Histological Staining Area Quantification

Run Workflow in Galaxy

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• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Collection\nROI image for staining analysis"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Sample ID"];
  2["header for total area"];
  3["Stain intensity normalization CLAHE"];
  0 -->|output| 3;
  4["Show image info"];
  0 -->|output| 4;
  5["Color Deconvolution"];
  3 -->|output| 5;
  b4393dde-25b8-49ad-b48c-5d2df47c1408["Output\nDeconvolved Image"];
  5 --> b4393dde-25b8-49ad-b48c-5d2df47c1408;
  style b4393dde-25b8-49ad-b48c-5d2df47c1408 stroke:#2c3143,stroke-width:4px;
  6["Width Extraction"];
  4 -->|output| 6;
  7["Height Extraction"];
  4 -->|output| 7;
  8["Split Image Channels for Staining Detection"];
  5 -->|output| 8;
  cbd8deec-7ea2-4715-bc9b-c1eea3c787fc["Output\nCollection: Individual Deconvolved Channels"];
  8 --> cbd8deec-7ea2-4715-bc9b-c1eea3c787fc;
  style cbd8deec-7ea2-4715-bc9b-c1eea3c787fc stroke:#2c3143,stroke-width:4px;
  9["Text transformation"];
  6 -->|out_file1| 9;
  10["Text transformation"];
  7 -->|out_file1| 10;
  11["Collection: Extract Stain Channel from Sub-Collections"];
  8 -->|output| 11;
  23ea738b-06ae-4688-ab4a-b29c196a9cfa["Output\nSelected Stain Channel"];
  11 --> 23ea738b-06ae-4688-ab4a-b29c196a9cfa;
  style 23ea738b-06ae-4688-ab4a-b29c196a9cfa stroke:#2c3143,stroke-width:4px;
  12["Paste"];
  9 -->|output| 12;
  10 -->|output| 12;
  13["Threshold Stain Channel Collection"];
  11 -->|output| 13;
  a3923c7b-8253-4578-9647-b11f5bbd91a6["Output\nSelected Stain Channel Thresholded"];
  13 --> a3923c7b-8253-4578-9647-b11f5bbd91a6;
  style a3923c7b-8253-4578-9647-b11f5bbd91a6 stroke:#2c3143,stroke-width:4px;
  14["Compute"];
  12 -->|out_file1| 14;
  15["Generate ROIs of stained region"];
  13 -->|output| 15;
  21505140-b70c-4dab-ba64-46e68c2121c7["Output\nROIs"];
  15 --> 21505140-b70c-4dab-ba64-46e68c2121c7;
  style 21505140-b70c-4dab-ba64-46e68c2121c7 stroke:#2c3143,stroke-width:4px;
  b05b07b2-2e6c-4d58-a92a-88c4c32828c3["Output\nROIs Image"];
  15 --> b05b07b2-2e6c-4d58-a92a-88c4c32828c3;
  style b05b07b2-2e6c-4d58-a92a-88c4c32828c3 stroke:#2c3143,stroke-width:4px;
  16["Extract Image Features"];
  13 -->|output| 16;
  11 -->|output| 16;
  19b9fc98-e80e-48f6-8bd9-a23a59e09e84["Output\nCollection of Tabular: Staining Quantification Results"];
  16 --> 19b9fc98-e80e-48f6-8bd9-a23a59e09e84;
  style 19b9fc98-e80e-48f6-8bd9-a23a59e09e84 stroke:#2c3143,stroke-width:4px;
  17["Cut"];
  14 -->|out_file1| 17;
  18["Prepare Header Source Dataset"];
  16 -->|output| 18;
  19["Extract"];
  16 -->|output| 19;
  20["Extract element identifiers"];
  16 -->|output| 20;
  21["Collapse Collection"];
  17 -->|out_file1| 21;
  22["Header Extraction"];
  18 -->|output| 22;
  23["Collapse Collection into one file"];
  19 -->|out_file1| 23;
  24["Concatenate datasets"];
  2 -->|outfile| 24;
  21 -->|output| 24;
  25["Paste header with Sample ID"];
  1 -->|outfile| 25;
  22 -->|out_file1| 25;
  26["Paste Sample Names with Tabular Results"];
  20 -->|output| 26;
  23 -->|output| 26;
  27["Tabular: Staining Feature Results"];
  25 -->|out_file1| 27;
  26 -->|out_file1| 27;
  28["Paste"];
  27 -->|out_file1| 28;
  24 -->|out_file1| 28;
  29["Percent area computation"];
  28 -->|out_file1| 29;
  1c3f7fd0-bad7-4891-9f95-f1346e44c20f["Output\nTabular File: Staining Feature Results"];
  29 --> 1c3f7fd0-bad7-4891-9f95-f1346e44c20f;
  style 1c3f7fd0-bad7-4891-9f95-f1346e44c20f stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

Tools

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Hands On: Importing a workflow

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. Provide your workflow
   • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
   • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/imaging/tutorials/stain-quantification-color-deconvolution/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows