Data

Tools

Indexes

Applications

Experiments

Open Source Science

multifish

EASI-FISH analysis pipeline for spatial transcriptomics

https://github.com/janeliascicomp/multifish

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.2%) to scientific vocabulary

Keywords

easi-fish ibm-platform-lsf nextflow pipeline
Last synced: 10 months ago · JSON representation ·

Repository

EASI-FISH analysis pipeline for spatial transcriptomics

Basic Info
  • Host: GitHub
  • Owner: JaneliaSciComp
  • License: bsd-3-clause
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage:
  • Size: 8.8 MB
Statistics
  • Stars: 34
  • Watchers: 5
  • Forks: 13
  • Open Issues: 19
  • Releases: 10
Topics
easi-fish ibm-platform-lsf nextflow pipeline
Created over 5 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

EASI-FISH Nextflow Pipeline

DOI Nextflow Run with Docker Run with Singularity Launch on Nextflow Tower

This pipeline analyzes imagery collected using the EASI-FISH (Expansion-Assisted Iterative Fluorescence In Situ Hybridization) method described in this paper. It includes automated image stitching, distributed multi-round image registration, cell segmentation, and distributed spot detection.

Pipeline Diagram

Documentation

Full documentation is available at https://janeliascicomp.github.io/multifish.

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 (version 20.10.0 or greater) and Singularity (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:

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

To install Singularity 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]

Owner

  • Name: Howard Hughes Medical Institute
  • Login: JaneliaSciComp
  • Kind: organization
  • Location: 19700 Helix Drive, Ashburn, VA 20147

GitHub organization maintained by Scientific Computing Software at HHMI's Janelia Research Campus for use by HHMI staff and external collaborators.

Citation (CITATION.cff) 

cff-version: 1.2.0
title: EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization
message: If you use this software, please cite it using the metadata from CITATION.cff
doi: 10.1016/j.cell.2021.11.024
date-released: 2021-12-01
authors:
  - given-names: Yuhan
    family-names: Wang
  - given-names: Mark
    family-names: Eddison
  - given-names: Greg
    family-names: Fleishman
  - given-names: Martin
    family-names: Weigert
  - given-names: Shengjin
    family-names: Xu
  - given-names: Tim
    family-names: Wang
  - given-names: Konrad
    family-names: Rokicki
  - given-names: Cristian
    family-names: Goina
  - given-names: Fredrick E
    family-names: Henry
  - given-names: Andrew L
    family-names: Lemire
  - given-names: Uwe
    family-names: Schmidt
  - given-names: Hui
    family-names: Yang
  - given-names: Karel
    family-names: Svoboda
  - given-names: Eugene W
    family-names: Myers
  - given-names: Stephan
    family-names: Saalfeld
  - given-names: Wyatt
    family-names: Korff
  - given-names: Scott M
    family-names: Sternson
  - given-names: Paul W
    family-names: Tillberg
type: software
repository-code: 'https://github.com/JaneliaSciComp/multifish'
url: 'https://janeliascicomp.github.io/multifish/'
license: BSD-3-Clause

GitHub Events

Total
  • Watch event: 3
  • Push event: 9
  • Fork event: 1
Last Year
  • Watch event: 3
  • Push event: 9
  • Fork event: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 47
  • Total pull requests: 3
  • Average time to close issues: 3 months
  • Average time to close pull requests: 4 months
  • Total issue authors: 18
  • Total pull request authors: 3
  • Average comments per issue: 3.64
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 minutes
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • FangmingXie (13)
  • krokicki (9)
  • bradleycolquitt (4)
  • KMSmichelle (3)
  • erkinacar5 (3)
  • neugun (2)
  • tm1101101 (2)
  • kenjp1223 (1)
  • liyongxin123 (1)
  • limingtan (1)
  • anaste123 (1)
  • orena1 (1)
  • azzhu (1)
  • JienaL (1)
  • Alex-de-Lecea (1)
Pull Request Authors
  • wangyuhan01 (1)
  • orena1 (1)
  • FangmingXie (1)
Top Labels
Issue Labels
bug (26) enhancement (14) question (1)
Pull Request Labels

