Capturing mitoflashes

imaging-detection-of-mitoflashes/capturing-mitoflashes

Author(s)
BMCV Group, Heidelberg University
Version
1
Last updated
Nov 20, 2024
License
CC-BY-4.0
Tags
mito-flash
mitochondrion_tracking

Features
Tutorial
Tracking of mitochondria and capturing mitoflashes
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["Mitochondrion detection"];
  b84bfb33-15eb-4984-b109-fab32f3813df["Output\nSpot Detection of Mitoflashes"];
  0 --> b84bfb33-15eb-4984-b109-fab32f3813df;
  style b84bfb33-15eb-4984-b109-fab32f3813df stroke:#2c3143,stroke-width:4px;
  1["Mitochondrion tracking"];
  0 -->|fn_out| 1;
  a25e8913-0019-4dd3-aed4-8138e7dd8da3["Output\nSpot Detection Across Frames"];
  1 --> a25e8913-0019-4dd3-aed4-8138e7dd8da3;
  style a25e8913-0019-4dd3-aed4-8138e7dd8da3 stroke:#2c3143,stroke-width:4px;
  2["Curve fitting to measured intensities"];
  1 -->|fn_out| 2;
  a978b043-f089-4d41-8f5d-0df99915dd45["Output\nCurve Fitting for Mitoflash Detection"];
  2 --> a978b043-f089-4d41-8f5d-0df99915dd45;
  style a978b043-f089-4d41-8f5d-0df99915dd45 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/imgteam/spot_detection_2d/ip_spot_detection_2d/0.0.1 Spot Detection Mitochondrion detection
toolshed.g2.bx.psu.edu/repos/imgteam/points_association_nn/ip_points_association_nn/0.0.3-2 Perform linking in time series (nearest neighbors) Mitochondrion tracking
toolshed.g2.bx.psu.edu/repos/imgteam/curve_fitting/ip_curve_fitting/0.0.3-2 Perform curve fitting Curve fitting to measured intensities

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/imgteam/curve_fitting/ip_curve_fitting/0.0.3-2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/points_association_nn/ip_points_association_nn/0.0.3-2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/spot_detection_2d/ip_spot_detection_2d/0.0.1 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
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • 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”
  • 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 92bc3176b 2024-11-12 12:48:42 workflow tests, test data and update

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/imaging/tutorials/detection-of-mitoflashes/workflows/Capturing-mitoflashes.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