Description

Unsupervised machine learning for cell type identification in multiplexed imaging using protein expression and cell neighborhood information without ground truth

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'test']

img_data{:bash}

:file

Quantification table with single cells as rows, markers (e.g. CD3 or CD8 but names do not have to match exactly) and X/Y coordinates as columns

*.csv

signature{:bash}

:file

Signature Matrix containing the definition of cell types according to markers

*.csv

high_thresholds{:bash}

:file

csv file with user-defined probability high thresholds for anchor cell (row 1) and index cell (row 2) definition

*.csv

low_thresholds{:bash}

:file

optional csv file with user-defined probability low thresholds for anchor cell (row 1) and index cell (row 2) definition

*.csv

Output

name:type
description
pattern

celltypes{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*results.csv{:bash}

:file

File with final celltype annotations concatenated to the original input quantification, due to the mechanism its non-deterministic

*.csv

quality{:bash}

*quality.csv{:bash}

:file

File with final calculated marker probabilities for inspection, non-deterministic

*.csv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

celesta
Apache-2.0

Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information

github.com/SchapiroLabor/mcmicro-celesta github.com/SchapiroLabor/mcmicro-celesta/blob/main/README.md https://github.com/plevritis-lab/CELESTA 10.1038/s41592-022-01498-z
maintainers
Github user LukasHats
Github user ArozHada
get in touch
Ask a question on Slack Open an issue on GitHub