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

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

The module runs the segmentation algorithm on a specific tile 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 runs the segmentation algorithm on a specific tile using Vizgen's post-processing tool.

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

include { VIZGENPOSTPROCESSING_RUNSEGMENTATIONONTILE } from 'nf-core/vizgenpostprocessing/runsegmentationontile'

MIT License

Process

`Name`	`VIZGENPOSTPROCESSING_RUNSEGMENTATIONONTILE`

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`
`tile_index` integer	The index of the tile to run the segmentation algorithm on.

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

`custom_weights` directory	Directory containing custom weights for the segmentation algorithm. Must be defined in the algorithm JSON file under "custom_weights" as directory name only (not full path).

Output 2 channels

#1 versions

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

#2 segmented_tile tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}/result_tiles/*.parquet` file	Parquet file containing the segmentation results for the specified tile.

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 19:22:53 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fvizgenpostprocessing%2Frunsegmentationontile/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/vizgenpostprocessing/runsegmentationontile/blobs/sha256:aa2f7b47d763d3d46ca07c788db51576ee382a22d4913e623a477797c770ef77
Size	3.2 KB
Checksum	sha256:aa2f7b47d763d3d46ca07c788db51576ee382a22d4913e623a477797c770ef77
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:22:53 (UTC)		1	3.2 KB	-