Image prediction with BioImage.IO model

imaging-process-image-bioimageio/main-workflow

Author(s)
Diana Chiang Jurado, Leonid Kostrykin
Version
2
Last updated
Apr 14, 2025
License
CC-BY-4.0
Tags
imaging

Features
Tutorial
Using BioImage.IO models for image analysis in Galaxy
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00324
RO-Crate logo with flask Download Workflow RO-Crate
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nBioImage.IO Model"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nImage for Prediction"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Process image with BioImage.IO model"];
  1 -->|output| 2;
  0 -->|output| 2;
  3["Split image along axes"];
  2 -->|output_predicted_image| 3;
  4["Extract dataset"];
  3 -->|output| 4;
  5["Extract dataset"];
  3 -->|output| 5;
  6["Process images using arithmetic expressions"];
  4 -->|output| 6;
  5 -->|output| 6;
  7["Threshold image"];
  6 -->|result| 7;
  049ccf2f-7737-4a0c-b5b6-aad261f7e9f4["Output\noutput"];
  7 --> 049ccf2f-7737-4a0c-b5b6-aad261f7e9f4;
  style 049ccf2f-7737-4a0c-b5b6-aad261f7e9f4 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset BioImage.IO Model
Input dataset Image for Prediction

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy3 Threshold image

Tools

Tool Links
__EXTRACT_DATASET__
toolshed.g2.bx.psu.edu/repos/bgruening/bioimage_inference/bioimage_inference/2.4.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/image_math/image_math/1.26.4+galaxy2 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
6 653fd4079 2025-04-14 13:32:31 Fix main_workflow.ga
5 11a74021d 2025-04-14 13:09:17 Fix main_workflow.ga
4 09d2fc75a 2025-04-14 11:31:53 Update workflow and tests
3 e12c27217 2025-04-09 06:49:13 Update main_workflow.ga
2 441b6a18e 2025-04-04 09:59:26 Update topics/imaging/tutorials/process-image-bioimageio/workflows/main_workflow.ga
1 8eb670c66 2025-04-01 13:07:58 Add tutorial and images for BioImage.IO model processing

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/imaging/tutorials/process-image-bioimageio/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