Description

Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information

transcripts{:bash}

:file

Transcript ids, genes, revised positions, assignment probability, etc.

*transcript-metadata.{csv.gz,csv,parquet}

mode{:bash}

:string

Proseg preset mode

transcript_metadata_fmt{:bash}

:string

Format of the transcript metadata file

cell_metadata_fmt{:bash}

:file

Format of the cell metadata file

expected_counts_fmt{:bash}

:file

Format of the expected counts file

Output

name:type
description
pattern

transcript_metadata{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*transcript-metadata.{csv,csv.gz,parquet}{:bash}

:file

Transcript ids, genes, revised positions, assignment probability, etc.

*transcript-metadata.{csv.gz,csv,parquet}

union_cell_polygons{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*cell-polygons-union.geojson.gz{:bash}

:file

Union cell polygons

*cell-polygons-union.geojson.gz

cell_polygons{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*cell-polygons.geojson.gz{:bash}

:file

Cell polygons file

*cell-polygons.geojson.gz

cell_metadata{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*cell-metadata.{csv,csv.gz,parquet}{:bash}

:file

Cell metadata file

*cell-metadata.{csv.gz,csv,parquet}

cell_polygons_layers{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*cell-polygons-layers.geojson.gz{:bash}

:file

Cell polygon layers file

*cell-polygons-layers.geojson.gz

expected_counts{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*expected-counts.{csv,csv.gz,parquet}{:bash}

:file

Expected transcript counts file

*expected-counts.{csv.gz,csv,parquet}

maxpost_counts{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*maxpost-counts.{csv,csv.gz,parquet}{:bash}

:file

point estimate of counts per cell

*maxpost-counts.{csv.gz,csv,parquet}

output_rates{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*output-rates.{csv,csv.gz,parquet}{:bash}

:file

Estimated poisson expression rates for each cell

*output-rates.{csv.gz,csv,parquet}

cell_hulls{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*cell-hulls.{csv,csv.gz,parquet}{:bash}

:file

Cell convex hulls

*cell-hulls.{csv.gz,csv,parquet}

gene_metadata{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*gene-metadata.{csv,csv.gz,parquet}{:bash}

:file

gene metadata

*gene-metadata.{csv.gz,csv,parquet}

metagene_rates{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*metagene-rates.{csv,csv.gz,parquet}{:bash}

:file

metagene rates

*metagene-rates.{csv.gz,csv,parquet}

metagene_loadings{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*metagene-loadings.{csv,csv.gz,parquet}{:bash}

:file

metagene loadings

*metagene-loadings.{csv.gz,csv,parquet}

cell_voxels{:bash}

meta{:bash}

:map

Groovy Map containing sample information

*cell-voxels.{csv,csv.gz,parquet}{:bash}

:file

table of each voxel in each cell

*cell-voxels.{csv.gz,csv,parquet}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

proseg
GPLv3

Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics.

github.com/dcjones/proseg 10.1038/s41592-025-02697-0
maintainer
Github user derrik-gratz
get in touch
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