Workflows

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, Leonid Kostrykin

Last updated Nov 6, 2024

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["Show image info"];
  0 -->|output| 1;
  2["Filter 2-D image"];
  0 -->|output| 2;
  3["Perform histogram equalization"];
  2 -->|output| 3;
  4["Threshold image"];
  2 -->|output| 4;
  5["Convert binary image to label map"];
  4 -->|output| 5;
  6["Overlay images"];
  3 -->|output| 6;
  5 -->|output| 6;
  d362c206-756d-4f04-82f0-bd6f24907e04["Output\nout_png"];
  6 --> d362c206-756d-4f04-82f0-bd6f24907e04;
  style d362c206-756d-4f04-82f0-bd6f24907e04 stroke:#2c3143,stroke-width:4px;
  7["Count objects in label map"];
  5 -->|output| 7;
  9c56017b-20c7-4ad3-8340-d36dd6b2e7b4["Output\noutput"];
  7 --> 9c56017b-20c7-4ad3-8340-d36dd6b2e7b4;
  style 9c56017b-20c7-4ad3-8340-d36dd6b2e7b4 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:

Video: Importing a workflow from URL