same for deepcell module

Author: BioinfoTongLI

…r/bioinfotongli/deepcell/environment.yml …/sanger/imaging/deepcell/environment.ymlmodules/sanger/bioinfotongli/deepcell/environment.yml renamed to modules/sanger/imaging/deepcell/environment.yml modules/sanger/bioinfotongli/deepcell/environment.yml renamed to modules/sanger/imaging/deepcell/environment.yml

@@ -1,4 +1,4 @@
-process BIOINFOTONGLI_DEEPCELL {
+process IMAGING_DEEPCELL {
     tag "${meta.id}"
     label 'process_medium'
 
@@ -33,7 +33,7 @@ process BIOINFOTONGLI_DEEPCELL {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bioinfotongli: \$(deepcell_helper.py version)
+        imaging: \$(deepcell_helper.py version)
     END_VERSIONS
     """
 
@@ -45,7 +45,7 @@ process BIOINFOTONGLI_DEEPCELL {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bioinfotongli: \$(deepcell_helper.py version)
+        imaging: \$(deepcell_helper.py version)
     END_VERSIONS
     """
 }

…es/sanger/bioinfotongli/deepcell/main.nf modules/sanger/imaging/deepcell/main.nfmodules/sanger/bioinfotongli/deepcell/main.nf renamed to modules/sanger/imaging/deepcell/main.nf modules/sanger/bioinfotongli/deepcell/main.nf renamed to modules/sanger/imaging/deepcell/main.nf

@@ -1,20 +1,20 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
-name: "bioinfotongli_deepcell"
+name: "imaging_deepcell"
 description: This module runs deepcell on a crop of an image
 keywords:
   - image analysis
   - image segmentation
   - imaging
 tools:
-  - "bioinfotongli":
+  - "imaging":
       description: "This module runs deepcell on a crop of an image"
       homepage: ""
       documentation: ""
       tool_dev_url: ""
       doi: ""
-      licence: 
-      identifier: 
+      licence:
+      identifier:
 
 input:
   - - meta:
@@ -41,21 +41,21 @@ input:
 
 output:
   - wkts:
-    - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. `[ id:'sample1' ]`
-    - "${output_name}":
-        type: file
-        description: WKT file
-        pattern: "*.wkt"
-          
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "${output_name}":
+          type: file
+          description: WKT file
+          pattern: "*.wkt"
+
   - versions:
-    - "versions.yml":
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 
 authors:
   - "@BioinfoTongLI"

…s/sanger/bioinfotongli/deepcell/meta.yml modules/sanger/imaging/deepcell/meta.ymlmodules/sanger/bioinfotongli/deepcell/meta.yml renamed to modules/sanger/imaging/deepcell/meta.yml modules/sanger/bioinfotongli/deepcell/meta.yml renamed to modules/sanger/imaging/deepcell/meta.yml

@@ -2,8 +2,7 @@
 # -*- coding: utf-8 -*-
 # Copyright (c) 2025 Wellcome Sanger Institute
 
-"""
-"""
+""" """
 import fire
 from deepcell.applications import NuclearSegmentation
 import numpy as np
@@ -18,6 +17,7 @@
 from imagetileprocessor import slice_and_crop_image
 
 import logging
+
 logger = logging.getLogger(__name__)
 
 
@@ -35,7 +35,7 @@ def get_largest_polygon(multi_polygon: MultiPolygon):
             largest_area = area
         largest_polygon = polygon
     if largest_polygon is None:
-        return multi_polygon 
+        return multi_polygon
     else:
         return largest_polygon
 
@@ -52,11 +52,9 @@ def get_shapely(label):
             continue
         cur_cell_label = i + 1
         msk = (label[bbox[0], bbox[1]] == cur_cell_label).astype(np.uint8).copy()
-        cnts, _ = cv2.findContours(
-            msk, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE
-        )
+        cnts, _ = cv2.findContours(msk, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
         # if len(cnts) > 1:
-            # print(len(cnts), cur_cell_label)
+        # print(len(cnts), cur_cell_label)
         current_polygons = [
             Polygon((cnt + [bbox[1].start, bbox[0].start]).squeeze())
             #             else Point((cnt + [bbox[1].start, bbox[0].start]).squeeze())
@@ -72,12 +70,15 @@ def get_shapely(label):
 
 
 def main(
-        image_path: str,
-        x_min: int, x_max: int, y_min: int, y_max: int,
-        output_name: str,
-        C: int = 0,
-        Z: int = 0,
-    ):
+    image_path: str,
+    x_min: int,
+    x_max: int,
+    y_min: int,
+    y_max: int,
+    output_name: str,
+    C: int = 0,
+    Z: int = 0,
+):
     model_dir = Path.home() / ".deepcell" / "models"
     # model_path = model_dir / MODEL_NAME
     model_path = model_dir / "NuclearSegmentation"
@@ -88,9 +89,16 @@ def main(
     # crop = img.get_image_dask_data("TYXC", Z=Z, T=T, C=C)[:, y_min:y_max, x_min:x_max, :]
 
     crop = slice_and_crop_image(
-        image_path, x_min, x_max, y_min, y_max, zs=np.array([Z]), channel=np.array([C]), resolution_level=0
+        image_path,
+        x_min,
+        x_max,
+        y_min,
+        y_max,
+        zs=np.array([Z]),
+        channel=np.array([C]),
+        resolution_level=0,
     )
-    if crop.ndim == 2: # special channel setting required by deepcell
+    if crop.ndim == 2:  # special channel setting required by deepcell
         crop = np.expand_dims(crop, axis=[-1, 0])
     segmentation_predictions = app.predict(
         np.array(crop).astype(np.uint16), image_mpp=0.5
@@ -103,11 +111,11 @@ def main(
                 translate(MultiPolygon(list(polys[1].values())), xoff=x_min, yoff=y_min)
             )
         )
-    
+
 
 if __name__ == "__main__":
     options = {
         "run": main,
         "version": "0.0.1",
     }
-    fire.Fire(options)
+    fire.Fire(options)

…ell/resources/usr/bin/deepcell_helper.py …ell/resources/usr/bin/deepcell_helper.pymodules/sanger/bioinfotongli/deepcell/resources/usr/bin/deepcell_helper.py renamed to modules/sanger/imaging/deepcell/resources/usr/bin/deepcell_helper.py modules/sanger/bioinfotongli/deepcell/resources/usr/bin/deepcell_helper.py renamed to modules/sanger/imaging/deepcell/resources/usr/bin/deepcell_helper.py

@@ -1,14 +1,14 @@
-// nf-core modules test bioinfotongli/deepcell
+// nf-core modules test imaging/deepcell
 nextflow_process {
 
-    name "Test Process BIOINFOTONGLI_DEEPCELL"
+    name "Test Process IMAGING_DEEPCELL"
     script "../main.nf"
-    process "BIOINFOTONGLI_DEEPCELL"
+    process "IMAGING_DEEPCELL"
 
     tag "modules"
     tag "modules_sanger"
-    tag "bioinfotongli"
-    tag "bioinfotongli/deepcell"
+    tag "imaging"
+    tag "imaging/deepcell"
 
     test("mouse_heart - tiff") {