MCMICRO reader does not support new nf-core/mcmicro output formats

[adamjtaylor]

We recently completed a port of MCMICRO to nf-core (https://nf-co.re/mcmicro/2.0.0). There are minor changes to expected output formats, and the current spatialdata_io.readers.mcmicro reader — written against the original labsyspharm/mcmicro layout — does not read nf-core output.

What changed between the two pipelines:

Aspect	labsyspharm/mcmicro	nf-core/mcmicro
Run config	qc/params.yml (workflow.tma)	pipeline_info/params*.json (tma_dearray, segmentation)
Registration	registration/<sample>.ome.tif	registration/ashlar/<sample>.ome.tif
Segmentation	segmentation/<module>-<sample>/{cell,nuclei}.ome.tif	segmentation/<segmenter>/<sample>_<tool-suffix>.tif
Quantification	quantification/<module>-<sample>_<comp>.csv	quantification/mcquant/<segmenter>/<sample>.csv
TMA cores	dearray/ + qc/coreograph/centroidsY-X.txt	tma_dearray/ (plus TMA_MAP.tif) + tma_dearray/centroidsY-X.txt
Markers	markers.csv at root	input sheet (often not copied to outdir); backsub/<sample>_backsub.csv when backsub runs
Samples / segmenters	single sample, typically one segmenter	multiple samples and multiple segmenters per run

Gotchas found while testing against real nf-core/mcmicro output that will need to be considered:

• Segmentation mask filenames are tool-specific, not a uniform _mask suffix — e.g. 1_cp_masks.tif (cellpose) vs exemplar-002_1_mask.tif (mesmer).
• The segmenter directory name differs between segmentation/ and quantification/mcquant/ (e.g. deepcell_mesmer vs mesmer), so tables can't be linked to labels by an exact directory-name match.
• With background subtraction, the registration image and the quantification tables carry different marker sets (e.g. 40 image channels vs 37 table markers).
• TMA core numbers must be parsed carefully — the sample name itself can contain digits (exemplar-002_1_mask → core 1, not 002) — and tma_dearray/ also contains TMA_MAP.tif, which is not a core.
• The prelude/markers_markersheet_mqc.tsv file is a long-format MultiQC validation report, not a usable wide marker sheet.

Proposal

Update the mcmicro reader to auto-detect the pipeline (with an explicit pipeline= override) and handle both layouts, including multiple samples and segmenters, in WSI and TMA modes. Backwards compatibility with labsyspharm output is preserved.