in #427
• Update final few lines to python 3.11 by @adamltyson in #428
• Moved force cpu into cellfinder function by @IgorTatarnikov in #430
• Remove test dependency duplication by @adamltyson in #431
• Update default inference batch size by @adamltyson in #432
• Enable MPS fallback by default by @IgorTatarnikov in #433
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #434

Full Changelog: v1.2.0...v1.3.0

v1.3.0rc2

What's Changed

• Remove test dependency duplication by @adamltyson in #431
• Update default inference batch size by @adamltyson in #432
• Enable MPS fallback by default by @IgorTatarnikov in #433

Full Changelog: v1.3.0rc1...v1.3.0rc2

v1.3.0rc1

What's Changed

• Update init.py by @adamltyson in #427
• Update final few lines to python 3.11 by @adamltyson in #428
• Moved force cpu into cellfinder function by @IgorTatarnikov in #430

Full Changelog: v1.3.0rc0...v1.3.0rc1

v1.3.0rc0

Release candidate to test move to torch

What's Changed

• Update caching by @adamltyson in #422
• Updating to Keras 3.0 and migrating to PyTorch by @IgorTatarnikov in #418

Full Changelog: v1.2.0...v1.3.0rc0

v1.2.0

Summary

• major performance improvements in cell candidate detection thanks to @matham 👏
• moved utility functionality to brainglobe-utils and re-use it here.
• tidying/maintenance of development related things (examples, CI)

What's Changed

• Import header from brainglobe-utils by @K-Meech in #399
• Separate napari image parameter to prevent magicgui slowdown by @matham in #401
• Add codecov token by @K-Meech in #403
• Allow turning off classification or detection in GUI by @matham in #402
• Support single z-stack tif file for input by @matham in #397
• Remove modular asv benchmarks by @sfmig in #406
• Adapt CI so it covers both new and old Macs, and installs required additional dependencies on M1 by @alessandrofelder in #408
• Optimize cell detection (#398) by @alessandrofelder in #407
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #412
• Simplify model download by @adamltyson in #414
• Remove examples by @adamltyson in #417
• Update badges to remove references to cellfinder-core by @adamltyson in #421
• Remove data loading code by @adamltyson in #420

Full Changelog: v1.1.3...v1.2.0

v1.1.3

What's Changed

• Cellfinder test fix by @IgorTatarnikov in #400

Full Changelog: v1.1.2...v1.1.3

v1.1.2

What's Changed

• Pin minimum brainglobe dependency versions by @K-Meech in #392
• basic fix avoiding writing to package files by @alessandrofelder in #394

New Contributors

• @K-Meech made their first contribution in #392

Full Changelog: v1.1.1...v1.1.2

v1.1.1

Fixes bug causing very long cell detection times

This bug affects many users, please update ASAP.

What's Changed

• Remove outdated info in the napari plugin init by @adamltyson in #358
• Raise more informative error message when data with a large z-spacing is used by @adamltyson in #359
• Update GitHub actions status badge by @adamltyson in #360
• Adds vertical scroll bar to the training widget by @adamltyson in #357
• Fix pyproject links by @adamltyson in #361
• Delete old training data saves and warn user by @adamltyson in #365
• Remove pytest-lazy-fixture due to incompatibility with pytest v8.0.0 by @willGraham01 in #369
• Update test_and_deploy.yml by @alessandrofelder in #370
• Add curation keyboard shortcuts by @adamltyson in #366
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #371
• Create CITATION.cff by @willGraham01 in #367
• Switch order of arguments passed to prep_model_weights in train_yml.py by @IgorTatarnikov in #384
• add a test for connect_four by @alessandrofelder in #385
• consistently use uint32 in candidate detection by @alessandrofelder in #388

New Contributors

• @IgorTatarnikov made their first contribution in #384

Full Changelog: v1.1.0...v1.1.1

v1.1.0

Remove Duplicate Function

Removes a duplicated function from the package (#272) and standardises the corresponding calls across other functions within the package.

Various developer-related updates are also going in with this PR, which do not affect anything in the package.

• Reinstating the brainmapper CI check, but as an optional check to indicate potential breakages
• Additional tests added
• Pre-commit config modified slightly.

What's Changed

• Reinstate brainmapper ci check by @willGraham01 in #347
• Update github link in widget by @adamltyson in #350
• Update tooling config by @adamltyson in #351
• Update tests by @adamltyson in #348
• Prep merge by @adamltyson in #349

Full Changelog: v1.0.0...v1.1.0

v1.0.0

Merging of cellfinder-core and cellfinder-napari

This package combines the old cellfinder-core and cellfinder-napari packages into a single package, called cellfinder.
You can read more about this merging of functionality on the brainglobe blog.
Additionally, see the full changelog on the brainglobe website for details on what this package offers.