Releases: brainglobe/cellfinder
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
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
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- Remove outdated info in the napari plugin init by @adamltyson in #358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 withpytest 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
withsafe_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