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Segger - #49

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EliHei2 wants to merge 30 commits into

mainfrom

segger

Open

Segger#49
EliHei2 wants to merge 30 commits into
mainfrom
segger

Commits on May 18, 2026
- Keep vendor cell_id in spatial_unlabelled as a segmentation prior
  
  EliHei2
  and
  claude
  committed
  da46c22
- Add segger method component
  
  EliHei2
  and
  claude
  committed
  a36fb57
- Apply suggestions from code review
  rcannood
  authored
  c2a3268
- Merge remote-tracking branch 'origin/main' into segger
  rcannood
  committed
  b9c4803
Commits on May 19, 2026
- Segger - use pytorch 25.04 instead of 26.02 as a base image (#33)
  rcannood
  authored
  3bc10ee
- Fix segger CI: replace cellpose min_size=-1 with 0 for NumPy 2.x
  
  EliHei2
  and
  claude
  committed
  5f74b6a
- Filter -1 / UNASSIGNED cell_id sentinels before rasterization
  
  EliHei2
  and
  claude
  committed
  1c10f12
- Align segger CLI flags with dpeerlab/segger@main
  
  EliHei2
  and
  claude
  committed
  11d203c
- Skip cudf driver validation on GPU-less runners
  
  EliHei2
  and
  claude
  committed
  770ca1b
- CPU stub-and-exit for segger + restore cuspatial install
  
  EliHei2
  and
  claude
  committed
  b9ae3e5
- Warn early when no CUDA GPU is detected for segger
  
  EliHei2
  and
  claude
  committed
  d8765d3
- Hard-fail segger when no CUDA GPU is available
  
  EliHei2
  and
  claude
  committed
  29d16d1
- Merge remote-tracking branch 'origin/main' into segger
  rcannood
  committed
  6e0ccd7
- bypass run test for segger
  rcannood
  committed
  bbb5f30
- add segger to wf
  rcannood
  committed
  c520074
- use different label
  rcannood
  committed
  8c8560a
- Merge remote-tracking branch 'origin/main' into segger
  EliHei2
  committed
  b5da903
- Export segger's full per-cell footprint, boundaries, and per-cell table
  
  EliHei2
  and
  claude
  committed
  3c2e808
- Minimal label image for segger: pixel-paint per assigned transcript
  
  EliHei2
  and
  claude
  committed
  48aed73
- Set production defaults for --init_segmentation and --cellpose_diameter
  
  EliHei2
  and
  claude
  committed
  4b3ddc8
- Switch segger raster to cKDTree-Voronoi for filled cell masks
  
  EliHei2
  and
  claude
  committed
  49b7938
- Replace segger's opencv-python with headless wheel
  
  EliHei2
  and
  claude
  committed
  113079d
- add missing packages
  rcannood
  committed
  a809166
- fix config
  rcannood
  committed
  8bdad1f
- removed unneeded deps?
  rcannood
  committed
  e4d6a33
- Merge branch 'main' into segger
  rcannood
  committed
  8782a00
- revert cv2 issues
  rcannood
  committed
  9dd0a20
- Write boundary cell_id as string for segger's preprocessor
  
  EliHei2
  and
  claude
  committed
  c22dc4b
- Trust per-transcript cell_id prior directly; fail loud on empty signal
  
  EliHei2
  and
  claude
  committed
  2baf179
- Drop transcripts whose cell has no boundary polygon
  
  EliHei2
  and
  claude
  committed
  f76c8ab

Commits

Commits on May 18, 2026

Commits on May 19, 2026