Segmentation_Values_Testing

imaging-parameter-tuning/segmentation-values-testing

Author(s)
Riccardo Massei
Version
1
Last updated
Apr 28, 2025
License
MIT
Tags
imaging

Features
Tutorial
Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy
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\nImage to segment"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nSigma Values"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nGround Truth Image"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Split by group"];
  1 -->|output| 3;
  4["Parse parameter value"];
  3 -->|split_output| 4;
  5["Filter 2-D image"];
  4 -->|float_param| 5;
  0 -->|output| 5;
  6["Perform histogram equalization"];
  5 -->|output| 6;
  7["Threshold image"];
  6 -->|output| 7;
  8["Compute image segmentation and object detection performance measures"];
  2 -->|output| 8;
  7 -->|output| 8;
  9["Collapse Collection"];
  8 -->|results| 9;
  54631b7f-9caa-476a-a194-1b8a862e12b6["Output\noutput"];
  9 --> 54631b7f-9caa-476a-a194-1b8a862e12b6;
  style 54631b7f-9caa-476a-a194-1b8a862e12b6 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset Image to segment
Input dataset Sigma Values
Input dataset Ground Truth Image

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 Collapse Collection

Tools

Tool Links
param_value_from_file
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6 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/2d_histogram_equalization/ip_histogram_equalization/0.18.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/1.12.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/segmetrics/ip_segmetrics/1.4.0-2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 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
5 17f4d874e 2025-04-25 13:31:12 small fixes
4 45da65db2 2025-04-25 13:09:45 Tutorial update with new images suggested in the review
3 83a3289fe 2025-04-22 20:47:09 Updated the workflow files
2 c9b8c1b9c 2025-04-22 20:40:22 Updated the workflow with good practices
1 1e52b6845 2025-04-22 17:12:05 Added workflow test

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/imaging/tutorials/parameter-tuning/workflows/Segmentation_Values_Testing.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