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openproblems-bio / task_spatial_segmentation Public

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Segger#46

Merged

rcannood merged 21 commits into

mainopenproblems-bio/task_spatial_segmentation:mainfrom

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

May 19, 2026

Conversation Commits21 (21)Checks Files changed

Merged

Segger#46
rcannood merged 21 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

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