Issues

• [Feature] Unify where default models are on hugging face

  enhancement
  brainglobe/cellfinder#665 · Filter by author alessandrofelder opened on Sep 25, 2026

• Explore depending on HF client library

  enhancement
  brainglobe/cellfinder#664 · Filter by author alessandrofelder opened on Sep 11, 2026
  

• Download weights only, for default models

  enhancement
  brainglobe/cellfinder#663 · Filter by author alessandrofelder opened on Sep 11, 2026

• [Maintenance] torch.jit.script deprecated

  enhancement
  brainglobe/cellfinder#652 · Filter by author alessandrofelder opened on Aug 9, 2026

• [Feature] Cache models from huggingface used in tests

  enhancement
  brainglobe/cellfinder#651 · Filter by author alessandrofelder opened on Aug 7, 2026
  2

• [Feature] Ability to (re)train a single channel model based on curated two-channel data

  enhancement
  brainglobe/cellfinder#645 · Filter by author alessandrofelder opened on Jul 24, 2026

• [Feature] Have a progress bar showing download of default single channel model

  enhancement
  brainglobe/cellfinder#641 · Filter by author alessandrofelder opened on Jul 7, 2026
  1

• Unseeded random sizes in test_image_processing.py make coverage nondeterministic

  brainglobe/cellfinder#638 · Filter by author aymuos15 opened on Jul 6, 2026
  1

• [Feature] progress bar during saving of curated data in the napari GUI

  enhancementgood first issue
  brainglobe/cellfinder#626 · Filter by author alessandrofelder opened on Jun 11, 2026
  2

• [Feature] Improve defaults for cellfinder 2.0

  enhancement
  brainglobe/cellfinder#625 · Filter by author alessandrofelder opened on Jun 11, 2026
  2

• Discuss pros/cons of keras compared to native pytorch

  brainglobe/cellfinder#618 · Filter by author alessandrofelder opened on May 22, 2026
  3

• [Feature] Consider publishing a normalised pre-trained model

  enhancement
  brainglobe/cellfinder#617 · Filter by author alessandrofelder opened on May 22, 2026
  3

• [BUG]: background channel is required even when skip_classification=True (single-channel flow breaks)

  bug
  brainglobe/cellfinder#605 · Filter by author ishansurdi opened on Mar 17, 2026
  3

• Unused global variables in cellfinder detection?

  brainglobe/cellfinder#601 · Filter by author alessandrofelder opened on Mar 12, 2026
  4

• Explore how data augmentation affects training

  enhancement
  brainglobe/cellfinder#587 · Filter by author adamltyson opened on Feb 3, 2026

• [Optimsation] Vectorised binning

  enhancement
  brainglobe/cellfinder#584 · Filter by author HarshdipSaha opened on Jan 24, 2026

• [BUG] Spike in memory usage end of cellfinder inference phase

  bug
  brainglobe/cellfinder#555 · Filter by author marcodallavecchia opened on Aug 12, 2025
  13

• Editable install reports incorrect version

  bug
  brainglobe/cellfinder#551 · Filter by author matham opened on Jun 23, 2025
  1

• A different tile thresholding strategy for CFOS-type data: can this be its own preprocessing step (local contrast enhancement)

  brainglobe/cellfinder#541 · Filter by author alessandrofelder opened on Jun 6, 2025
  3

• automate evaluation as far as possible, so results can be reported in a standard way at each PR

  brainglobe/cellfinder#538 · Filter by author alessandrofelder opened on Jun 6, 2025
  1

• Benchmarking and validation functionality to evaluate cellfinder, as semi-automated high-level integration tests

  brainglobe/cellfinder#537 · Filter by author alessandrofelder opened on Jun 6, 2025
  3

• Document a list of real-life, diverse(CFOS and rabies-tracing) test datasets that allow us to evaluate correctness and performance of cellfinder

  brainglobe/cellfinder#536 · Filter by author alessandrofelder opened on Jun 6, 2025
  2

• [Feature] Make cellfinder CFOS ready

  enhancement
  brainglobe/cellfinder#535 · Filter by author alessandrofelder opened on Jun 6, 2025
  1

  

• [Feature] Run cell detection on subvolume of an image and not just select z planes

  enhancement
  brainglobe/cellfinder#468 · Filter by author IgorTatarnikov opened on Nov 7, 2024
  3

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

  enhancement
  brainglobe/cellfinder#464 · Filter by author alessandrofelder opened on Oct 18, 2024
  6