GTN_Exemplar_002_TMA

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

Associated Tutorial

This workflows is part of the tutorial GTN_Exemplar_002_TMA_workflow, available in the GTN

Tutorial Author(s): Cameron Watson, Allison Creason

Inputs

ID	Name	Description	Type
Input Dataset Collection	#main/Input Dataset Collection	n/a	array containing File
PhenotypeWorkflow	#main/PhenotypeWorkflow	n/a	File
markers.csv	#main/markers.csv	n/a	File

Steps

ID	Name	Description
3	BaSiC Illumination	toolshed.g2.bx.psu.edu/repos/perssond/basic_illumination/basic_illumination/1.0.3+galaxy1
4	ASHLAR	toolshed.g2.bx.psu.edu/repos/perssond/ashlar/ashlar/1.14.0+galaxy1
5	UNetCoreograph	toolshed.g2.bx.psu.edu/repos/perssond/coreograph/unet_coreograph/2.2.8+galaxy1
6	Mesmer	toolshed.g2.bx.psu.edu/repos/goeckslab/mesmer/mesmer/0.12.3+galaxy2
7	Convert image	toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy0
8	MCQUANT	toolshed.g2.bx.psu.edu/repos/perssond/quantification/quantification/1.5.3+galaxy1
9	Rename OME-TIFF Channels	toolshed.g2.bx.psu.edu/repos/goeckslab/rename_tiff_channels/rename_tiff_channels/0.0.1+galaxy1
10	Convert McMicro Output to Anndata	toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_mcmicro_to_anndata/scimap_mcmicro_to_anndata/0.17.7+galaxy0
11	Single Cell Phenotyping	toolshed.g2.bx.psu.edu/repos/goeckslab/scimap_phenotyping/scimap_phenotyping/0.17.7+galaxy0
12	Vitessce Visualization	toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/1.0.4+galaxy0

Outputs

ID	Name	Description	Type
Mesmer on input dataset(s): Mask	#main/Mesmer on input dataset(s): Mask	n/a	File
Primary Mask Quantification	#main/Primary Mask Quantification	n/a	File
_anonymous_output_1	#main/_anonymous_output_1	n/a	File
_anonymous_output_10	#main/_anonymous_output_10	n/a	File
_anonymous_output_11	#main/_anonymous_output_11	n/a	File
_anonymous_output_2	#main/_anonymous_output_2	n/a	File
_anonymous_output_3	#main/_anonymous_output_3	n/a	File
_anonymous_output_4	#main/_anonymous_output_4	n/a	File
_anonymous_output_5	#main/_anonymous_output_5	n/a	File
_anonymous_output_6	#main/_anonymous_output_6	n/a	File
_anonymous_output_7	#main/_anonymous_output_7	n/a	File
_anonymous_output_8	#main/_anonymous_output_8	n/a	File
_anonymous_output_9	#main/_anonymous_output_9	n/a	File

Version History

Added/updated 4 files

Open master 759b4a3

Added/updated 4 files

Frozen 3.0 346a035