Nextflow Registry | nf-core/vizgenpostprocessing/runsegmentationontile@0.0.0-3fc6d40

nf-core/vizgenpostprocessing/runsegmentationontile @ 0.0.0-3fc6d40

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

vpt vizgen segmentation microscopy spatial transcriptomics

Latest version: 0.0.0-3fc6d40

Total downloads: 4

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	0.0.0-3fc6d40
Commit ID	3fc6d40d163d89ae44d40a00b9017d5a9df5170e
Release Date	22 Apr 2026 15:36:31 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fvizgenpostprocessing%2Frunsegmentationontile/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/vizgenpostprocessing/runsegmentationontile/blobs/sha256:097c2eb841f9094e8ce9e0819d7e957eef868a3f40afa1318fcf70c1340d4c66
Size	3.2 KB
Checksum	sha256:097c2eb841f9094e8ce9e0819d7e957eef868a3f40afa1318fcf70c1340d4c66
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-3fc6d40	22 Apr 2026 15:36:31 (UTC)		3	3.2 KB
0.0.0-0c7146d	08 Apr 2026 19:47:07 (UTC)		1	3.2 KB