docs(workflow): 📝 update relation output docs for the xlsx change

.csv -> .xlsx in config/multi.yaml's example outputs, and document
the two-sheet layout (per-a-object incl. unmatched, per-b-object
incl. zero-match) in guide/snakemake.md.

Author: Laurent Guerard

docs/guide/snakemake.md

@@ -303,7 +303,7 @@ segmentations:
 relations:
   - a: nuclei_labels
     b: cyto_labels
-    output: nuclei_to_cyto.csv # written into work_dir
+    output: nuclei_to_cyto.xlsx # written into work_dir
 ```
 
 ```bash
@@ -317,6 +317,19 @@ Every listed segmentation config must share the same `work_dir` (so
 script checks this and errors out otherwise. `relations` is optional; omit it
 to just chain segmentations without a relation step.
 
+Each `output:` is an Excel workbook (`openpyxl`, part of the `workflow`
+extra) with two sheets:
+
+| Sheet | One row per | Columns |
+| --- | --- | --- |
+| `<a>` | every non-background `a` label, **including unmatched ones** | `<a>_id`, `<b>_id` (blank if unmatched), `overlap_voxels`, `overlap_fraction` (0 if unmatched) |
+| `<b>` | every non-background `b` label, **including ones with zero matches** | `<b>_id`, `<a>_count`, `total_overlap_voxels` |
+
+Unlike calling `label_relations()` directly (which only returns matched `a`
+labels — see below), the workbook always covers every object in both
+segmentations, so counts (e.g. "how many nuclei have no matching cell",
+"how many cells have zero cilia") aren't silently dropped.
+
 Both lists are ordinary lists, so 3+ segmentations work the same way — add
 more entries to `segmentations`, then list whichever pairs to relate. There's
 no automatic "chain": list every pair explicitly, e.g. for nuclei + cyto +

workflow/config/multi.yaml

@@ -1,6 +1,8 @@
 # Drives `pixi run multi` / `scripts/run_multi.py`: runs several segmentation
 # configs (in order) against the same work_dir, then relates their labels by
-# voxel overlap (patchworks.label_relations) and writes a CSV per pair.
+# voxel overlap (patchworks.label_relations) and writes an Excel workbook per
+# pair (two sheets: one row per a-object incl. unmatched ones, one row per
+# b-object incl. ones with zero matches — see docs/guide/snakemake.md).
 #
 # All listed segmentation configs must share the same work_dir/image.zarr and
 # the same tile_shape/level, so the resulting label arrays are directly
@@ -19,10 +21,10 @@ segmentations:
 relations:
 - a: nuclei_labels
   b: cyto_labels
-  output: nuclei_to_cyto.csv
+  output: nuclei_to_cyto.xlsx
 - a: cilia_labels
   b: cyto_labels
-  output: cilia_to_cell.csv
+  output: cilia_to_cell.xlsx
 - a: cilia_labels
   b: nuclei_labels
-  output: cilia_to_nucleus.csv
+  output: cilia_to_nucleus.xlsx