feat(workflow): ✨ wire dilate_labels into build_fn via cfg["dilate"]

Applies to every method (cellpose/threshold/custom) uniformly, since
build_fn wraps its single return point rather than each branch. Adds a
commented-out dilate: N example to both config.yaml and config_cilia.yaml.

Author: lguerard

workflow/config/config.yaml

@@ -30,6 +30,7 @@ empty_threshold: null # null → Otsu; or a number
 
 # ---- segmentation -----------------------------------------------------------
 method: "cellpose" # "cellpose" (GPU), "threshold" (no GPU; testing), "custom"
+# dilate: 2 # optional: pixels to grow labels by after segmentation, any method
 # Also namespaces this run's intermediate files under work_dir/<label_name>/,
 # so a second segmentation (different label_name, e.g. nuclei vs cytoplasm)
 # can safely target the same work_dir — see docs/guide/snakemake.md

workflow/config/config_cilia.yaml

@@ -25,6 +25,7 @@ skip_empty: true
 empty_threshold: null
 
 method: "custom"
+# dilate: 2 # optional: pixels to grow labels by after segmentation
 label_name: "cilia_labels"
 custom:
   module: "patchworks.plugins.dog"

workflow/scripts/_pw.py

@@ -133,7 +133,34 @@ def build_fn(cfg):
     cfg : dict
         Snakemake config. ``method`` selects ``"cellpose"`` (default), a simple
         ``"threshold"`` (testing / no-GPU), or ``"custom"`` to import your own
-        function (``cfg["custom"] = {module, function, kwargs}``).
+        function (``cfg["custom"] = {module, function, kwargs}``). Optional
+        ``cfg["dilate"]``: int, pixels to grow labels by after segmentation
+        (via ``patchworks.dilate_labels``), applied regardless of ``method``.
+        Omitted/0 disables dilation.
+
+    Returns
+    -------
+    callable
+        ``(ndarray) -> ndarray`` returning integer labels.
+    """
+    fn = _build_method_fn(cfg)
+
+    dilate = cfg.get("dilate")
+    if dilate:
+        from patchworks import dilate_labels
+
+        fn = dilate_labels(fn, iterations=dilate)
+
+    return fn
+
+
+def _build_method_fn(cfg):
+    """Build the per-tile segmentation function for ``cfg["method"]``.
+
+    Parameters
+    ----------
+    cfg : dict
+        Snakemake config, see :func:`build_fn`.
 
     Returns
     -------