Fixes #681, hopefully cannot build website locally right now...

NEUBIAS · May 16, 2024 · dab0f76 · dab0f76
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diff --git a/...lei_measure_shape_scijava_imagejmacro.ijm → ...h_measure_nuclei_shape_scijava_ijmacro.md b/...lei_measure_shape_scijava_imagejmacro.ijm → ...h_measure_nuclei_shape_scijava_ijmacro.md
diff --git a/_includes/batch_processing/measure_nuclei_shapes.md b/_includes/batch_processing/measure_nuclei_shapes.md
@@ -0,0 +1,4 @@
+<h4 id="batchshape"><a href="#batchshape">Batch analysis of nuclear shapes</a></h4>
+
+- In a previous module [there is a workflow to measure the shapes of nuclei in one image](https://neubias.github.io/training-resources/workflow_segment_2d_nuclei_measure_shape/index.html#2dnuclei)
+- Adapt this workflow for automated batch analysis of many images
diff --git a/_includes/workflow_segment_2d_nuclei_measure_shape/segment_2d_nuclei.md b/_includes/workflow_segment_2d_nuclei_measure_shape/segment_2d_nuclei.md
@@ -1,4 +1,4 @@
-<h4 id="2dnuclei"><a href="#2dnuclei">Segment 2D nuclei</a></h4>
+<h4 id="2dnuclei"><a href="#2dnuclei">Segment 2D nuclei and measure their shapes</a></h4>
 - Input images
   - [xy_8bit__mitocheck_incenp_t1.tif](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__mitocheck_incenp_t1.tif)
   - [xy_8bit__mitocheck_incenp_t70.tif](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__mitocheck_incenp_t70.tif)

diff --git a/_modules/batch_processing.md b/_modules/batch_processing.md
@@ -3,6 +3,7 @@ title: Batch processing
 layout: module
 tags: ["scripting"]
 prerequisites:
+  - "[Working with Strings](../string_concat)"
 objectives:
   - "Automatically process a number of images"
 motivation: |
@@ -20,14 +21,8 @@ concept_map: >
 figure: /figures/batch_processing.png
 figure_legend: Batch processing of many images, yielding many tables.
 
-activity_preface: |
-  - Batch process several images containing nuclei.
-  - Download the images in [image_data/batch_process](https://github.com/NEUBIAS/training-resources/tree/master/image_data/batch_process).
-    - For each image
-      - Segment the nuclei and save the label mask.
-      - Measure the nuclei area and save the results in a table.
-activities:
-  - ["ImageJ Macro Scijava","batch_processing/activities/nuclei_measure_shape_scijava_imagejmacro.ijm", "Java"]
+multiactivities:
+  - ["batch_processing/measure_nuclei_shapes.md", [["ImageJ SciJava Macro", "batch_processing/batch_measure_nuclei_shape_scijava_ijmacro.md"]]]
 
 exercises_preface: |
   - Download those two images