Issues

• [add] Tool for image alingment

  enhancementprio3
  nf-core/spatialaxe#211 · Filter by author heylf opened on Sep 1, 2026

• [add] Support UNZIP and UNTAR for input

  enhancementprio1
  nf-core/spatialaxe#209 · Filter by author heylf opened on Aug 21, 2026 · 2.0.0

• [add] Extend and create summary, multisample QC report with spatialaxe

  enhancementprio1
  nf-core/spatialaxe#208 · Filter by author heylf opened on Aug 17, 2026 · 2.0.0

• [add] Make test runs with different Xenium data version

  enhancementprio2
  nf-core/spatialaxe#207 · Filter by author heylf opened on Aug 17, 2026

• [fix] nextflow.config

  enhancement
  nf-core/spatialaxe#187 · Filter by author khersameesh24 opened on Jul 3, 2026

• [add] Baysor Scaling factor

  enhancementprio1
  nf-core/spatialaxe#185 · Filter by author khersameesh24 opened on Jun 28, 2026

• [add] bento tools

  enhancement
  nf-core/spatialaxe#181 · Filter by author heylf opened on Jun 25, 2026
  

• [add] Enhance QC stuff part Altos

  enhancementprio1
  nf-core/spatialaxe#179 · Filter by author heylf opened on Jun 24, 2026 · 1.1.0
  

• [update] existing nf-core modules

  enhancementprio1
  nf-core/spatialaxe#178 · Filter by author heylf opened on Jun 24, 2026 · 1.1.0
  

• [update] Base config

  enhancementprio1
  nf-core/spatialaxe#177 · Filter by author heylf opened on Jun 24, 2026 · 2.0.0

• [bug] Allow for a bigger test run

  enhancementprio2
  nf-core/spatialaxe#176 · Filter by author heylf opened on Jun 24, 2026 · 1.1.0
  1

• [update] Full documentation

  enhancementprio2
  nf-core/spatialaxe#175 · Filter by author heylf opened on Jun 24, 2026 · 2.0.0

• [add] support for seurat object

  enhancementprio2
  nf-core/spatialaxe#174 · Filter by author khersameesh24 opened on Jun 18, 2026 · 2.0.0
  

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

  nf-core/spatialaxe#169 · Filter by author 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)

  nf-core/spatialaxe#168 · Filter by author an-altosian opened on May 28, 2026

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

  nf-core/spatialaxe#167 · Filter by author an-altosian opened on May 28, 2026

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

  nf-core/spatialaxe#166 · Filter by author 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)

  nf-core/spatialaxe#164 · Filter by author an-altosian opened on May 28, 2026

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

  nf-core/spatialaxe#165 · Filter by author an-altosian opened on May 28, 2026

• [bug] Prior segmentation confidence

  bug
  nf-core/spatialaxe#163 · Filter by author khersameesh24 opened on May 28, 2026

• [bug] RESIZE TIFF awlays runs with cellpose-baysor subworkflow

  bug
  nf-core/spatialaxe#161 · Filter by author khersameesh24 opened on May 22, 2026

• [add] Generate segmentation patches for faster ROI-based segmentation

  enhancement
  nf-core/spatialaxe#157 · Filter by author khersameesh24 opened on May 13, 2026

• [add] DenoIST

  moduleprio3qc
  nf-core/spatialaxe#128 · Filter by author heylf opened on Mar 10, 2026 · 2.0.0
  

• [add] module CellAdmix

  moduleprio3qc
  nf-core/spatialaxe#127 · Filter by author heylf opened on Mar 10, 2026

• [add] module SCS

  moduleqcsegmentation
  nf-core/spatialaxe#126 · Filter by author heylf opened on Mar 10, 2026