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hslci_pipeline

Data analysis pipeline for HSLCI screening data https://www.biorxiv.org/content/10.1101/2021.10.03.462896v3. This pipeline takes a directory containing MATLAB files with the unwrapped data from the interferometer and segments the images to identify the boundaries of the organoids in each frame. The output files are also .mat files. DOI

Contents

Running the Pipeline

Pipeline Inputs

The pipeline requires 3 inputs to run properly:

  1. Full path to a directory containing MATLAB files of interest.
  2. Full path to a corresponding well template with information on the various conditions. A template can be found under the inputs folder.
  3. A path for the location of outputs.

These 3 paths need to be modified and specified within the configuration file hslci_pipeline.config

Running with Nextflow

Install nextflow if not already in system. Additional information on installation can be found here

wget -qO- https://get.nextflow.io | bash

# Or if you prefer curl
#curl -s https://get.nextflow.io | bash

With nextflow already installed and the docker image already pulled or built in the system, modify the hslci_pipeline.config with the necessary paths and then run the pipeline.

nextflow run main.nf -c hslci_pipeline.config

Building the Docker image

  • Docker support is necessary to run the pipeline. Notes on how to install can be found here: docker
  • To pull the docker image:
docker pull soragnilab/unetsegmentation:1.0.0
  • The docker image is automatically pulled from dockerhub within the pipeline, but if no internet connection it can be built locally before running. Dockerfile can be found in the docker/base_docker directory.
docker build -t soragnilab/unetsegmentation:1.0.0 .

Additional Guidance

Installing Docker

O.S. Notes

  • Pipeline testing and validation was done both locally in linux and MAC-O.S, aswell as a CentOS/slurm cluster.

License

This project is covered under the GNU General Public License, version 2.0 (GPL-2.0).

License Author: Peyton Tebon (ptebon@mednet.ucla.edu), Bowen Wang (bowenwang410@g.ucla.edu), Alice Soragni (alices@mednet.ucla.edu) hslci_pipeline is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license. hslci_pipeline takes processes imaging data collected from a high-speed live cell interferometer to segment, track, and quantify organoids. Copyright (C) 2022 University of California Los Angeles (“Soragni Lab”) All rights reserved. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.