Cellular Dynamics Nextflow Modules

A collection of Nextflow modules for analyzing cellular dynamics in cell monolayers using imaging data.

Features

• Image processing modules for nuclei segmentation and cell approximation
• Cell tracking and trajectory analysis
• Graph-based analysis of cellular neighborhoods
• Measures for cellular motion ($D^2_\text{min}$, cage-relative squared displacement ($CRSD$))
• Structure and density analysis

Quick Start

1. Add this repository as a submodule to your Nextflow pipeline:

git submodule add https://github.com/lettlini/cellular-dynamics-nf-modules

2. Import modules in your pipeline script:

include { nuclei_segmentation } from './cellular-dynamics-nf-modules/modules/image_processing/nuclei_segmentation/main.nf'
include { cage_relative_squared_displacement } from './cellular-dynamics-nf-modules/modules/tracking/cage_relative_squared_displacement/main.nf'

3. Use the modules in your workflow:

workflow {
    nuclei_segmentation(
        input_channel,
        stardist_probability_threshold,
        min_nucleus_area_pxsq,
        parent_dir_out
    )
}

Documentation

Full documentation is available at https://lettlini.github.io/cellular-dynamics-nf-modules/