Segmentation of Anatomical Structures in Medical Images

Run Workflow in Galaxy

• Galaxy Main
• Galaxy Europe
• Galaxy France
• Galaxy Australia
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Parameter\nbones_threshold_huv"];
  style 0 fill:#ded,stroke:#393,stroke-width:4px;
  1["ℹ️ Input Parameter\ny_tol_bones_px"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Collection\ndicom_series"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Create header"];
  4["Compose text parameter value"];
  1 -->|output| 4;
  5["Convert DICOM to TIFF"];
  2 -->|output| 5;
  6["Add ”centroid_y” rule"];
  3 -->|outfile| 6;
  7["Add ”label” rule"];
  3 -->|outfile| 7;
  8["Concatenate images or channels"];
  5 -->|output| 8;
  9["Convert"];
  6 -->|outfile| 9;
  10["Convert"];
  7 -->|outfile| 10;
  11["Scale image"];
  8 -->|output| 11;
  12["Clip image intensities"];
  11 -->|output| 12;
  13["Threshold image"];
  12 -->|output| 13;
  0 -->|output| 13;
  14["Apply ridge filter"];
  12 -->|output| 14;
  15["Convert binary image to label map"];
  13 -->|output| 15;
  16["Threshold image"];
  14 -->|output| 16;
  17["Extract image features"];
  15 -->|output| 17;
  18["Convert binary image to label map"];
  16 -->|output| 18;
  19["Query Tabular"];
  17 -->|output| 19;
  20["Extract image features"];
  18 -->|output| 20;
  21["Compute"];
  19 -->|output| 21;
  4 -->|out1| 21;
  22["Query Tabular"];
  20 -->|output| 22;
  23["Parse parameter value"];
  21 -->|out_file1| 23;
  24["Parse parameter value"];
  22 -->|output| 24;
  25["Replace Text"];
  9 -->|out_file1| 25;
  23 -->|text_param| 25;
  26["Replace Text"];
  10 -->|out_file1| 26;
  24 -->|text_param| 26;
  27["Filter label map by rules"];
  17 -->|output| 27;
  15 -->|output| 27;
  25 -->|outfile| 27;
  8fa03bee-9e05-4f98-9816-20a6ab4d37cb["Output\nsegm_bones"];
  27 --> 8fa03bee-9e05-4f98-9816-20a6ab4d37cb;
  style 8fa03bee-9e05-4f98-9816-20a6ab4d37cb stroke:#2c3143,stroke-width:4px;
  28["Filter label map by rules"];
  20 -->|output| 28;
  18 -->|output| 28;
  26 -->|outfile| 28;
  9d82b7c6-8f5c-4523-aac2-21ec66030e62["Output\nsegm_aorticbif"];
  28 --> 9d82b7c6-8f5c-4523-aac2-21ec66030e62;
  style 9d82b7c6-8f5c-4523-aac2-21ec66030e62 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/dicom-anatomical-3d/workflows/dicom-anatomical-3d.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