multiplex-tissue-microarray-analysis/main

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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

SEEK ID: https://workflowhub.eu/workflows/1745?version=2

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
  • File?
Markers File Markers File File specifying marker names and autofluorescence channels to subtract
  • File
Phenotype workflow Phenotype workflow Scimap phenotype workflow
  • File
Registered Images Registered Images Collection of registered OME-TIFF images
  • File[]

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 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
  • File
Background subtracted markers Background subtracted markers n/a
  • File
Segmented Multiplexed Mask Segmented Multiplexed Mask n/a
  • File
Primary Mask Quantification Primary Mask Quantification n/a
  • File
phenotyped adata phenotyped adata n/a
  • File
Squidpy Spatial Scatterplots Squidpy Spatial Scatterplots n/a
  • File
Vitessce HTML Vitessce HTML n/a
  • File
Merged anndata Merged anndata n/a
  • File
Spatial Scatterplot Montage Spatial Scatterplot Montage n/a
  • File
Vitessce Dashboard Vitessce Dashboard n/a
  • File
Interaction Matrix Plot Interaction Matrix Plot n/a
  • File
Interaction Matrix Anndata Interaction Matrix Anndata n/a
  • File
Multisample barplot Multisample barplot n/a
  • File
Spatial Interaction Montage Spatial Interaction Montage n/a
  • File

Version History

v0.1.1 (latest) Created 24th Jun 2025 at 03:01 by WorkflowHub Bot

Updated to v0.1.1


Frozen v0.1.1 a130ec0

v0.1 (earliest) Created 22nd Jun 2025 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 1929e69
help Creators and Submitter
Creator
  • Cameron Watson
Submitter
Tool
anndata
License
MIT License
Activity

Views: 19   Downloads: 3   Runs: 0

Created: 22nd Jun 2025 at 03:01

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