Dependencies

aws-batch/package-lock.json npm
  • 366 dependencies
aws-batch/package.json npm
  • serverless ^3.8.0 development
docs/Gemfile rubygems
  • github-pages ~> 219 development
  • tzinfo ~> 1.2
  • tzinfo-data >= 0
  • wdm ~> 0.1.1
docs/Gemfile.lock rubygems
  • activesupport 6.0.4.1
  • addressable 2.8.0
  • coffee-script 2.4.1
  • coffee-script-source 1.11.1
  • colorator 1.1.0
  • commonmarker 0.17.13
  • concurrent-ruby 1.1.9
  • dnsruby 1.61.7
  • em-websocket 0.5.2
  • ethon 0.14.0
  • eventmachine 1.2.7
  • execjs 2.8.1
  • faraday 1.8.0
  • faraday-em_http 1.0.0
  • faraday-em_synchrony 1.0.0
  • faraday-excon 1.1.0
  • faraday-httpclient 1.0.1
  • faraday-net_http 1.0.1
  • faraday-net_http_persistent 1.2.0
  • faraday-patron 1.0.0
  • faraday-rack 1.0.0
  • ffi 1.15.4
  • forwardable-extended 2.6.0
  • gemoji 3.0.1
  • github-pages 219
  • github-pages-health-check 1.17.7
  • html-pipeline 2.14.0
  • http_parser.rb 0.6.0
  • i18n 0.9.5
  • jekyll 3.9.0
  • jekyll-avatar 0.7.0
  • jekyll-coffeescript 1.1.1
  • jekyll-commonmark 1.3.1
  • jekyll-commonmark-ghpages 0.1.6
  • jekyll-default-layout 0.1.4
  • jekyll-feed 0.15.1
  • jekyll-gist 1.5.0
  • jekyll-github-metadata 2.13.0
  • jekyll-mentions 1.6.0
  • jekyll-optional-front-matter 0.3.2
  • jekyll-paginate 1.1.0
  • jekyll-readme-index 0.3.0
  • jekyll-redirect-from 0.16.0
  • jekyll-relative-links 0.6.1
  • jekyll-remote-theme 0.4.3
  • jekyll-sass-converter 1.5.2
  • jekyll-seo-tag 2.7.1
  • jekyll-sitemap 1.4.0
  • jekyll-swiss 1.0.0
  • jekyll-theme-architect 0.2.0
  • jekyll-theme-cayman 0.2.0
  • jekyll-theme-dinky 0.2.0
  • jekyll-theme-hacker 0.2.0
  • jekyll-theme-leap-day 0.2.0
  • jekyll-theme-merlot 0.2.0
  • jekyll-theme-midnight 0.2.0
  • jekyll-theme-minimal 0.2.0
  • jekyll-theme-modernist 0.2.0
  • jekyll-theme-primer 0.6.0
  • jekyll-theme-slate 0.2.0
  • jekyll-theme-tactile 0.2.0
  • jekyll-theme-time-machine 0.2.0
  • jekyll-titles-from-headings 0.5.3
  • jekyll-watch 2.2.1
  • jemoji 0.12.0
  • kramdown 2.3.1
  • kramdown-parser-gfm 1.1.0
  • liquid 4.0.3
  • listen 3.7.0
  • mercenary 0.3.6
  • minima 2.5.1
  • minitest 5.14.4
  • multipart-post 2.1.1
  • nokogiri 1.12.5
  • octokit 4.21.0
  • pathutil 0.16.2
  • public_suffix 4.0.6
  • racc 1.5.2
  • rb-fsevent 0.11.0
  • rb-inotify 0.10.1
  • rexml 3.2.5
  • rouge 3.26.0
  • ruby-enum 0.9.0
  • ruby2_keywords 0.0.5
  • rubyzip 2.3.2
  • safe_yaml 1.0.5
  • sass 3.7.4
  • sass-listen 4.0.0
  • sawyer 0.8.2
  • simpleidn 0.2.1
  • terminal-table 1.8.0
  • thread_safe 0.3.6
  • typhoeus 1.4.0
  • tzinfo 1.2.9
  • unf 0.1.4
  • unf_ext 0.0.8
  • unicode-display_width 1.8.0
  • zeitwerk 2.4.2
containers/downloader/Dockerfile docker
  • alpine 3.8 build
containers/registration/Dockerfile docker
  • continuumio/miniconda3 4.9.2 build
  • janeliascicomp/builder 1.2.1 build
containers/rs_fish/Dockerfile docker
  • janeliascicomp/builder 1.2.1 build
  • multifish/spark 3.0.1-hadoop3.2 build
containers/segmentation/Dockerfile docker
  • oraclelinux 8 build
containers/spot_assignment/Dockerfile docker
  • oraclelinux 8 build
containers/spot_extraction/Dockerfile docker
  • oraclelinux 8 build
containers/stitching/Dockerfile docker
  • janeliascicomp/builder 1.2.1 build
  • multifish/spark 3.0.1-hadoop3.2 build
containers/spot_extraction/compiled_matlab/setup.py pypi
containers/registration/environment.yml pypi
  • argparse ==1.4.0
  • cycler ==0.10.0
  • decorator ==4.4.2
  • fasteners ==0.16
  • greedypy ==0.0.6
  • imageio ==2.9.0
  • kiwisolver ==1.3.1
  • matplotlib ==3.3.3
  • networkx ==2.5
  • nibabel ==3.2.1
  • numcodecs ==0.7.2
  • numpy ==1.20.3
  • opencv-python ==4.5.1.48
  • packaging ==20.8
  • pillow ==8.1.0
  • pyfftw ==0.12.0
  • pynrrd ==0.4.2
  • pyparsing ==3.0.0b2
  • python-dateutil ==2.8.1
  • pywavelets ==1.1.1
  • scikit-image ==0.18.1
  • scipy ==1.6.0
  • six ==1.15.0
  • tifffile ==2021.1.14
  • zarr ==2.6.1