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[upgrade] Proseg: bump v3.1.0 → v3.1.1 (patch release)

Status: Open.

#169 In nf-core/spatialaxe;

· an-altosian opened on May 28, 2026

[investigate] Segger: clarify version 1.0.14 source — dongzehe/segger container vs upstream dpeerlab/segger (canonical) / EliHei2/segger_dev (legacy)

Status: Open.

#168 In nf-core/spatialaxe;

· an-altosian opened on May 28, 2026

[upgrade] StarDist: identify current Wave-container version pin vs upstream 0.9.2

Status: Open.

#167 In nf-core/spatialaxe;

· an-altosian opened on May 28, 2026

[upgrade] Cellpose: identify current Wave-container version pin vs upstream v4.1.1

Status: Open.

#166 In nf-core/spatialaxe;

· an-altosian opened on May 28, 2026

[upgrade] Baysor: migrate Julia v0.7.1 → C++ cpp-0.8.2 (eliminates PARQUET_TO_CSV for Baysor paths)

Status: Open.

#164 In nf-core/spatialaxe;

· an-altosian opened on May 28, 2026

[upgrade] Ficture: migrate seqscope/ficture (Python) → Yichen-Si/punkst (C++)

Status: Open.

#165 In nf-core/spatialaxe;

· an-altosian opened on May 28, 2026

Prior segmentation confidence

bugSomething isn't workingSomething isn't working

Status: Open.

#163 In nf-core/spatialaxe;

· khersameesh24 opened on May 28, 2026

RESIZE TIFF awlays runs with cellpose-baysor subworkflow

bugSomething isn't workingSomething isn't working

Status: Open.

#161 In nf-core/spatialaxe;

· khersameesh24 opened on May 22, 2026

Generate segmentation patches for faster ROI-based segmentation

enhancementNew feature or requestNew feature or request

Status: Open.

#157 In nf-core/spatialaxe;

· khersameesh24 opened on May 13, 2026

Track and resolve outstanding TODOs in workflows/spatialxe.nf

Status: Open.

#149 In nf-core/spatialaxe;

· an-altosian opened on Apr 30, 2026

OPT modules needs updating

Status: Open.

#146 In nf-core/spatialaxe;

· heylf opened on Apr 30, 2026

DenoIST

module

prio3

qc

Status: Open.

#128 In nf-core/spatialaxe;

· heylf opened on Mar 10, 2026