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

179 stars 39 forks source link

issues

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Schedule weekly tests

#458 IgorTatarnikov closed 2 weeks ago
1
Unpin numpy

#457 adamltyson closed 3 weeks ago
0
Add to conda-forge

#456 adamltyson opened 3 weeks ago
0
[pre-commit.ci] pre-commit autoupdate

#455 pre-commit-ci[bot] closed 1 month ago
0
[Feature] Inform the user when they supply just the weights in place of the full model

#454 IgorTatarnikov opened 1 month ago
0
Remove x86 macOS runners from the test suite

#453 IgorTatarnikov closed 1 month ago
3
Unpin numpy

#452 IgorTatarnikov closed 1 month ago
5
Update pytorch version

#451 adamltyson opened 1 month ago
0
[Feature] an (existing, like ImageJ model zoo - or new) place to share cellfinder models

#450 alessandrofelder opened 1 month 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 1 month ago
3
temporarily depend on numpy<2

#448 alessandrofelder closed 1 month ago
0
Conform to new linting rules

#447 IgorTatarnikov closed 1 month ago
0
[BUG] Keras's incompatibility with `numpy>=2` breaks `cellfinder`'s model training

#446 alessandrofelder closed 3 weeks ago
4
[pre-commit.ci] pre-commit autoupdate

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

#444 IgorTatarnikov closed 2 months ago
0
Tests are failing with napari 0.5.0

#443 adamltyson opened 2 months ago
6
Standardise contact information in readme

#442 adamltyson closed 2 months ago
1
[pre-commit.ci] pre-commit autoupdate

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

#440 matham opened 3 months ago
12
Add citation to readme

#438 adamltyson closed 3 months ago
0
Prevent zero underflow in volume

#437 matham closed 3 months ago
1
[Feature] Use a registry file for test data instead of hard-coding paths in `conftest.py`

#439 alessandrofelder opened 4 months ago
5
Update supported Python versions

#436 adamltyson closed 4 months ago
0
Structure splitting unsigned underflow

#435 matham closed 3 months ago
2
[pre-commit.ci] pre-commit autoupdate

#434 pre-commit-ci[bot] closed 4 months ago
0
Enable MPS fallback by default

#433 IgorTatarnikov closed 4 months ago
0
Update default inference batch size

#432 adamltyson closed 4 months ago
0
Remove test dependency duplication

#431 adamltyson closed 4 months ago
0
Moved force cpu into cellfinder function

#430 IgorTatarnikov closed 4 months ago
0
Force backend during testing

#429 IgorTatarnikov closed 4 months ago
0
Update final few lines to python 3.11

#428 adamltyson closed 4 months ago
0
Update __init__.py

#427 adamltyson closed 4 months ago
0
Check performance on Windows

#426 adamltyson opened 4 months ago
0
napari plugin does not allow use of trained weights (without model file)

#425 adamltyson opened 4 months ago
0
Improve printing & logging

#424 adamltyson opened 4 months ago
0
Move imports out of functions

#423 adamltyson opened 4 months ago
0
Update caching

#422 adamltyson closed 4 months ago
0
Update badges to remove references to cellfinder-core

#421 adamltyson closed 4 months ago
0
Remove data loading code

#420 adamltyson closed 4 months ago
0
Cellfinder benchmarks

#419 sfmig closed 3 months ago
1
Updating to Keras 3.0 and migrating to PyTorch

#418 IgorTatarnikov closed 4 months ago
12
Remove examples

#417 adamltyson closed 4 months ago
0
Remove examples?

#416 adamltyson closed 4 months ago
1
[BUG] Kernel crashes when running the example

#415 priya-velu5 opened 5 months ago
4
Simplify model download

#414 adamltyson closed 4 months ago
0
Standardise the use of axes in cellfinder

#413 adamltyson opened 5 months ago
2
[pre-commit.ci] pre-commit autoupdate

#412 pre-commit-ci[bot] closed 5 months ago
0
Investigate why there's a transpose operation that cannot be removed.

#411 adamltyson closed 5 months ago
8
Add timeout and continue on error flags to numba disabled tests

#410 IgorTatarnikov closed 4 months ago
1
[BUG] Cellfinder seems to get stuck on structure splitting in some situations?

#409 alessandrofelder closed 4 months ago
4