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Look into making coreograph output mask/ROIs rather than physically splitting image

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#145 In nf-core/mcmicro;

· jmuhlich opened on Feb 9, 2026

Cellpose and Mesmer need the label <code>process_gpu</code>

Status: Open.

#144 In nf-core/mcmicro;

· adamjtaylor opened on Feb 4, 2026

mcCellpose incompatiable with Coreograph outputs.

Status: Open.

#143 In nf-core/mcmicro;

· adamjtaylor opened on Feb 3, 2026

Should illlumination be a boolean parameter in the schema

Status: Open.

#142 In nf-core/mcmicro;

· adamjtaylor opened on Feb 3, 2026

CELLPOSE process fails on AWS Batch when not selected in segmentation parameter

Status: Open.

#140 In nf-core/mcmicro;

· adamjtaylor opened on Feb 3, 2026

bftools showinf should omit extra annotations

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#132 In nf-core/mcmicro;

· jmuhlich opened on Jan 9, 2026

Evaluate instanseg for segmentation

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

#131 In nf-core/mcmicro;

· jmuhlich opened on Dec 4, 2025

all ome-tiff output should include channel name metadata

enhancementImprovement for existing functionalityImprovement for existing functionality

Status: Open.

Enhancement

#130 In nf-core/mcmicro;

· jmuhlich opened on Nov 20, 2025

some omevalidation checks are too strict or misapplied

bugSomething isn't workingSomething isn't working

Status: Open.

#121 In nf-core/mcmicro;

· jmuhlich opened on Oct 20, 2025

Registration processes are not launched until all illumination processes complete

bugSomething isn't workingSomething isn't working

Status: Open.

#105 In nf-core/mcmicro;

· jmuhlich opened on Oct 2, 2025

Add a test that multi-cycle samples produce the expected number of output files

Status: Open.

Task

#102 In nf-core/mcmicro;

· jmuhlich opened on Sep 24, 2025

Color heterogeneity

Status: Open.

#92 In nf-core/mcmicro;

· tkcaccia opened on Jun 18, 2025