CP_pipeline_IDR_training

Run Workflow in Galaxy

• Galaxy Main
• Galaxy Europe
• Galaxy France
• Galaxy Australia
• Import to another server (≥23.0+ only!)

flowchart TD
  0["Starting modules"];
  1["Download images"];
  2["Segment complete nuclei"];
  0 -->|output_pipeline| 2;
  3["Segmentation mask complete nuclei"];
  2 -->|output_pipeline| 3;
  4["Label nuclei"];
  3 -->|output_pipeline| 4;
  5["Save labelled nuclei"];
  4 -->|output_pipeline| 5;
  6["Detect dark holes in nuclei"];
  5 -->|output_pipeline| 6;
  7["Segment nucleoli that fall inside nuclei"];
  6 -->|output_pipeline| 7;
  8["Segment nucleoli"];
  7 -->|output_pipeline| 8;
  9["Convert the segmented nucleoli into an image"];
  8 -->|output_pipeline| 9;
  10["Combine masks nuclei + nucleoli"];
  9 -->|output_pipeline| 10;
  11["Save combined segmentation masks"];
  10 -->|output_pipeline| 11;
  12["Segment all nuclei"];
  11 -->|output_pipeline| 12;
  13["Segmentation mask nucleoli including cells touching borders"];
  12 -->|output_pipeline| 13;
  14["Extract background"];
  13 -->|output_pipeline| 14;
  15["Measure the image granularity"];
  14 -->|output_pipeline| 15;
  16["Measure the nuclei texture"];
  15 -->|output_pipeline| 16;
  17["Measure the nuclei intensity"];
  16 -->|output_pipeline| 17;
  18["Measure size and shape of nuclei and nucleoli"];
  17 -->|output_pipeline| 18;
  19["Relate nucleoli with their parent nuclei"];
  18 -->|output_pipeline| 19;
  20["Measure the image quality"];
  19 -->|output_pipeline| 20;
  21["Measure the area occupied by nuclei and nucleoli"];
  20 -->|output_pipeline| 21;
  22["Measure the image intensity"];
  21 -->|output_pipeline| 22;
  23["Export measurements"];
  22 -->|output_pipeline| 23;
  24["Run CellProfiler"];
  1 -->|output_tar| 24;
  23 -->|output_pipeline| 24;

Inputs

Outputs

Tools

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

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 galaxy-upload 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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/imaging/tutorials/tutorial-CP/workflows/main_workflow.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