Nextflow Registry | nf-core/vizgenpostprocessing/compiletilesegmentation@0.0.0-0c7146d

nf-core/vizgenpostprocessing/compiletilesegmentation @ 0.0.0-0c7146d

The module compiles segmentation tiles using Vizgen's post-processing tool.

vpt vizgen segmentation microscopy spatial transcriptomics

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @mcmero

Maintainers: @mcmero

The module compiles segmentation tiles using Vizgen's post-processing tool.

Add the following snippet to your workflow script to include this module.

include { VIZGENPOSTPROCESSING_COMPILETILESEGMENTATION } from 'nf-core/vizgenpostprocessing/compiletilesegmentation'

MIT License

Process

`Name`	`VIZGENPOSTPROCESSING_COMPILETILESEGMENTATION`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
`input_images` directory	Path to the input images directory to be used for segmentation.
`segmentation_params` file	Path to the segmentation parameters (algorithm specification) JSON file generated by the preparesegmentation module. `*.json`

`algorithm_json` file	JSON file containing the algorithm parameters. `*.json`

`segmentation_tiles` file	Parquet files containing the segmentation results for tiles to compile. `*.parquet`

Output 3 channels

#1 versions

`versions.yml` file	File containing software versions `versions.yml`

#2 micron_space tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}/*_micron_space.parquet` file	Parquet file containing the compiled segmentation results in micron space.

#3 mosaic_space tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}/*_mosaic_space.parquet` file	Parquet file containing the compiled segmentation results in mosaic space.

Tool	Description	Homepage
vizgenpostprocessing	Vizgen's post-processing tool	https://github.com/Vizgen/vizgen-postprocessing

Version	0.0.0-0c7146d
Commit ID	4e8e48c04e24c2159a5589a36bae0f038809cd48
Release Date	08 Apr 2026 19:22:49 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fvizgenpostprocessing%2Fcompiletilesegmentation/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/vizgenpostprocessing/compiletilesegmentation/blobs/sha256:fc60bc483656059d005102747c949659469254e0b47f44367d67a9ac66ac4898
Size	3.3 KB
Checksum	sha256:fc60bc483656059d005102747c949659469254e0b47f44367d67a9ac66ac4898
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:22:49 (UTC)		1	3.3 KB	-