These workflows are associated with Introduction to image analysis using Galaxy

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.

Workflow constructed from Tutorial 'Introduction to image analysis using Galaxy'
Till Korten

Last updated Nov 8, 2023

Launch in Tutorial Mode question
License: MIT
Tests: ✅ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Dataset\ninput_image"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Histogram equalization"];
  0 -->|output| 1;
  2["Image Info"];
  0 -->|output| 2;
  3["Filter Image"];
  0 -->|output| 3;
  4["Filter Image"];
  0 -->|output| 4;
  5["Convert image"];
  0 -->|output| 5;
  6["Convert image"];
  1 -->|output| 6;
  7["Auto Threshold"];
  3 -->|output| 7;
  8["Histogram equalization"];
  3 -->|output| 8;
  9["Binary 2 Label"];
  7 -->|output| 9;
  10["Convert image"];
  8 -->|output| 10;
  11["Overlay Images"];
  6 -->|output| 11;
  9 -->|output| 11;
  11 --> 85029ccb-ebb3-4a91-9ba3-d1daefd13efc;
  style 85029ccb-ebb3-4a91-9ba3-d1daefd13efc stroke:#2c3143,stroke-width:4px;
  12["Convert image"];
  9 -->|output| 12;
  13["Count Objects"];
  9 -->|output| 13;
  13 --> 1446f4bf-b031-405a-84f0-88acc1a5c8a3;
  style 1446f4bf-b031-405a-84f0-88acc1a5c8a3 stroke:#2c3143,stroke-width:4px;

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on galaxy-upload Import at the top-right of the screen
  • 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”
  • Click the Import workflow button

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