{"id":18964161,"url":"https://github.com/janeliascicomp/nf-rsfish","last_synced_at":"2026-03-19T07:22:43.412Z","repository":{"id":224260468,"uuid":"762778041","full_name":"JaneliaSciComp/nf-rsfish","owner":"JaneliaSciComp","description":"Nextflow wrapper for RS-FISH-Spark","archived":false,"fork":false,"pushed_at":"2024-02-27T16:10:00.000Z","size":2009,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":7,"default_branch":"main","last_synced_at":"2025-01-01T05:29:36.072Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Nextflow","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":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2024-02-24T17:03:02.000Z","updated_at":"2024-04-02T19:52:14.000Z","dependencies_parsed_at":"2024-02-27T17:28:56.205Z","dependency_job_id":"6c35566a-57c7-4e7b-85c3-07ac4dc179cb","html_url":"https://github.com/JaneliaSciComp/nf-rsfish","commit_stats":null,"previous_names":["janeliascicomp/nf-rsfish"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fnf-rsfish","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fnf-rsfish/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fnf-rsfish/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fnf-rsfish/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JaneliaSciComp","download_url":"https://codeload.github.com/JaneliaSciComp/nf-rsfish/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239959947,"owners_count":19725221,"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":[],"created_at":"2024-11-08T14:23:05.762Z","updated_at":"2026-01-27T23:44:52.998Z","avatar_url":"https://github.com/JaneliaSciComp.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# RS-FISH Nextflow Pipeline\n\nNextflow pipeline wrapper for [PreibischLab/RS-FISH-Spark](https://github.com/PreibischLab/RS-FISH-Spark) which implements \"precise, interactive, fast, and scalable FISH spot detection.\" This pipeline allows you to easily run RS-FISH at scale on any infrastructure supported by Nextflow. \n\n## Quick Start\n\nThe only software requirements for running this pipeline are [Nextflow](https://www.nextflow.io) (version 20.10.0 or greater) and either Docker or [Singularity](https://sylabs.io) (version 3.5 or greater). If you are running in an HPC cluster, ask your system administrator to install Singularity on all the cluster nodes.\n\nTo [install Nextflow](https://www.nextflow.io/docs/latest/getstarted.html):\n\n    curl -s https://get.nextflow.io | bash \n\nAlternatively, you can install it as a conda package:\n\n    conda create --name nextflow -c bioconda nextflow\n\nTo [install Singularity](https://sylabs.io/guides/3.7/admin-guide/installation.html) on CentOS Linux:\n\n    sudo yum install singularity\n\nNow you can run the pipeline and it will download everything else it needs. The following command will analyze one input image in N5 format and save a CSV of detected spots to the `./output` directory. \n\n    nextflow run JaneliaSciComp/nf-rsfish --input_image /path/to/image.n5 \\\n        --input_dataset /c0/s0 --outdir ./output -profile singularity \\\n        --rsfish_opts \"--anisotropy 0.53 --minIntensity 5401 --maxIntensity 61053\"\n\nBy default, the pipeline runs a local Java process. To scale to larger data sizes, you can run with a Spark cluster, e.g.\n\n    nextflow run JaneliaSciComp/nf-rsfish --input_image /path/to/image.n5 \\\n        --input_dataset /c0/s0 --outdir ./output -profile janelia \\\n        --spark_cluster=true --spark_workers=2 --spark_worker_cores=4 --spark_gb_per_core=15 \\\n        --rsfish_opts \"--anisotropy 0.53 --minIntensity 5401 --maxIntensity 61053\"\n\n\n## Interactive Parameter Finding\n\nYou can use the RS-FISH Fiji Plugin to interactively find the correct parameters for your data as follows.\n\n1. Use File-\u003eImport-\u003eN5 to open your data set and select the \"Crop\" option to cut out a small but interesting region for testing spot detection.\n2. File-\u003eSave As-\u003eTiff... and reopen the TIFF image.\n3. Install RS-FISH plugins: Help-\u003eUpdate... then click \"Manage Update Sites\" and enable \"Radial Symmetry\" then click Close and restart Fiji. \n4. Plugins -\u003e RS-FISH -\u003e Tools -\u003e Calculate Anisotropy Coefficient. Save this coefficient for later use. It should stay consistent when using the same microscope.\n5. Plugins -\u003e RS-FISH -\u003e RS-FISH \n    * Set the anisotropy coefficient from step 4\n    * Click Ok and Done on the options dialog\n    * Set the minimum value in the intensity distribution\n    * Click \"OK press to proceed to final results\"\n6. RS-FISH -\u003e Tools -\u003e Show Detections in BigDataViewer\n\nIteratively adjust the parameters until you are detecting all the spots you want.\n\nAt the end, you can choose RS-FISH -\u003e Advanced to view all of parameter values, or record to a macro to save them. This will give you all the parameters you need to run the pipeline:\n\n```\nrun(\"RS-FISH\", \"image=cropped.tif mode=Advanced anisotropy=0.7213 robust_fitting=RANSAC compute_min/max use_anisotropy sigma=1.50000 threshold=0.00500 support=3 min_inlier_ratio=0.10 max_error=1.50 spot_intensity_threshold=269.54 background=[No background subtraction] background_subtraction_max_error=0.05 background_subtraction_min_inlier_ratio=0.10 results_file=[]\");\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjaneliascicomp%2Fnf-rsfish","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjaneliascicomp%2Fnf-rsfish","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjaneliascicomp%2Fnf-rsfish/lists"}