GTN_Exemplar_002_TMA_workflow

imaging-multiplex-tissue-imaging-TMA/main-workflow

Author(s)

Version
1
Last updated
Feb 14, 2023
License
None Specified, defaults to CC-BY-4.0
Tags
imaging

Features
Tutorial
End-to-End Tissue Microarray Image Analysis with Galaxy-ME
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00104
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 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;

Inputs

Input Label
Input dataset collection Input Dataset Collection
Input dataset markers.csv
Input dataset PhenotypeWorkflow

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/1.0.3+galaxy1 BaSiC Illumination
toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/1.14.0+galaxy1 ASHLAR
toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/2.2.8+galaxy1 UNetCoreograph
toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/0.12.3+galaxy2 Mesmer
toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy0 Convert image
toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/1.5.3+galaxy1 MCQUANT
toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/rename_tiff_channels/0.0.1+galaxy1 Rename OME-TIFF Channels
toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/0.17.7+galaxy0 Convert McMicro Output to Anndata
toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/0.17.7+galaxy0 Single Cell Phenotyping
toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/1.0.4+galaxy0 Vitessce Visualization

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/0.12.3+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/rename_tiff_channels/0.0.1+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/0.17.7+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/0.17.7+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/1.0.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/1.14.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/1.0.3+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/2.2.8+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/1.5.3+galaxy1 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
3 74c571972 2023-02-10 00:02:35 update tool IDs, params to tutorial; add updated workflow; add hands-on avivator example to tutorial
2 b0bac7415 2022-07-07 16:57:26 update tool IDs in MTI workflow for linting
1 aa2aba190 2022-07-04 04:58:40 Multiplex Imaging tutorial - initial push

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/imaging/tutorials/multiplex-tissue-imaging-TMA/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