Issues

• Cleanup: 6 unmerged branches without a PR (decide: delete, PR or keep)

  CellMigrationLab/morphobricks-preprocessing#297 · Filter by author guijacquemet opened on Nov 14, 2026

• Read TIFF-based whole-slide formats (SVS/NDPI/SCN) as RGB units; a conversion helper for WebP/PNG/JPEG

  CellMigrationLab/morphobricks-preprocessing#294 · Filter by author guijacquemet opened on Nov 13, 2026

• Removing every member of a biological repeat is refused with R_USED_ID_DROPPED at used_ids.repeats

  CellMigrationLab/morphobricks-preprocessing#283 · Filter by author guijacquemet opened on Nov 11, 2026

• Step 1 previews: read a lower pyramid level for large OME-Zarr images

  CellMigrationLab/morphobricks-preprocessing#251 · Filter by author guijacquemet opened on Nov 9, 2026

• Design: windowed (lazy) Y/X reads of one plane for very large images (whole-slide OME-Zarr)

  CellMigrationLab/morphobricks-preprocessing#179 · Filter by author guijacquemet opened on Nov 6, 2026

• Recorded Z-projection step (moved from CellPatcher)

  CellMigrationLab/morphobricks-preprocessing#176 · Filter by author guijacquemet opened on Nov 6, 2026

• Expand experimental metadata to condition annotations, own controls and explicit contrasts

  CellMigrationLab/morphobricks-preprocessing#172 · Filter by author guijacquemet opened on Nov 5, 2026

• Add explicit channel-aware canonical dataset export to OME-TIFF or OME-Zarr

  CellMigrationLab/morphobricks-preprocessing#171 · Filter by author guijacquemet opened on Nov 5, 2026

• Allow users to define canonical experiment channel names and record them in the run manifest

  CellMigrationLab/morphobricks-preprocessing#170 · Filter by author guijacquemet opened on Nov 5, 2026

• Add representative image/channel QC with safe notebook visualization

  CellMigrationLab/morphobricks-preprocessing#169 · Filter by author guijacquemet opened on Nov 5, 2026

• Show phase-aware progress and ETA while checking folders and image headers

  CellMigrationLab/morphobricks-preprocessing#168 · Filter by author guijacquemet opened on Nov 5, 2026

• Document the before/during/after segmentation workflow with one shared MorphoBricks step pattern

  CellMigrationLab/morphobricks-preprocessing#167 · Filter by author guijacquemet opened on Nov 5, 2026

• Record completeness and segmentation snapshot provenance in mask_relationships.json

  CellMigrationLab/morphobricks-preprocessing#166 · Filter by author guijacquemet opened on Nov 5, 2026

• Make the mask relationship scan resumable per FOV

  CellMigrationLab/morphobricks-preprocessing#164 · Filter by author guijacquemet opened on Nov 5, 2026

• Read-memory estimate is slightly low for tiny uncompressed tiles

  CellMigrationLab/morphobricks-preprocessing#157 · Filter by author guijacquemet opened on Nov 5, 2026

• Consumer checks need exact commit SHAs, not tags

  CellMigrationLab/morphobricks-preprocessing#154 · Filter by author guijacquemet opened on Nov 5, 2026

• Uncommitted 238-case --log test matrix

  CellMigrationLab/morphobricks-preprocessing#152 · Filter by author guijacquemet opened on Nov 5, 2026

• write_target TOCTOU between check and write (documented)

  CellMigrationLab/morphobricks-preprocessing#151 · Filter by author guijacquemet opened on Nov 5, 2026

• convert: accept a stated page reshape (e.g. --pages CZ=2x3) and/or reorder copies into the common order (plan Q73)

  CellMigrationLab/morphobricks-preprocessing#144 · Filter by author guijacquemet opened on Nov 3, 2026

• Conversion reopens TIFF headers for pixel reads and memory checks (performance follow-up of #96)

  CellMigrationLab/morphobricks-preprocessing#141 · Filter by author guijacquemet opened on Nov 3, 2026

• [Sad Catapella][Performance/Architecture] Add optional FOV-level worker parallelism to mask relationship scans

  CellMigrationLab/morphobricks-preprocessing#108 · Filter by author guijacquemet opened on Nov 1, 2026

• [Performance] Add simple resource-aware FOV-level parallel preprocessing

  CellMigrationLab/morphobricks-preprocessing#107 · Filter by author guijacquemet opened on Nov 1, 2026

• [Sad Catapella B9][Performance infrastructure] Add reproducible end-to-end and kernel benchmarks before Numba acceleration

  CellMigrationLab/morphobricks-preprocessing#106 · Filter by author guijacquemet opened on Nov 1, 2026

• [Sad Catapella B8][Performance] Notebook plan rebuild repeatedly stats every TIFF and reparses the manifest on settings edits

  CellMigrationLab/morphobricks-preprocessing#102 · Filter by author guijacquemet opened on Nov 1, 2026

• [Sad Catapella B8][Notebook reliability] Failed folder preflight escapes the widget handler without clearing the prior checked state

  CellMigrationLab/morphobricks-preprocessing#101 · Filter by author guijacquemet opened on Nov 1, 2026