feature_extraction

imaging-hela-screen-analysis/feature-extraction

Author(s)
Till Korten, Leonid Kostrykin
Version
6
Last updated
Nov 6, 2024
License
MIT
Tags
imaging

Features
Tutorial
Analyse HeLa fluorescence siRNA screen
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00102
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\ninput image"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nfilter rules"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Filter 2-D image"];
  0 -->|output| 2;
  3["Threshold image"];
  2 -->|output| 3;
  4["Convert binary image to label map"];
  3 -->|output| 4;
  5["Extract image features"];
  4 -->|output| 5;
  6["Filter label map by rules"];
  5 -->|output| 6;
  4 -->|output| 6;
  1 -->|output| 6;
  f6f7f638-0f3c-404e-ab2e-5281a0393060["Output\noutput"];
  6 --> f6f7f638-0f3c-404e-ab2e-5281a0393060;
  style f6f7f638-0f3c-404e-ab2e-5281a0393060 stroke:#2c3143,stroke-width:4px;
  7["Extract image features"];
  6 -->|output| 7;
  0 -->|output| 7;
  31da5e27-19fe-465e-95f0-96d3f6dcaba4["Output\noutput"];
  7 --> 31da5e27-19fe-465e-95f0-96d3f6dcaba4;
  style 31da5e27-19fe-465e-95f0-96d3f6dcaba4 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset input image
Input dataset filter rules

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features/0.0.1-4 Filter label map by rules
toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.18.1+galaxy0 Extract image features

Tools

Tool Links
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_feature_extraction/ip_2d_feature_extraction/0.18.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/2d_filter_segmentation_by_features/ip_2d_filter_segmentation_by_features/0.0.1-4 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/binary2labelimage/ip_binary_to_labelimage/0.5+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
  • 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
8 347a40757 2024-11-06 15:33:40 Update feature_extraction.ga and fix tests
7 d1e807a66 2023-11-08 10:56:10 fixed json syntax
6 e34767b4a 2023-11-08 10:48:59 added `creator` and `license` fields
5 574ce45a0 2023-11-07 17:02:48 updated feature_extraction.ga
4 667ff3de9 2020-01-22 10:59:29 annotation
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 faf6d298a 2019-12-12 13:02:33 unflatten workflows
1 96462d6dc 2019-08-06 12:50:14 added second tutorial

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/imaging/tutorials/hela-screen-analysis/workflows/feature_extraction.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