Removed python-dependent code from general activities

NEUBIAS · Jul 30, 2024 · 9c71833 · 9c71833
1 parent c2a0cf2
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Showing 2 changed files with 12 additions and 7 deletions.
diff --git a/_includes/batch_processing/batch_measure_nuclei_shapes.md b/_includes/batch_processing/batch_measure_nuclei_shapes.md
@@ -5,14 +5,17 @@
 - Adapt this workflow for automated batch analysis of many images
 - Start by building the skeleton of the workflow without filling in the functionality;
 
-  Note that the code below runs fine, but does not produce any results:
+  Note that the pseudo-code below will run fine, but does not produce any results:
 
 ```
-def analyse(image_path, output_folder):
-    print("Analyzing:", image_path)
-    
-for image_path in image_paths:
-    analyse(image_path, output_dir)
+FUNCTION analyse(image_path, output_folder)
+    PRINT "Analyzing:", image_path
+END FUNCTION
+
+FOR each image_path in image_paths
+    CALL analyse(image_path, output_dir)
+END FOR
 ```
 
- - Make sure the loop with the (almost) empty analyse function runs without error before filling in the image analysis steps
+ - Make sure the loop with the (almost) empty analyse function runs without error before filling in the image analysis steps
+ - Inspect the analysis results in a suitable software
diff --git a/_modules/batch_processing.md b/_modules/batch_processing.md
@@ -41,4 +41,6 @@ learn_next:
 
 external_links:
   - "[Batch processing in ImageJ](https://imagej.net/scripting/batch)"
+  - [MoBIE](https://github.com/mobie/mobie-viewer-fiji)
+  - [ImageDataExplorer](https://git.embl.de/heriche/image-data-explorer)
 ---