tissue-microarray-analysis/main

Complete 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	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+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	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 Config	#main/Vitessce Dashboard Config	n/a	File
Vitessce dashboard	#main/Vitessce dashboard	n/a	File

tissue-microarray-analysis/main
v0.1

Inputs

Steps

Outputs

Version History

v0.1 (earliest) Created 14th Apr 2025 at 03:02 by WorkflowHub Bot

Creator

Submitter

tissue-microarray-analysis/main v0.1

Inputs

Steps

Outputs

Version History

v0.1 (earliest) Created 14th Apr 2025 at 03:02 by WorkflowHub Bot

Creator

Submitter

Related items

tissue-microarray-analysis/main
v0.1