GTN_Exemplar_002_TMA_workflow_Feb2025
1.0

Workflow Type: Galaxy

End-to-End Tissue Microarray Analysis with Galaxy-ME

Associated Tutorial

This workflows is part of the tutorial End-to-End Tissue Microarray Image Analysis with Galaxy-ME, available in the GTN

Features

Thanks to...

Workflow Author(s): Cameron Watson

Tutorial Author(s): Cameron Watson, Allison Creason

Tutorial Contributor(s): Leonid Kostrykin, Beatriz Serrano-Solano, Helena Rasche, Saskia Hiltemann, Cameron Watson

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
PhenotypeWorkflow #main/PhenotypeWorkflow Scimap formatted phenotype workflow
  • File
Raw cycle images #main/Raw cycle images Raw TIFF images (CZI, TIFF) in an round-ordered list
  • array containing
    • File
markers.csv #main/markers.csv CSV file containing marker names
  • File

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+galaxy0
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
  • File
Converted image #main/Converted image n/a
  • File
DFP images #main/DFP images n/a
  • File
Dearray images #main/Dearray images n/a
  • File
Dearray masks #main/Dearray masks n/a
  • File
FFP images #main/FFP images n/a
  • File
Nuclear mask #main/Nuclear mask n/a
  • File
Phenotyped feature table #main/Phenotyped feature table n/a
  • File
Primary Mask Quantification #main/Primary Mask Quantification n/a
  • File
Registered image #main/Registered image n/a
  • File
Renamed image #main/Renamed image n/a
  • File
TMA dearray map #main/TMA dearray map n/a
  • File
Vitessce dashboard #main/Vitessce dashboard n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:56 by GTN Bot

Added/updated 4 files


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Created: 2nd Jun 2025 at 10:56

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