{"id":18964059,"url":"https://github.com/JaneliaSciComp/multifish","last_synced_at":"2025-04-16T05:31:47.726Z","repository":{"id":43026118,"uuid":"329431552","full_name":"JaneliaSciComp/multifish","owner":"JaneliaSciComp","description":"EASI-FISH analysis pipeline for spatial transcriptomics","archived":false,"fork":false,"pushed_at":"2024-10-29T14:30:32.000Z","size":9213,"stargazers_count":33,"open_issues_count":19,"forks_count":13,"subscribers_count":6,"default_branch":"master","last_synced_at":"2024-10-29T17:42:41.083Z","etag":null,"topics":["easi-fish","ibm-platform-lsf","nextflow","pipeline"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/JaneliaSciComp.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-01-13T21:06:12.000Z","updated_at":"2024-10-23T18:39:23.000Z","dependencies_parsed_at":"2024-04-15T15:54:42.237Z","dependency_job_id":"c1b96196-b1d7-41b7-8376-7f34732e5fa6","html_url":"https://github.com/JaneliaSciComp/multifish","commit_stats":null,"previous_names":[],"tags_count":13,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fmultifish","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fmultifish/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fmultifish/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fmultifish/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JaneliaSciComp","download_url":"https://codeload.github.com/JaneliaSciComp/multifish/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":223697532,"owners_count":17187820,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["easi-fish","ibm-platform-lsf","nextflow","pipeline"],"created_at":"2024-11-08T14:22:38.606Z","updated_at":"2024-11-08T14:22:51.425Z","avatar_url":"https://github.com/JaneliaSciComp.png","language":"Jupyter Notebook","readme":"# EASI-FISH Nextflow Pipeline\n\n[![DOI](https://zenodo.org/badge/329431552.svg)](https://zenodo.org/badge/latestdoi/329431552)\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.04.1-23aa62.svg)](https://www.nextflow.io/)\n[![Run with Docker](https://img.shields.io/badge/run%20with-docker-0db7ed?logo=docker)](https://www.docker.com/)\n[![Run with Singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg)](https://sylabs.io/docs/)\n[![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)\n\n\nThis 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.\n\n![Pipeline Diagram](docs/images/pipeline_diagram.png)\n\n## Documentation\n\nFull documentation is available at \u003chttps://janeliascicomp.github.io/multifish\u003e.\n\n## Command-line Quick Start\n\nFor 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. 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