Voronoi segmentation

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nImage"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nSeeds"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Convert image format"];
  0 -->|output| 2;
  09e98f2a-17b3-429b-877d-93de63ca7e1a["Output\nSingle channel image"];
  2 --> 09e98f2a-17b3-429b-877d-93de63ca7e1a;
  style 09e98f2a-17b3-429b-877d-93de63ca7e1a stroke:#2c3143,stroke-width:4px;
  3["Convert binary image to label map"];
  1 -->|output| 3;
  4d2a861c-3746-4c24-9b81-96d8f7a710d4["Output\nlabel map"];
  3 --> 4d2a861c-3746-4c24-9b81-96d8f7a710d4;
  style 4d2a861c-3746-4c24-9b81-96d8f7a710d4 stroke:#2c3143,stroke-width:4px;
  4["Convert single-channel to multi-channel image"];
  2 -->|output| 4;
  66990d3d-7b19-43f6-ac5a-ecd5557bff35["Output\nmulti-channel image"];
  4 --> 66990d3d-7b19-43f6-ac5a-ecd5557bff35;
  style 66990d3d-7b19-43f6-ac5a-ecd5557bff35 stroke:#2c3143,stroke-width:4px;
  5["Filter 2-D image"];
  2 -->|output| 5;
  e030c644-5cb4-4c1e-8287-8fc6d2950490["Output\nSmoothed image"];
  5 --> e030c644-5cb4-4c1e-8287-8fc6d2950490;
  style e030c644-5cb4-4c1e-8287-8fc6d2950490 stroke:#2c3143,stroke-width:4px;
  6["Compute Voronoi tessellation"];
  3 -->|output| 6;
  af96320e-5fa7-49d2-831b-bb438f8b2d73["Output\ntesselation"];
  6 --> af96320e-5fa7-49d2-831b-bb438f8b2d73;
  style af96320e-5fa7-49d2-831b-bb438f8b2d73 stroke:#2c3143,stroke-width:4px;
  7["Threshold image"];
  5 -->|output| 7;
  633e495b-ca86-451b-836c-bfceeb8d25ee["Output\nmask"];
  7 --> 633e495b-ca86-451b-836c-bfceeb8d25ee;
  style 633e495b-ca86-451b-836c-bfceeb8d25ee stroke:#2c3143,stroke-width:4px;
  8["Count objects in label map"];
  6 -->|result| 8;
  b977eb0c-e874-439f-b42b-756d6a864112["Output\nobject count"];
  8 --> b977eb0c-e874-439f-b42b-756d6a864112;
  style b977eb0c-e874-439f-b42b-756d6a864112 stroke:#2c3143,stroke-width:4px;
  9["Extract image features"];
  6 -->|result| 9;
  2 -->|output| 9;
  5a94a425-9000-4083-aae7-232ea01ae215["Output\nimage features"];
  9 --> 5a94a425-9000-4083-aae7-232ea01ae215;
  style 5a94a425-9000-4083-aae7-232ea01ae215 stroke:#2c3143,stroke-width:4px;
  10["Process images using arithmetic expressions"];
  6 -->|result| 10;
  1 -->|output| 10;
  7 -->|output| 10;
  45f919dd-298f-4e94-a390-e73537b5fedb["Output\nsegmentation"];
  10 --> 45f919dd-298f-4e94-a390-e73537b5fedb;
  style 45f919dd-298f-4e94-a390-e73537b5fedb stroke:#2c3143,stroke-width:4px;
  11["Colorize label map"];
  10 -->|result| 11;
  6903fd1b-304a-4e4a-a529-8f3643bcd445["Output\ncolorized label map"];
  11 --> 6903fd1b-304a-4e4a-a529-8f3643bcd445;
  style 6903fd1b-304a-4e4a-a529-8f3643bcd445 stroke:#2c3143,stroke-width:4px;
  12["Overlay images"];
  4 -->|output| 12;
  11 -->|output| 12;
  2adb0afd-923f-4641-bafb-10eaca09a4e0["Output\nsegmented image"];
  12 --> 2adb0afd-923f-4641-bafb-10eaca09a4e0;
  style 2adb0afd-923f-4641-bafb-10eaca09a4e0 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/voronoi-segmentation/workflows/Voronoi-segmentation.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