Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of cellfinder

cellfinder - v1.7.0

What's Changed

  • Remove save weights option from training widget by @parharti in https://github.com/brainglobe/cellfinder/pull/499
  • Inform the user when they supply just the weights in place of the full model by @parharti in https://github.com/brainglobe/cellfinder/pull/490
  • Pull Request: Implementing Issue #295 – "Check Location of Detected Cells in Tests" by @Menna1812 in https://github.com/brainglobe/cellfinder/pull/509
  • Update pinned pytorch version by @ayush2281 in https://github.com/brainglobe/cellfinder/pull/519
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/cellfinder/pull/521
  • Fix #423 : Clean up TensorFlow-related code after migrating to Keras 3.0 with PyTorch backend by @0Anshu1 in https://github.com/brainglobe/cellfinder/pull/523
  • Improve printing & logging by @parharti in https://github.com/brainglobe/cellfinder/pull/507
  • Fix for deleted layers hanging around in CurationWidget by @DPWebster in https://github.com/brainglobe/cellfinder/pull/497
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/cellfinder/pull/529
  • Don't deepcopy input arrays to prevent loading into RAM by @matham in https://github.com/brainglobe/cellfinder/pull/531
  • Expose CPU/GPU selection in Napari (default to GPU), remove usescipy param (always True on CPU), and improve batchsize docstring (#464) by @Fede2717 in https://github.com/brainglobe/cellfinder/pull/503
  • Run scheduled tests on napari main by @IgorTatarnikov in https://github.com/brainglobe/cellfinder/pull/533

New Contributors

  • @parharti made their first contribution in https://github.com/brainglobe/cellfinder/pull/499
  • @Menna1812 made their first contribution in https://github.com/brainglobe/cellfinder/pull/509
  • @ayush2281 made their first contribution in https://github.com/brainglobe/cellfinder/pull/519
  • @0Anshu1 made their first contribution in https://github.com/brainglobe/cellfinder/pull/523
  • @DPWebster made their first contribution in https://github.com/brainglobe/cellfinder/pull/497
  • @Fede2717 made their first contribution in https://github.com/brainglobe/cellfinder/pull/503

Full Changelog: https://github.com/brainglobe/cellfinder/compare/1.6.0...v1.7.0

- Python
Published by alessandrofelder 9 months ago

cellfinder - v1.6.0

What's Changed

  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/cellfinder/pull/489
  • Standardize .yml and .yaml Extensions for Consistency by @nischitkumar in https://github.com/brainglobe/cellfinder/pull/488

New Contributors

  • @nischitkumar made their first contribution in https://github.com/brainglobe/cellfinder/pull/488

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.5.1...v1.6.0

- Python
Published by adamltyson 12 months ago

cellfinder - v1.5.1

What's Changed

  • Move qt-niu dependency by @adamltyson in https://github.com/brainglobe/cellfinder/pull/486

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.5.0...v1.5.1

- Python
Published by adamltyson about 1 year ago

cellfinder - v1.5.0

What's Changed

  • Import Qt elements from qt-niu by @adamltyson in https://github.com/brainglobe/cellfinder/pull/485

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.4.1...v1.5.0

- Python
Published by adamltyson about 1 year ago

cellfinder - v1.4.1

What's Changed

  • Replaced NIU upload action with separate steps by @IgorTatarnikov in https://github.com/brainglobe/cellfinder/pull/478
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/cellfinder/pull/480
  • Use pypa/gh-action-pypi-publish stable release v1 by @lochhh in https://github.com/brainglobe/cellfinder/pull/481
  • Use explicit len(arr)-count instead of just -count to handle count=0 by @matham in https://github.com/brainglobe/cellfinder/pull/484

New Contributors

  • @lochhh made their first contribution in https://github.com/brainglobe/cellfinder/pull/481

