brainglobe/cellfinder

Issues

• Use yaml or yml consistently.

  #465 opened 22 days ago by adamltyson
  0

• [Feature] expose GPU/CPU choice and other parameters to pytorch cellfinder version

  #464 opened a month ago by alessandrofelder
  0

• [BUG] Training stalls at the end of the first epoch with keras 3.6.0

  #463 opened a month ago by IgorTatarnikov
  1

• [Feature] Load model weights via the napari GUI

  #459 opened a month ago by IgorTatarnikov
  0

• [BUG] Keras's incompatibility with `numpy>=2` breaks `cellfinder`'s model training

  #446 opened 2 months ago by alessandrofelder
  4

• Add to conda-forge

  #456 opened 2 months ago by adamltyson
  0

• [Feature] Inform the user when they supply just the weights in place of the full model

  #454 opened 3 months ago by IgorTatarnikov
  0

• Update pytorch version

  #451 opened 3 months ago by adamltyson
  0

• [Feature] an (existing, like ImageJ model zoo - or new) place to share cellfinder models

  #450 opened 3 months ago by alessandrofelder
  1

• For 2D filtering in the detection step, option for a fixed threshold instead of the n_sds_above_mean_thresh

  #449 opened 3 months ago by xmikezheng20
  3

• Tests are failing with napari 0.5.0

  #443 opened 4 months ago by adamltyson
  6

• [Feature] Use a registry file for test data instead of hard-coding paths in `conftest.py`

  #439 opened 5 months ago by alessandrofelder
  5

• Structure splitting unsigned underflow

  #435 opened 5 months ago by matham
  2

• Update to Python 3.11

  #266 opened 6 months ago by adamltyson
  0

• Check performance on Windows

  #426 opened 6 months ago by adamltyson
  0

• napari plugin does not allow use of trained weights (without model file)

  #425 opened 6 months ago by adamltyson
  0

• Improve printing & logging

  #424 opened 6 months ago by adamltyson
  0

• Move imports out of functions

  #423 opened 6 months ago by adamltyson
  0

• Move data loading code to `brainglobe_utils.image_io.load`

  #405 opened 6 months ago by adamltyson
  0

• Remove examples?

  #416 opened 6 months ago by adamltyson
  1

• [BUG] Cellfinder seems to get stuck on structure splitting in some situations?

  #409 opened 6 months ago by alessandrofelder
  4

• [BUG] Intermittent Segmentation Faults on CI

  #404 opened 6 months ago by willGraham01
  14

• Downloading the trained model crashes if the model directory already exists

  #390 opened 6 months ago by adamltyson
  0

• Save models into e.g. `.brainglobe/cellfinder/models`

  #268 opened 6 months ago by adamltyson
  0

• [BUG] Kernel crashes when running the example

  #415 opened 6 months ago by priya-velu5
  4

• Standardise the use of axes in cellfinder

  #413 opened 6 months ago by adamltyson
  2

• Investigate why there's a transpose operation that cannot be removed.

  #411 opened 6 months ago by adamltyson
  8

• [BUG] Writing custom config is not possible on HPC with shared installation of BrainGlobe

  #393 opened 8 months ago by alessandrofelder
  0

• [Feature] Benchmark napari versus brainmapper code

  #391 opened 9 months ago by alessandrofelder
  0

• [BUG] Inappropriate handling of unsigned integer data types

  #383 opened 9 months ago by alessandrofelder
  1

• Analysis csv output does not include data about all cells classified

  #389 opened 9 months ago by Eddymorphling
  0

• [BUG] Multiprocessing threading causing timeouts

  #372 opened 9 months ago by willGraham01
  7

• [Feature] Use uint16 for cell candidate detection when signal_array is small, to save memory

  #386 opened 9 months ago by alessandrofelder
  3

• [Feature] Refactor so THRESHOLD and SOMA_CENTRE_VALUE are defined in one place

  #387 opened 9 months ago by alessandrofelder
  0

• [Feature] Add keyboard shortcuts to the curation interface

  #364 opened 9 months ago by adamltyson
  0

• [BUG] CI breaks with pytest v8.0.0

  #368 opened 9 months ago by willGraham01
  1

• Update cell classification network

  #267 opened a year ago by adamltyson
  1

• [Feature] Warn the user when overwriting training data in the curation interface

  #363 opened 10 months ago by adamltyson
  0

• [Feature] Allow the user to select points from more than one layer at once in the curation interface

  #362 opened 10 months ago by adamltyson
  2

• Raise a more informative error message with 2.5D data

  #269 opened 10 months ago by adamltyson
  0

• How are `prep_classification` and `prep_training` different?

  #272 opened 10 months ago by sfmig
  1

• Remove `test/data/brain` directory

  #271 opened 10 months ago by adamltyson
  0

• Update the sample data

  #305 opened a year ago by adamltyson
  0

• Add benchmarks for training [Feature]

  #274 opened a year ago by sfmig
  0

• Investigate parameter combinations causing cellfinder to stall

  #270 opened a year ago by adamltyson
  0

• Deprecation of pandas.DataFrame.append() causing cellfinder to crash

  #254 opened a year ago by adamltyson
  0

• [Feature] Migrate to `setuptools_scm`

  #242 opened a year ago by willGraham01
  0

• [BUG] CLI scripts raise errors due to missing functions.

  #246 opened a year ago by willGraham01
  1

• [BUG] Napari and brainreg-segment dependencies not fetched

  #245 opened a year ago by willGraham01
  4

• [BUG] Tests fail on py3.8

  #235 opened a year ago by willGraham01
  2