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• Remove outdated info in the napari plugin init by @adamltyson in #358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.

v0.8.1

cellfinder has migrated!

v0.8.1 marks the end of the cellfinder package's current lifecycle, as it prepares for it's new role in BrainGlobe version 1.

Users are recommended to head over to brainglobe-workflows and install that package if they want to continue using the cellfinder command-line interface.

What's Changed

• Replace pandas.df.append with safe_concat by @alessandrofelder in #259
• Prepare for migration by @willGraham01 in #261

New Contributors

• @alessandrofelder made their first contribution in #259

Full Changelog: v0.8.0...v0.8.1

Update to comply with `brainreg` v1.0.0

Update to depend on brainreg v1.0.0

Users may wish to uninstall brainreg-napari and brainreg-segment before updating. For details, see our blog post.

What's Changed

• Update to brainreg v1 compliance by @willGraham01 in #255

Full Changelog: v0.7.1...v0.8.0

Version 0.3.12

Main updates

• Windows bug fix thanks to @EmanPaoli
• Prebuilt wheels now released for Linux, Windows and macOS (untested)

Developers

• Update dependencies & refactor usage of amap api

Version 0.3.11

Further refactoring

Version 0.3.10

Minor refactoring

Version 0.3.9

Version 0.3.9 (2020-03-11)

Added

Training can now be saved every N epochs using --checkpoint-interval

Fixed

• Bug fixed in cellfinder_xml_crop
• Pandas dependencies updated thanks to @amedyukhina

Version 0.3.9rc1

v0.3.9rc1

bump (#74)