Workflows

These workflows are associated with End-to-End Tissue Microarray Image Analysis with Galaxy-ME

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.

GTN_Exemplar_002_TMA_workflow

Last updated Feb 14, 2023

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Tests: ❌ Results: Not yet automated

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flowchart TD
  0["ℹ️ Input Collection\nInput Dataset Collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nmarkers.csv"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nPhenotypeWorkflow"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["BaSiC Illumination"];
  0 -->|output| 3;
  4["ASHLAR"];
  3 -->|output_dfp| 4;
  3 -->|output_ffp| 4;
  0 -->|output| 4;
  1 -->|output| 4;
  5["UNetCoreograph"];
  4 -->|output| 5;
  6["Mesmer"];
  5 -->|tma_sections| 6;
  ee73bee3-59e7-4e1c-87fd-197b8eac7e15["Output\nMesmer on input dataset(s): Mask"];
  6 --> ee73bee3-59e7-4e1c-87fd-197b8eac7e15;
  style ee73bee3-59e7-4e1c-87fd-197b8eac7e15 stroke:#2c3143,stroke-width:4px;
  7["Convert image"];
  5 -->|tma_sections| 7;
  8["MCQUANT"];
  1 -->|output| 8;
  5 -->|tma_sections| 8;
  6 -->|mask| 8;
  fe28534a-2b3f-4ecc-8ba9-a106b2d1425c["Output\nPrimary Mask Quantification"];
  8 --> fe28534a-2b3f-4ecc-8ba9-a106b2d1425c;
  style fe28534a-2b3f-4ecc-8ba9-a106b2d1425c stroke:#2c3143,stroke-width:4px;
  9["Rename OME-TIFF Channels"];
  1 -->|output| 9;
  7 -->|output| 9;
  10["Convert McMicro Output to Anndata"];
  8 -->|cellmask| 10;
  11["Single Cell Phenotyping"];
  10 -->|outfile| 11;
  2 -->|output| 11;
  12["Vitessce Visualization"];
  11 -->|output| 12;
  9 -->|renamed_image| 12;
  6 -->|mask| 12;

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