multiplex-tissue-microarray-analysis/main
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Workflow Type: Galaxy
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Perform background subtraction, nuclear segmentation, feature quantification, cellular phenotyping, spatial analysis, and interactive visualization of registered TMA core multiplex tissue images
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Manual Gates | Manual Gates | CSV with log1p intensity manual gates per marker. Markers not specified will be GMM auto thresholded |
|
| Markers File | Markers File | File specifying marker names and autofluorescence channels to subtract |
|
| Phenotype workflow | Phenotype workflow | Scimap phenotype workflow |
|
| Registered Images | Registered Images | Collection of registered OME-TIFF images |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Extract element identifiers | toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2 |
| 5 | Background subtraction | toolshed.g2.bx.psu.edu/repos/goeckslab/backsub/backsub/0.4.1+galaxy0 |
| 6 | Select first | Show beginning1 |
| 7 | Perform segmentation of multiplexed tissue data | toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/0.12.3+galaxy3 |
| 8 | MCQUANT | toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/1.6.0+galaxy0 |
| 9 | Convert McMicro Output to Anndata | toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/2.1.0+galaxy3 |
| 10 | Single Cell Phenotyping | toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/2.1.0+galaxy3 |
| 11 | AnnData Operations | toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0 |
| 12 | Extract dataset | __EXTRACT_DATASET__ |
| 13 | Filter collection | __FILTER_FROM_FILE__ |
| 14 | Create spatial scatterplot | toolshed.g2.bx.psu.edu/repos/goeckslab/squidpy_scatter/squidpy_scatter/1.5.0+galaxy2 |
| 15 | Vitessce | toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/3.5.1+galaxy2 |
| 16 | Create spatial neighbors | toolshed.g2.bx.psu.edu/repos/goeckslab/squidpy_spatial/squidpy_spatial/1.5.0+galaxy2 |
| 17 | Merge anndata files | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy1 |
| 18 | Create Scatterplot Montage | toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.45+galaxy0 |
| 19 | Replace | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.5+galaxy2 |
| 20 | Compute interaction matrix for clusters | toolshed.g2.bx.psu.edu/repos/goeckslab/squidpy_spatial/squidpy_spatial/1.5.0+galaxy2 |
| 21 | Spatial plotting functions | toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_plotting/scimap_plotting/2.1.0+galaxy3 |
| 22 | Extract first vitessce config | __EXTRACT_DATASET__ |
| 23 | Create Spatial Interaction Montage | toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage/1.3.45+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Background subtracted images | Background subtracted images | n/a |
|
| Background subtracted markers | Background subtracted markers | n/a |
|
| Segmented Multiplexed Mask | Segmented Multiplexed Mask | n/a |
|
| Primary Mask Quantification | Primary Mask Quantification | n/a |
|
| phenotyped adata | phenotyped adata | n/a |
|
| Squidpy Spatial Scatterplots | Squidpy Spatial Scatterplots | n/a |
|
| Vitessce HTML | Vitessce HTML | n/a |
|
| Merged anndata | Merged anndata | n/a |
|
| Spatial Scatterplot Montage | Spatial Scatterplot Montage | n/a |
|
| Vitessce Dashboard | Vitessce Dashboard | n/a |
|
| Interaction Matrix Anndata | Interaction Matrix Anndata | n/a |
|
| Interaction Matrix Plot | Interaction Matrix Plot | n/a |
|
| Multisample barplot | Multisample barplot | n/a |
|
| Final Dashboard for Report | Final Dashboard for Report | n/a |
|
| Spatial Interaction Montage | Spatial Interaction Montage | n/a |
|
Version History
v0.1.1 (latest) Created 24th Jun 2025 at 03:01 by WorkflowHub Bot
Updated to v0.1.1
Frozen
v0.1.1a130ec0
v0.1 (earliest) Created 22nd Jun 2025 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
1929e69
Creators and Submitter
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Views: 1322 Downloads: 1438 Runs: 1
Created: 22nd Jun 2025 at 03:01
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