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.4.0...v1.4.1

- Python
Published by adamltyson about 1 year ago

cellfinder - v1.4.0

What's Changed

  • Move detection (2d/3d filtering, structure splitting) to PyTorch by @matham in https://github.com/brainglobe/cellfinder/pull/440
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/cellfinder/pull/467
  • Notify slack on scheduled test failure by @IgorTatarnikov in https://github.com/brainglobe/cellfinder/pull/469
  • ensure trained_model is a Path before calling .suffix by @alessandrofelder in https://github.com/brainglobe/cellfinder/pull/471
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/cellfinder/pull/472
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/cellfinder/pull/474
  • Unpin keras by @IgorTatarnikov in https://github.com/brainglobe/cellfinder/pull/475
  • bump headless display action 2->3 by @alessandrofelder in https://github.com/brainglobe/cellfinder/pull/476

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.3.3...v1.4.0

- Python
Published by IgorTatarnikov about 1 year ago

cellfinder - v1.4.0-alpha.0

What's Changed

  • Move detection (2d/3d filtering, structure splitting) to PyTorch by @matham in https://github.com/brainglobe/cellfinder/pull/440

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.3.3...v1.4.0alpha0

- Python
Published by alessandrofelder over 1 year ago

cellfinder - v1.3.3

What's Changed

  • Unpin numpy by @IgorTatarnikov in https://github.com/brainglobe/cellfinder/pull/452
  • Remove x86 macOS runners from the test suite by @IgorTatarnikov in https://github.com/brainglobe/cellfinder/pull/453
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/cellfinder/pull/455
  • Unpin numpy by @adamltyson in https://github.com/brainglobe/cellfinder/pull/457
  • Schedule weekly tests by @IgorTatarnikov in https://github.com/brainglobe/cellfinder/pull/458
  • Pin keras version to 3.5.0 by @IgorTatarnikov in https://github.com/brainglobe/cellfinder/pull/462
  • Allow napari GUI to accept custom weights by @IgorTatarnikov in https://github.com/brainglobe/cellfinder/pull/460
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/cellfinder/pull/461

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.3.2...v1.3.3

- Python
Published by IgorTatarnikov over 1 year ago

cellfinder - v1.3.2

What's Changed

  • Conform to new linting rules by @IgorTatarnikov in https://github.com/brainglobe/cellfinder/pull/447
  • temporarily depend on numpy<2 by @alessandrofelder in https://github.com/brainglobe/cellfinder/pull/448
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/cellfinder/pull/445

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.3.1...v1.3.2

- Python
Published by alessandrofelder over 1 year ago

cellfinder - v1.3.1

What's Changed

  • Update supported Python versions by @adamltyson in https://github.com/brainglobe/cellfinder/pull/436
  • Add citation to readme by @adamltyson in https://github.com/brainglobe/cellfinder/pull/438
  • Prevent zero underflow in volume by @matham in https://github.com/brainglobe/cellfinder/pull/437
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/brainglobe/cellfinder/pull/441
  • Standardise contact information in readme by @adamltyson in https://github.com/brainglobe/cellfinder/pull/442
  • Added xfail to tests that fail due to logging bug by @IgorTatarnikov in https://github.com/brainglobe/cellfinder/pull/444

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.3.0...v1.3.1

- Python
Published by alessandrofelder over 1 year ago

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

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.2.0...v1.3.0

- Python
Published by adamltyson over 1 year ago

cellfinder - v1.3.0rc2

What's Changed

  • Remove test dependency duplication by @adamltyson in https://github.com/brainglobe/cellfinder/pull/431
  • Update default inference batch size by @adamltyson in https://github.com/brainglobe/cellfinder/pull/432
  • Enable MPS fallback by default by @IgorTatarnikov in https://github.com/brainglobe/cellfinder/pull/433

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.3.0rc1...v1.3.0rc2

- Python
Published by adamltyson over 1 year ago

cellfinder - v1.3.0rc1

What's Changed

  • Update init.py by @adamltyson in https://github.com/brainglobe/cellfinder/pull/427
  • Update final few lines to python 3.11 by @adamltyson in https://github.com/brainglobe/cellfinder/pull/428
  • Moved force cpu into cellfinder function by @IgorTatarnikov in https://github.com/brainglobe/cellfinder/pull/430

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.3.0rc0...v1.3.0rc1

- Python
Published by adamltyson over 1 year ago

cellfinder - v1.3.0rc0

Release candidate to test move to torch

What's Changed

  • Update caching by @adamltyson in https://github.com/brainglobe/cellfinder/pull/422
  • Updating to Keras 3.0 and migrating to PyTorch by @IgorTatarnikov in https://github.com/brainglobe/cellfinder/pull/418

