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openproblems-bio / task_spatial_segmentation Public

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Segger#49

Open

EliHei2 wants to merge 30 commits into

mainopenproblems-bio/task_spatial_segmentation:mainfrom

seggeropenproblems-bio/task_spatial_segmentation:seggerCopy head branch name to clipboard

Conversation Commits30 (30)Checks Files changed

Open

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

Commits

Commits on May 18, 2026

Keep vendor cell_id in spatial_unlabelled as a segmentation prior

EliHei2
and
claude
committed
Add segger method component

EliHei2
and
claude
committed
Apply suggestions from code review
rcannood
authored
Merge remote-tracking branch 'origin/main' into segger
rcannood
committed

Commits on May 19, 2026

Segger - use pytorch 25.04 instead of 26.02 as a base image (#33)
rcannood
authored
Fix segger CI: replace cellpose min_size=-1 with 0 for NumPy 2.x

EliHei2
and
claude
committed
Filter -1 / UNASSIGNED cell_id sentinels before rasterization

EliHei2
and
claude
committed
Align segger CLI flags with dpeerlab/segger@main

EliHei2
and
claude
committed
Skip cudf driver validation on GPU-less runners

EliHei2
and
claude
committed
CPU stub-and-exit for segger + restore cuspatial install

EliHei2
and
claude
committed
Warn early when no CUDA GPU is detected for segger

EliHei2
and
claude
committed
Hard-fail segger when no CUDA GPU is available

EliHei2
and
claude
committed
Merge remote-tracking branch 'origin/main' into segger
rcannood
committed
bypass run test for segger
rcannood
committed
add segger to wf
rcannood
committed
use different label
rcannood
committed
Merge remote-tracking branch 'origin/main' into segger
EliHei2
committed
Export segger's full per-cell footprint, boundaries, and per-cell table

EliHei2
and
claude
committed
Minimal label image for segger: pixel-paint per assigned transcript

EliHei2
and
claude
committed
Set production defaults for --init_segmentation and --cellpose_diameter

EliHei2
and
claude
committed
Switch segger raster to cKDTree-Voronoi for filled cell masks

EliHei2
and
claude
committed
Replace segger's opencv-python with headless wheel

EliHei2
and
claude
committed
add missing packages
rcannood
committed
fix config
rcannood
committed
removed unneeded deps?
rcannood
committed
Merge branch 'main' into segger
rcannood
committed
revert cv2 issues
rcannood
committed
Write boundary cell_id as string for segger's preprocessor

EliHei2
and
claude
committed
Trust per-transcript cell_id prior directly; fail loud on empty signal

EliHei2
and
claude
committed
Drop transcripts whose cell has no boundary polygon

EliHei2
and
claude
committed

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