YOLO training and segmentation workflow

imaging-yolo-segmentation-training/main-workflow

Author(s)
nfdi4bioimage, Yi Sun, Arif Khan
Version
1
Last updated
Jul 25, 2025
License
GPL-3.0-or-later
Tags
yolo
bioimage

Features
Tutorial
Training Custom YOLO Models for Object Detection and Segmentation in Bioimages
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 Collection\nInput Images"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nYOLO Class File"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Perform histogram equalization"];
  0 -->|output| 2;
  3["Convert image format"];
  2 -->|output| 3;
  4["AnyLabeling Interactive"];
  3 -->|output| 4;
  5["Convert AnyLabeling JSON to YOLO text"];
  1 -->|output| 5;
  4 -->|al_output| 5;
  6["Perform YOLO training"];
  3 -->|output| 6;
  5 -->|output_yolo| 6;

Inputs

Input Label
Input dataset collection Input Images
Input dataset YOLO Class File

Outputs

From Output Label

Tools

Tool Links
interactive_tool_anylabeling
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/bgruening/json2yolosegment/json2yolosegment/8.3.0+galaxy2
toolshed.g2.bx.psu.edu/repos/bgruening/yolo_training/yolo_training/8.3.0+galaxy2
toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.18.1+galaxy0 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 de584b705 2025-07-25 10:02:08 new yolo training tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/imaging/tutorials/yolo-segmentation-training/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