ISCC - image analysis workflow example

imaging-iscc-suite/iscc---image-analysis-workflow-example

Author(s)
Maarten W. Paul
Version
1
Last updated
Feb 14, 2026
License
Apache-2.0
Tags
imaging
bioimaging

Features
Tutorial
Content Tracking and Verification in Galaxy Workflows with ISCC-SUM
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\noriginal_image"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nChannel selection"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Dataset\nsegmented image"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Split image along axes"];
  0 -->|output| 3;
  4["Generate ISCC-CODE"];
  2 -->|output| 4;
  5["Extract dataset"];
  3 -->|output| 5;
  1 -->|output| 5;
  6["Parse parameter value"];
  4 -->|output_file| 6;
  7["Otsu"];
  5 -->|output| 7;
  33221213-66f9-453f-b2a3-d69fcdaa7eb3["Output\notsu_segmented"];
  7 --> 33221213-66f9-453f-b2a3-d69fcdaa7eb3;
  style 33221213-66f9-453f-b2a3-d69fcdaa7eb3 stroke:#2c3143,stroke-width:4px;
  8["Verify ISCC-CODE"];
  6 -->|text_param| 8;
  7 -->|output| 8;
  4edb3676-7cb6-4c65-a497-09d71fb8caa9["Output\nISCC-code"];
  8 --> 4edb3676-7cb6-4c65-a497-09d71fb8caa9;
  style 4edb3676-7cb6-4c65-a497-09d71fb8caa9 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset original_image
Input parameter Channel selection
Input dataset segmented image

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.25.0+galaxy0 Threshold image Otsu
toolshed.g2.bx.psu.edu/repos/imgteam/iscc_sum_verify/iscc_sum_verify/0.1.0+galaxy1 Verify ISCC-CODE

Tools

Tool Links
__EXTRACT_DATASET__
param_value_from_file
toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.25.0+galaxy0
toolshed.g2.bx.psu.edu/repos/imgteam/iscc_sum/iscc_sum/0.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/imgteam/iscc_sum_verify/iscc_sum_verify/0.1.0+galaxy1
toolshed.g2.bx.psu.edu/repos/imgteam/split_image/ip_split_image/2.3.5+galaxy0

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 051cdfed6 2026-02-11 17:05:03 Add ISCC image analysis workflow example and related test files

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/imaging/tutorials/iscc-suite/workflows/ISCC---image-analysis-workflow-example.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