Issues

• scikit-image is imported directly but only installed through optional extras

  Biohub/biahub#470 · Filter by author tayllatheodoro opened on Nov 10, 2026

• More interpolation kinds for apply-transform and Transform.apply

  Biohub/biahub#469 · Filter by author tayllatheodoro opened on Nov 10, 2026

• Library functions print with click.echo: log instead, so callers can filter it

  Biohub/biahub#467 · Filter by author tayllatheodoro opened on Nov 9, 2026
  1

• Update deconvolve cli to run Richards-Lucy deconvolution

  Biohub/biahub#462 · Filter by author tayllatheodoro opened on Nov 6, 2026
  

• dca-finalize: support neuromast (zebrafish) reconstructions

  Biohub/biahub#456 · Filter by author aofei-liu opened on Nov 3, 2026
  1

• project: match the training Z window for fluorescence channels; set real NA and wavelength for focus

  Biohub/biahub#451 · Filter by author ieivanov opened on Oct 29, 2026
  1

  

• Division classifier: score and cut false divisions after tracking (on hold: needs more annotations)

  Biohub/biahub#447 · Filter by author tayllatheodoro opened on Oct 27, 2026
  1

• segment: make cpdino / cpdino-vitb usable (dinov3 dependency and licence)

  Biohub/biahub#445 · Filter by author tayllatheodoro opened on Oct 27, 2026
  1

• Tracking follow-up: choose the A549 default tracker, downsample for HOCT/Trackastra, three-way divisions, division classifier

  Biohub/biahub#444 · Filter by author tayllatheodoro opened on Oct 27, 2026
  4

• track: write tracks.geff for every tracker, not only ultrack

  Biohub/biahub#441 · Filter by author ieivanov opened on Oct 26, 2026
  4

• Remove the legacy registration / stabilization code

  Biohub/biahub#417 · Filter by author tayllatheodoro opened on Oct 13, 2026

• Nextflow: a step's config change does not invalidate downstream steps

  Biohub/biahub#406 · Filter by author ieivanov opened on Oct 6, 2026

• Add inference-readiness preprocessing for focus and intensity metadata

  Biohub/biahub#400 · Filter by author edyoshikun opened on Oct 2, 2026
  1

• nextflow a549 qc.yaml hard-codes GFP and mCherry SNR floors, so QC gate fails on stores lacking either channel

  Biohub/biahub#389 · Filter by author tayllatheodoro opened on Sep 28, 2026
  1

• DCA: make mantis-v2 pipeline outputs DCA v0.2 compliant

  enhancement
  Biohub/biahub#363 · Filter by author ieivanov opened on Sep 24, 2026
  8

• DCA: write normalization statistics into dca (reuse QC intensity stats)

  enhancement
  Biohub/biahub#358 · Filter by author ieivanov opened on Sep 24, 2026
  1

  

• DCA: write the dca metadata block from AirTable

  enhancement
  Biohub/biahub#357 · Filter by author ieivanov opened on Sep 24, 2026
  1

  

• feat(nextflow): Restructure Nextflow DAG to work across positions rather than across reconstruction steps

  Biohub/biahub#304 · Filter by author ieivanov opened on Aug 5, 2026
  2

  

• feat(cli): scaffold an experiment folder (configs + run script) from an acquisition path

  Biohub/biahub#293 · Filter by author tayllatheodoro opened on Jul 27, 2026

• feat(cli): add a command to edit zarr channels (drop / rename)

  enhancement
  Biohub/biahub#274 · Filter by author tayllatheodoro opened on Jul 8, 2026
  3

• Inherit pixel sizes from zarr stores by default in reconstruction pipelines

  Biohub/biahub#270 · Filter by author ieivanov opened on Jun 11, 2026

• Transition to using Typer for CLI

  Biohub/biahub#253 · Filter by author ieivanov opened on May 28, 2026
  

• Migrate biahub to uv workspace with independent subpackages

  Biohub/biahub#228 · Filter by author ieivanov opened on Apr 7, 2026
  1

  

• Include main biahub API method in __init__.py __all__ for easy import

  Biohub/biahub#227 · Filter by author ieivanov opened on Apr 7, 2026
  

• concatenate pollutes stdout by repetitively printing channel indices

  Biohub/biahub#210 · Filter by author alxndrkalinin opened on Mar 5, 2026