nf-core/vizgenpostprocessing_runsegmentationontile

module

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

vpt vizgen segmentation microscopy spatial transcriptomics

Module Information

Repository: https://github.com/nf-core/modules/tree/master/modules/nf-core/vizgenpostprocessing/runsegmentationontile
Source: nf-core
Organization: nf-core
Authors: @mcmero
Maintainers: @mcmero

Tools

vizgenpostprocessing

Vizgen's post-processing tool

License: Apache-2.0

Inputs

Name	Type	Description
0
algorithm_json	file	JSON file containing the algorithm parameters.
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).

Quick Start

Include this module in your Nextflow pipeline:

include { VIZGENPOSTPROCESSING_RUNSEGMENTATIONONTILE } from 'https://github.com/nf-core/modules/tree/master/modules/nf-core/vizgenpostprocessing/runsegmentationontile'

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