Image Learner - HAM10000

statistics-image_learner/main-workflow

Author(s)
Khai Dang, Paulo Cilas Morais Lyra Junior, Junhao Qiu, Jeremy Goecks
Version
1
Last updated
Jan 28, 2026
License
AGPL-3.0-or-later
Tags
HAM10000
Image_Classification
Skin_Lesion
Deep_Learning
Image_Learner
GLEAM

Features
Tutorial
GLEAM Image Learner - Validating Skin Lesion Classification on HAM10000
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\nselected_HAM10000_img_metadata_aug.csv"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nselected_HAM10000_img_96_size.zip"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Image Learner"];
  1 -->|output| 2;
  0 -->|output| 2;

Inputs

Input Label
Input dataset selected_HAM10000_img_metadata_aug.csv
Input dataset selected_HAM10000_img_96_size.zip

Outputs

From Output Label

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/goeckslab/image_learner/image_learner/0.1.5

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
2 6a8eb6666 2026-01-27 19:56:22 leakage‑aware testing
1 7d08e0c69 2025-12-24 21:59:08 image learner tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/statistics/tutorials/image_learner/workflows/main_workflow.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