brainglobe cellfinder issues

brainglobe / cellfinder

Automated 3D cell detection in very large images

https://brainglobe.info/documentation/cellfinder/index.html

BSD 3-Clause "New" or "Revised" License

181 stars 39 forks source link

issues

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ensure trained_model is a Path before calling .suffix

#471 alessandrofelder closed 1 week ago
0
[BUG] Path to trained model from `brainmapper` is a str, and doesn't have `.suffix` attribute

#470 alessandrofelder closed 1 week ago
0
Notify slack on scheduled test failure

#469 IgorTatarnikov closed 1 week ago
0
[Feature] Run cell detection on subvolume of an image and not just select z planes

#468 IgorTatarnikov opened 2 weeks ago
0
[pre-commit.ci] pre-commit autoupdate

#467 pre-commit-ci[bot] closed 2 weeks ago
0
2-D WSI Images

#466 eshasadia closed 3 weeks ago
1
Use yaml or yml consistently.

#465 adamltyson opened 1 month ago
0
[Feature] expose GPU/CPU choice and other parameters to pytorch cellfinder version

#464 alessandrofelder opened 1 month ago
0
[BUG] Training stalls at the end of the first epoch with keras 3.6.0

#463 IgorTatarnikov opened 1 month ago
2
Pin `keras` version to 3.5.0

#462 IgorTatarnikov closed 1 month ago
0
[pre-commit.ci] pre-commit autoupdate

#461 pre-commit-ci[bot] closed 1 month ago
0
Allow napari GUI to accept custom weights

#460 IgorTatarnikov closed 1 month ago
0
[Feature] Load model weights via the napari GUI

#459 IgorTatarnikov closed 1 month ago
0
Schedule weekly tests

#458 IgorTatarnikov closed 2 months ago
1
Unpin numpy

#457 adamltyson closed 2 months ago
0
Add to conda-forge

#456 adamltyson opened 2 months ago
0
[pre-commit.ci] pre-commit autoupdate

#455 pre-commit-ci[bot] closed 2 months ago
0
[Feature] Inform the user when they supply just the weights in place of the full model

#454 IgorTatarnikov opened 3 months ago
0
Remove x86 macOS runners from the test suite

#453 IgorTatarnikov closed 3 months ago
3
Unpin numpy

#452 IgorTatarnikov closed 3 months ago
5
Update pytorch version

#451 adamltyson opened 3 months ago
0
[Feature] an (existing, like ImageJ model zoo - or new) place to share cellfinder models

#450 alessandrofelder opened 3 months ago
1
For 2D filtering in the detection step, option for a fixed threshold instead of the n_sds_above_mean_thresh

#449 xmikezheng20 closed 3 months ago
3
temporarily depend on numpy<2

#448 alessandrofelder closed 3 months ago
0
Conform to new linting rules

#447 IgorTatarnikov closed 3 months ago
0
[BUG] Keras's incompatibility with `numpy>=2` breaks `cellfinder`'s model training

#446 alessandrofelder closed 2 months ago
4
[pre-commit.ci] pre-commit autoupdate

#445 pre-commit-ci[bot] closed 3 months ago
1
Added xfail to tests that fail due to logging bug

#444 IgorTatarnikov closed 4 months ago
0
Tests are failing with napari 0.5.0

#443 adamltyson opened 4 months ago
6
Standardise contact information in readme

#442 adamltyson closed 4 months ago
1
[pre-commit.ci] pre-commit autoupdate

#441 pre-commit-ci[bot] closed 4 months ago
0
Move detection (2d/3d filtering, structure splitting) to PyTorch

#440 matham closed 3 weeks ago
14
Add citation to readme

#438 adamltyson closed 5 months ago
0
Prevent zero underflow in volume

#437 matham closed 5 months ago
1
[Feature] Use a registry file for test data instead of hard-coding paths in `conftest.py`

#439 alessandrofelder opened 5 months ago
5
Update supported Python versions

#436 adamltyson closed 5 months ago
0
Structure splitting unsigned underflow

#435 matham closed 5 months ago
2
[pre-commit.ci] pre-commit autoupdate

#434 pre-commit-ci[bot] closed 5 months ago
0
Enable MPS fallback by default

#433 IgorTatarnikov closed 5 months ago
0
Update default inference batch size

#432 adamltyson closed 5 months ago
0
Remove test dependency duplication

#431 adamltyson closed 5 months ago
0
Moved force cpu into cellfinder function

#430 IgorTatarnikov closed 5 months ago
0
Force backend during testing

#429 IgorTatarnikov closed 5 months ago
0
Update final few lines to python 3.11

#428 adamltyson closed 5 months ago
0
Update __init__.py

#427 adamltyson closed 5 months ago
0
Check performance on Windows

#426 adamltyson opened 5 months ago
0
napari plugin does not allow use of trained weights (without model file)

#425 adamltyson opened 5 months ago
0
Improve printing & logging

#424 adamltyson opened 6 months ago
0
Move imports out of functions

#423 adamltyson opened 6 months ago
0
Update caching

#422 adamltyson closed 6 months ago
0