Electrophoresis-Gel-Bands-Image-Analysis

imaging-electrophoresis-gel-bands-image-analysis/galaxy-workflow-electrophoresis-gel-bands-image-analysis

Author(s)
Reyhaneh Tavakoli-Koopaei, Diana Chiang Jurado
Version
1
Last updated
Aug 11, 2025
License
MIT
Tags
name:Bioimaging
name:Band_Intensity
name:QuPath
ROI
Electrophoresis_Gel

Features
Tutorial
Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:
RO-Crate logo with flask Download Workflow RO-Crate
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nElectropheresis-Gel.jpg"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Convert coordinates to label map"];
  2["Convert image format"];
  0 -->|output| 2;
  3["Extract image features"];
  1 -->|output| 3;
  4["Show image info"];
  2 -->|output| 4;
  5["Split image along axes"];
  2 -->|output| 5;
  6["QuPath"];
  2 -->|output| 6;
  ecf5b534-95d3-40d0-af1d-28480b447188["Output\noutputs"];
  6 --> ecf5b534-95d3-40d0-af1d-28480b447188;
  style ecf5b534-95d3-40d0-af1d-28480b447188 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Electropheresis-Gel.jpg

Outputs

From Output Label
interactive_tool_qupath QuPath

Tools

Tool Links
interactive_tool_qupath
toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_convert/graphicsmagick_image_convert/1.3.45+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.18.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/image_info/ip_imageinfo/5.7.1+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/points2labelimage/ip_points_to_label/0.4.1+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/split_image/ip_split_image/2.2.3+galaxy1 View in ToolShed

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

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands On: Importing a workflow
  1. Click on 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 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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
1 152686cfd 2025-08-04 05:20:01 The Galaxy workflow was updated

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/imaging/tutorials/electrophoresis-gel-bands-image-analysis/workflows/Galaxy-Workflow-Electrophoresis-Gel-Bands-Image-Analysis.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