imbg-ua/fastlbp-nextflow

A versatile Nextflow pipeline for unsupervised image segmentation

Nextflow pipeline for LBP-based image segmentation

Key points

The pipeline supports the following modes:

• GridSearch, where you can specify lists of parameters for each step to run the pipeline using all possible combinations.
• SingleImage to process a single image.
• MultiImage to process a folder of images.

How to use

Find best parameters combinations

To launch in the GridSearch mode, use the corresponding template grid_search_template.yaml and type:

nextflow run grid_search.nf -profile conda -params-file templates/grid_search_template.yaml -entry Pipeline

Just process my images

To run in either SingleImage or MultiImage mode, choose the corresponding template (e.g. single_image.yaml) and run:

nextflow run main.nf -profile conda -params-file templates/single_image.yaml -entry Pipeline