Workflows

These workflows are associated with Object tracking using CellProfiler

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.

CP_object_tracking_example

Last updated Mar 17, 2021

Launch in Tutorial Mode
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Main Galaxy Europe Galaxy Australia Galaxy France Import to another server (≥23.0+ only!) 
flowchart TD
  0["Starting Modules"];
  1["ℹ️ Input Dataset\nInput dataset"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ColorToGray"];
  0 -->|output_pipeline| 2;
  3["Unzip"];
  1 -->|output| 3;
  4["IdentifyPrimaryObjects"];
  2 -->|output_pipeline| 4;
  5["MeasureObjectSizeShape"];
  4 -->|output_pipeline| 5;
  6["MeasureObjectIntensity"];
  5 -->|output_pipeline| 6;
  7["TrackObjects"];
  6 -->|output_pipeline| 7;
  8["OverlayOutlines"];
  7 -->|output_pipeline| 8;
  9["Tile"];
  8 -->|output_pipeline| 9;
  10["SaveImages"];
  9 -->|output_pipeline| 10;
  11["ExportToSpreadsheet"];
  10 -->|output_pipeline| 11;
  12["CellProfiler"];
  3 -->|unzipped| 12;
  11 -->|output_pipeline| 12;
  dab4a9ee-fb53-4c74-93f5-8a0c7f7eb13e["Output\nCellProfiler pipeline output files"];
  12 --> dab4a9ee-fb53-4c74-93f5-8a0c7f7eb13e;
  style dab4a9ee-fb53-4c74-93f5-8a0c7f7eb13e stroke:#2c3143,stroke-width:4px;

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