tissue-microarray-analysis/main
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Run on GalaxyComplete multiplex tissue image (MTI) analysis pipeline for tissue microarray (TMA) data imaged using cyclic immunofluorescence: Performs illumination correction, stitching and registration, and tissue microarray segmentation. Tissue-segmented images undergo nuclear segmentation, cell/nuclei feature quantification (mean marker intensities, cell coordinates, and morphological features), and cell phenotyping. Produces outputs that are compatible with downstream single-cell/spatial analysis and interactive image viewers including: Pyramidal OME-TIFF images, nuclear segmentation masks (TIFF), quantified feature tables (CSV, h5ad) with cell type annotations, and an interactive Vitessce dashboard that combines image viewing with linked single-cell data visualizations.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| PhenotypeWorkflow | #main/PhenotypeWorkflow | Scimap formatted phenotype workflow |
|
| Raw cycle images | #main/Raw cycle images | Raw TIFF images (CZI, TIFF) in an round-ordered list |
|
| markers.csv | #main/markers.csv | CSV file containing marker names |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Illumination correction with Basic | Illumination correction toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/1.1.1+galaxy2 |
| 4 | Stitching and registration with Ashlar | Stitching and registration toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/1.18.0+galaxy1 |
| 5 | TMA dearray with UNetCoreograph | TMA dearray toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/2.2.8+galaxy1 |
| 6 | Nuclear segmentation | Nuclear segmentation toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/0.12.3+galaxy3 |
| 7 | Convert dearray images to OME-TIFF | Convert to OME-TIFF toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy3 |
| 8 | Cell feature quantification with MC-Quant | Quantify cell features toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/1.6.0+galaxy0 |
| 9 | Rename OME-TIFF channels | Rename OME-TIFF channels toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/rename_tiff_channels/0.0.2+galaxy1 |
| 10 | Convert to Anndata | Convert to Anndata toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/2.1.0+galaxy2 |
| 11 | Scimap phenotyping | Scimap phenotyping toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/2.1.0+galaxy2 |
| 12 | Create a Vitessce dashboard | Create a Vitessce dashboard toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/3.5.1+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Anndata feature table | #main/Anndata feature table | n/a |
|
| Converted image | #main/Converted image | n/a |
|
| DFP images | #main/DFP images | n/a |
|
| Dearray images | #main/Dearray images | n/a |
|
| Dearray masks | #main/Dearray masks | n/a |
|
| FFP images | #main/FFP images | n/a |
|
| Nuclear mask | #main/Nuclear mask | n/a |
|
| Phenotyped feature table | #main/Phenotyped feature table | n/a |
|
| Primary Mask Quantification | #main/Primary Mask Quantification | n/a |
|
| Registered image | #main/Registered image | n/a |
|
| Renamed image | #main/Renamed image | n/a |
|
| TMA dearray map | #main/TMA dearray map | n/a |
|
| Vitessce Dashboard Config | #main/Vitessce Dashboard Config | n/a |
|
| Vitessce dashboard | #main/Vitessce dashboard | n/a |
|
Version History
v0.1.1 (latest) Created 22nd Jun 2025 at 03:01 by WorkflowHub Bot
Updated to v0.1.1
Frozen
v0.1.1ba7bdd3
v0.1 (earliest) Created 14th Apr 2025 at 03:02 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
f804a80
Creators and Submitter
Views: 1793 Downloads: 1678 Runs: 2
Created: 14th Apr 2025 at 03:01
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Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
The Intergalactic Workflow Commission releases vetted analysis pipelines for the Galaxy platform.
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Public web page: https://iwc.galaxyproject.org/