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.2.0...v1.3.0rc0

- Python
Published by adamltyson almost 2 years ago

cellfinder - v1.2.0

Summary

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

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.1.3...v1.2.0

- Python
Published by alessandrofelder almost 2 years ago

cellfinder - v1.1.3

What's Changed

  • Cellfinder test fix by @IgorTatarnikov in https://github.com/brainglobe/cellfinder/pull/400

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.1.2...v1.1.3

- Python
Published by alessandrofelder almost 2 years ago

cellfinder - v1.1.2

What's Changed

  • Pin minimum brainglobe dependency versions by @K-Meech in https://github.com/brainglobe/cellfinder/pull/392
  • basic fix avoiding writing to package files by @alessandrofelder in https://github.com/brainglobe/cellfinder/pull/394

New Contributors

  • @K-Meech made their first contribution in https://github.com/brainglobe/cellfinder/pull/392

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.1.1...v1.1.2

- Python
Published by alessandrofelder almost 2 years ago

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

New Contributors

  • @IgorTatarnikov made their first contribution in https://github.com/brainglobe/cellfinder/pull/384

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.1.0...v1.1.1

- Python
Published by adamltyson about 2 years ago

cellfinder - v1.1.0

Remove Duplicate Function

Removes a duplicated function from the package (https://github.com/brainglobe/cellfinder/issues/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 https://github.com/brainglobe/cellfinder/pull/347
  • Update github link in widget by @adamltyson in https://github.com/brainglobe/cellfinder/pull/350
  • Update tooling config by @adamltyson in https://github.com/brainglobe/cellfinder/pull/351
  • Update tests by @adamltyson in https://github.com/brainglobe/cellfinder/pull/348
  • Prep merge by @adamltyson in https://github.com/brainglobe/cellfinder/pull/349

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v1.0.0...v1.1.0

- Python
Published by willGraham01 about 2 years ago

cellfinder - 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.

- Python
Published by willGraham01 about 2 years ago

cellfinder - 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 https://github.com/brainglobe/cellfinder/pull/259
  • Prepare for migration by @willGraham01 in https://github.com/brainglobe/cellfinder/pull/261

New Contributors

  • @alessandrofelder made their first contribution in https://github.com/brainglobe/cellfinder/pull/259

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v0.8.0...v0.8.1

- Python
Published by willGraham01 about 2 years ago

cellfinder - 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 https://github.com/brainglobe/cellfinder/pull/255

Full Changelog: https://github.com/brainglobe/cellfinder/compare/v0.7.1...v0.8.0

- Python
Published by willGraham01 over 2 years ago

cellfinder - 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

- Python
Published by adamltyson almost 6 years ago

cellfinder - Version 0.3.11

Further refactoring

- Python
Published by adamltyson almost 6 years ago

cellfinder - Version 0.3.10

Minor refactoring

- Python
Published by adamltyson almost 6 years ago

cellfinder - 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

- Python
Published by adamltyson almost 6 years ago

cellfinder - Version 0.3.9rc1

- Python
Published by adamltyson almost 6 years ago

cellfinder - Version 0.3.9rc0

- Python
Published by adamltyson almost 6 years ago

cellfinder - Version 0.3.8

Fix memory leak in training

- Python
Published by adamltyson about 6 years ago

cellfinder - Version 0.3.8 rc0

- Python
Published by adamltyson about 6 years ago

cellfinder - Version 0.3.7

- Python
Published by adamltyson about 6 years ago

cellfinder - Version 0.3.6 release candidate 0

- Python
Published by adamltyson about 6 years ago

cellfinder - Version 0.3.5 (2020-02-03)

Main updates

  • New all python training data generation interface, cellfinder_curate. Details here

Developers

  • Heatmap and converting cells to brainrender format moved to neuro
  • Lots of utility functions moved to imlib
  • Automatic deployment with Travis

- Python
Published by adamltyson about 6 years ago

cellfinder - v0.3.4

- Python
Published by adamltyson about 6 years ago

cellfinder - v0.3.4rc3

- Python
Published by adamltyson about 6 years ago