Merge pull request #345 from kostrykin/add_otsu_workflow

Add workflow for segmentation and counting of cell nuclei in fluorescence microscopy images

Author: mvdbeek

workflows/imaging/fluorescence-nuclei-segmentation-and-counting/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /segmentation-and-counting.ga
+  testParameterFiles:
+  - /segmentation-and-counting-tests.yml
+  authors:
+  - name: Leonid Kostrykin
+    orcid: 0000-0003-1323-3762
+    url: https://github.com/kostrykin/

workflows/imaging/fluorescence-nuclei-segmentation-and-counting/CHANGELOG.md

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+# Changelog
+
+## [0.1] - 2024-02-29
+
+- Creation of workflow for segmentation and counting of cell nuclei in fluorescence microscopy images.

workflows/imaging/fluorescence-nuclei-segmentation-and-counting/README.md

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+# Segmentation and counting of cell nuclei in fluorescence microscopy images
+
+This workflow performs segmentation and counting of cell nuclei using fluorescence microscopy images. The segmentation step is performed using Otsu thresholding (Otsu, 1979). The workflow is based on the tutorial: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/tutorial.html
+
+![](test-data/overlay_image.png)
+
+## Inputs
+
+**`input_image`:** The fluorescence microscopy images to be segmented. Must be the single image channel, which contains the cell nuclei.
+
+## Outputs
+
+**`overlay_image`:** An overlay of the original image and the outlines of the segmentated objects, each also annotated with a unique number.
+
+**`objects_count`:** Table with a single column `objects` and a single row (the actual number of objects).
+
+**`label_image`:** The segmentation result (label map, which contains a unique label for each segmented object).

workflows/imaging/fluorescence-nuclei-segmentation-and-counting/segmentation-and-counting-tests.yml

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+- doc: Test outline for segmentation-and-counting.ga
+  job:
+    input_image:
+      class: File
+      path: test-data/input_image.tiff
+      filetype: tiff
+  outputs:
+    overlay_image:
+      path: test-data/overlay_image.png
+      compare: sim_size
+      delta: 100
+    objects_count:
+      path: test-data/objects_count.tabular
+      compare: diff
+      lines_diff: 0
+    label_image:
+      path: test-data/label_image.tiff
+      compare: sim_size
+      delta: 100