modules/proseg_proseg

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

segmentationspatialtranscriptomics

https://github.com/nf-core/modules/[...]/modules/nf-core/proseg/proseg

Description

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

Input

name:type

description

pattern

`meta:map`

Groovy Map containing sample information

`transcripts:file`

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

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

`mode:string`

Proseg preset mode

`transcript_metadata_fmt:string`

Format of the transcript metadata file

`cell_metadata_fmt:file`

Format of the cell metadata file

`expected_counts_fmt:file`

Format of the expected counts file

Output

name:type

description

pattern

`transcript_metadata`

`meta:map`

Groovy Map containing sample information

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

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

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

`union_cell_polygons`

`meta:map`

Groovy Map containing sample information

`*cell-polygons-union.geojson.gz:file`

Union cell polygons

*cell-polygons-union.geojson.gz

`cell_polygons`

`meta:map`

Groovy Map containing sample information

`*cell-polygons.geojson.gz:file`

Cell polygons file

*cell-polygons.geojson.gz

`cell_metadata`

`meta:map`

Groovy Map containing sample information

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

Cell metadata file

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

`cell_polygons_layers`

`meta:map`

Groovy Map containing sample information

`*cell-polygons-layers.geojson.gz:file`

Cell polygon layers file

*cell-polygons-layers.geojson.gz

`expected_counts`

`meta:map`

Groovy Map containing sample information

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

Expected transcript counts file

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

`maxpost_counts`

`meta:map`

Groovy Map containing sample information

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

point estimate of counts per cell

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

`output_rates`

`meta:map`

Groovy Map containing sample information

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

Estimated poisson expression rates for each cell

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

`cell_hulls`

`meta:map`

Groovy Map containing sample information

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

Cell convex hulls

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

`gene_metadata`

`meta:map`

Groovy Map containing sample information

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

gene metadata

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

`metagene_rates`

`meta:map`

Groovy Map containing sample information

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

metagene rates

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

`metagene_loadings`

`meta:map`

Groovy Map containing sample information

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

metagene loadings

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

`cell_voxels`

`meta:map`

Groovy Map containing sample information

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

table of each voxel in each cell

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

`versions`

`versions.yml: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

modules/proseg_proseg

Description

Input

meta:map

transcripts:file

mode:string

transcript_metadata_fmt:string

cell_metadata_fmt:file

expected_counts_fmt:file

Output

transcript_metadata

meta:map

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

union_cell_polygons

meta:map

*cell-polygons-union.geojson.gz:file

cell_polygons

meta:map

*cell-polygons.geojson.gz:file

cell_metadata

meta:map

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

cell_polygons_layers

meta:map

*cell-polygons-layers.geojson.gz:file

expected_counts

meta:map

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

maxpost_counts

meta:map

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

output_rates

meta:map

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

cell_hulls

meta:map

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

gene_metadata

meta:map

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

metagene_rates

meta:map

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

metagene_loadings

meta:map

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

cell_voxels

meta:map

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

versions

versions.yml:file

Tools

proseg GPLv3

maintainer

get in touch

`meta:map`

`transcripts:file`

`mode:string`

`transcript_metadata_fmt:string`

`cell_metadata_fmt:file`

`expected_counts_fmt:file`

`transcript_metadata`

`meta:map`

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

`union_cell_polygons`

`meta:map`

`*cell-polygons-union.geojson.gz:file`

`cell_polygons`

`meta:map`

`*cell-polygons.geojson.gz:file`

`cell_metadata`

`meta:map`

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

`cell_polygons_layers`

`meta:map`

`*cell-polygons-layers.geojson.gz:file`

`expected_counts`

`meta:map`

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

`maxpost_counts`

`meta:map`

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

`output_rates`

`meta:map`

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

`cell_hulls`

`meta:map`

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

`gene_metadata`

`meta:map`

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

`metagene_rates`

`meta:map`

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

`metagene_loadings`

`meta:map`

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

`cell_voxels`

`meta:map`

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

`versions`

`versions.yml:file`

proseg
GPLv3