https://github.com/JaneliaSciComp/multifish

EASI-FISH analysis pipeline for spatial transcriptomics
https://github.com/JaneliaSciComp/multifish

easi-fish ibm-platform-lsf nextflow pipeline

Last synced: 3 months ago
JSON representation

EASI-FISH analysis pipeline for spatial transcriptomics

• Host: GitHub
• URL: https://github.com/JaneliaSciComp/multifish
• Owner: JaneliaSciComp
• License: bsd-3-clause
• Created: 2021-01-13T21:06:12.000Z (about 4 years ago)
• Default Branch: master
• Last Pushed: 2024-10-29T14:30:32.000Z (3 months ago)
• Last Synced: 2024-10-29T17:42:41.083Z (3 months ago)
• Topics: easi-fish, ibm-platform-lsf, nextflow, pipeline
• Language: Jupyter Notebook
• Homepage:
• Size: 8.79 MB
• Stars: 33
• Watchers: 6
• Forks: 13
• Open Issues: 19
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Citation: CITATION.cff

Awesome Lists containing this project

• awesome-janelia-software - EASI-FISH Pipeline - Spatial transcriptomics using the EASI-FISH protocol (Nextflow Pipelines)
• awesome-janelia-software - EASI-FISH Pipeline - Spatial transcriptomics using the EASI-FISH protocol (Nextflow Pipelines)

README

        
# EASI-FISH Nextflow Pipeline

[![DOI](https://zenodo.org/badge/329431552.svg)](https://zenodo.org/badge/latestdoi/329431552)

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.04.1-23aa62.svg)](https://www.nextflow.io/)

[![Run with Docker](https://img.shields.io/badge/run%20with-docker-0db7ed?logo=docker)](https://www.docker.com/)

[![Run with Singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg)](https://sylabs.io/docs/)

[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/JaneliaSciComp/multifish)

This pipeline analyzes imagery collected using the [EASI-FISH](https://github.com/multiFISH/EASI-FISH) (Expansion-Assisted Iterative Fluorescence *In Situ* Hybridization) method described in [this paper](https://doi.org/10.1016/j.cell.2021.11.024). It includes automated image stitching, distributed multi-round image registration, cell segmentation, and distributed spot detection.

![Pipeline Diagram](docs/images/pipeline_diagram.png)

## Documentation

Full documentation is available at .

## Command-line Quick Start

For tech-saavy users, the pipeline can be invoked from the command-line and runs on any workstation or cluster. The only prerequisites for running this pipeline are [Nextflow](https://www.nextflow.io) (version 20.10.0 or greater) and [Singularity](https://sylabs.io) (version 3.5 or greater). If you are running on an HPC cluster, ask your system administrator to install Singularity on all the cluster nodes. Singularity is a popular HPC containerization tool, so many institutional clusters already support it.

To [install Nextflow](https://www.nextflow.io/docs/latest/getstarted.html):

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

To [install Singularity](https://sylabs.io/guides/3.7/admin-guide/installation.html) on CentOS Linux:

    sudo yum install singularity

Clone this repository with the following command:

    git clone --recursive https://github.com/JaneliaSciComp/multifish.git

Before running the pipeline for the first time, run setup to pull in external dependencies:

    ./setup.sh

You can now launch the pipeline using:

    ./main.nf [arguments]