2025_2D_spot_detection

imaging-2D-spot-detection/2025-2d-spot-detection

Author(s)
Riccardo
Version
1
Last updated
Mar 20, 2025
License
MIT
Tags
Segmentation
bioimaging
smFISH
IDR

Features
Tutorial
Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00321
RO-Crate logo with flask Download Workflow RO-Crate
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Parameter\nIDR IDs"];
  style 0 fill:#ded,stroke:#393,stroke-width:4px;
  1["ℹ️ Input Parameter\nChannel to analyze"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Parameter\nz-stack"];
  style 2 fill:#ded,stroke:#393,stroke-width:4px;
  3["Download IDR/OMERO"];
  0 -->|output| 3;
  1 -->|output| 3;
  2 -->|output| 3;
  4["Unzip"];
  3 -->|output_tar| 4;
  5["IDR Image IDs"];
  4 -->|unzipped| 5;
  6["Perform 2-D spot detection"];
  5 -->|output| 6;
  7["Convert point coordinates to label map"];
  6 -->|fn_out| 7;
  8["Overlay images"];
  5 -->|output| 8;
  7 -->|output| 8;
  f3538bf0-0dc6-4237-a2ad-bdf539b01c70["Output\nout_png"];
  8 --> f3538bf0-0dc6-4237-a2ad-bdf539b01c70;
  style f3538bf0-0dc6-4237-a2ad-bdf539b01c70 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input parameter IDR IDs
Input parameter Channel to analyze
Input parameter z-stack

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.4+galaxy4 Overlay images

Tools

Tool Links
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/overlay_images/ip_overlay_images/0.0.4+galaxy4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/points2labelimage/ip_points_to_label/0.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/spot_detection_2d/ip_spot_detection_2d/0.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/0.45 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
4 99ec37984 2025-03-19 20:37:04 Fix the workflo folder
3 8e8f1b8e8 2025-03-19 10:20:14 added the workflow file
2 5db67eef2 2025-03-18 21:09:35 remove workflow
1 d37575ec5 2025-03-18 19:46:04 Add the 2D spot detection tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/imaging/tutorials/2D-spot-detection/workflows/2025_2D_spot_detection.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