soragnilab/unetsegmentation repository overview

⁠hslci_pipeline

Docker container image for data analysis pipeline used to process HSLCI screening data https://www.biorxiv.org/content/10.1101/2021.10.03.462896v3⁠. This pipeline is available on Github: https://github.com/uclahs-soragnilab/hslci_pipeline⁠

⁠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 ([email protected]⁠), Bowen Wang ([email protected]⁠), Alice Soragni ([email protected]⁠) 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.