MCMICRO reader does not support new nf-core/mcmicro output formats
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调研方向
从 spatialdata_io.readers.mcmicro 开始，将其假设与 issue 中列出的两种输出布局进行比较。跟踪 registration、segmentation、quantification、markers 和 TMA cores 是如何被发现的，然后为多个样本和 segmenters、pipeline 自动检测以及显式 override 定义验证用例。完成的标准是 labsyspharm 和 nf-core 的输出都仍然可读，包括 WSI 和 TMA 用例。
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描述
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
_masksuffix — e.g.1_cp_masks.tif(cellpose) vsexemplar-002_1_mask.tif(mesmer). - The segmenter directory name differs between
segmentation/andquantification/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→ core1, not002) — andtma_dearray/also containsTMA_MAP.tif, which is not a core. - The
prelude/markers_markersheet_mqc.tsvfile 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.
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