This repository contains code to replicate a denoising+segmentation pipeline either on a local machine, SLURM cluster or make an AWS cloud deployment. It relies on Nextflow capabilities to achieve that goal and is pulling docker repositories in the process. Specific deployments could require setting up the nextflow.config file. We provide an example nextflow.config file for deployment to a SLURM cluster.

1. Install nextflow at the root of the repository using

curl -s https://get.nextflow.io | bash

For more instructins, see https://www.nextflow.io/docs/latest/getstarted.html

2. Once installed, run individual nextflow files as :

./nextflow deepinterpolation.nf

nf files contains all required instruction to pull environments (dockers, ...) and launch the underlying figures code.

Please reach out [email protected] for any questions. If this is useful to you, 👋 are welcome! Credits are due to David Feng and the Code Ocean team. This repo results from the work of a lot of people.