optinist

calcium imaging pipeline tool

https://github.com/oist/optinist

Science Score: 49.0%

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

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
Found 3 DOI reference(s) in README
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Academic publication links
Links to: plos.org
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Scientific vocabulary similarity
Low similarity (13.0%) to scientific vocabulary

Keywords

calcium-imaging neuroscience

Last synced: 7 months ago · JSON representation

Repository

calcium imaging pipeline tool

Basic Info

Host: GitHub
Owner: oist
License: gpl-3.0
Language: TypeScript
Default Branch: main
Homepage:
Size: 743 MB

Statistics

Stars: 47
Watchers: 10
Forks: 14
Open Issues: 33
Releases: 26

Topics

calcium-imaging neuroscience

Created over 4 years ago · Last pushed 7 months ago

Metadata Files

Readme License Codemeta

OptiNiSt

OptiNiSt(Optical Neuroimage Studio) is a GUI based workflow pipeline tools for processing two-photon calcium imaging data.

OptiNiSt helps researchers try multiple data analysis methods, visualize the results, and construct the data analysis pipelines easily and quickly on GUI. OptiNiSt's data-saving format follows NWB standards.

OptiNiSt also supports reproducibility of scientific research, standardization of analysis protocols, and developments of novel analysis tools as plug-in.

Support Library

ROI detection

[x] Suite2p
[x] CaImAn
[x] LCCD

Postprocessing

[x] Basic Neural Analysis (Event Trigger Average...)
[x] Dimension Reduction (PCA...)
[x] Neural Decoding (LDA...)
[x] Neural Population Analysis (Correlation...)

Saving Format

[x] NWB

Key Features

:beginner: Easy-To-Create Workflow

zero-knowledge of coding: OptiNiSt allows you to create analysis pipelines easily on the GUI.

:zap: Visualizing analysis results

quick visualization: OptiNiSt supports you visualize the analysis results by plotly.

:rocket: Managing Workflows

recording and reproducing: OptiNiSt records and reproduces the workflow pipelines easily.

Installation

Need anaconda or miniconda or miniforge environment.

conda create -n optinist python=3.9 conda activate optinist

Install from pip.

pip install optinist

launch.

run_optinist

Open browser. http://localhost:8000

Documentation

https://optinist.readthedocs.io/en/latest/

Using GUI

Workflow

OptiNiSt allows you to make your analysis pipelines by graph style using nodes and edges on GUI. Parameters for each analysis are easily changeable.

Visualize

OptiNiSt allows you to visualize the analysis results with one click by plotly. It supports a variety of plotting styles.

Record

OptiNiSt supports you in recording and reproducing workflow pipelines in an organized manner.

Contributors

References

[Suite2p] Marius Pachitariu, Carsen Stringer, Mario Dipoppa, Sylvia Schrder, L. Federico Rossi, Henry Dalgleish, Matteo Carandini, Kenneth D. Harris. "Suite2p: beyond 10,000 neurons with standard two-photon microscopy". 2017 [CaImAn] Andrea Giovannucci Is a corresponding author, Johannes Friedrich, Pat Gunn, Jrmie Kalfon, Brandon L Brown, Sue Ann Koay, Jiannis Taxidis, Farzaneh Najafi, Jeffrey L Gauthier, Pengcheng Zhou, Baljit S Khakh, David W Tank, Dmitri B Chklovskii, Eftychios A Pnevmatikakis. "CaImAn: An open source tool for scalable Calcium Imaging data Analysis". 2019 [LCCD] Tsubasa Ito, Keisuke Ota, Kanako Ueno, Yasuhiro Oisi, Chie Matsubara, Kenta Kobayashi, Masamichi Ohkura, Junichi Nakai, Masanori Murayama, Toru Aonishi, "Low computational-cost cell detection method for calcium imaging data", 2022 [PyNWB] Oliver Rbel, Andrew Tritt, Ryan Ly, Benjamin K. Dichter, Satrajit Ghosh, Lawrence Niu, Ivan Soltesz, Karel Svoboda, Loren Frank, Kristofer E. Bouchard, "The Neurodata Without Borders ecosystem for neurophysiological data science", bioRxiv 2021.03.13.435173, March 15, 2021

Citation

If you use this software, please cite our paper: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1013087

@misc{OptiNiSt, author = {Yamane, Yukako and Li, Yuzhe and Matsumoto, Keita and Kanai, Ryota and Desforges, Miles and Gutierrez, Carlos Enrique and Doya, Kenji}, title = {Optical Neuroimage Studio (OptiNiSt): intuitive, scalable, extendable framework for optical neuroimage data analysis}, volume = {21}, issue = {5}, year = {2025}, doi = {10.1371/journal.pcbi.1013087}, journal = {PLOS Computational Biology} }

Join Our User Community on Slack

We've launched a Slack workspace to provide a more casual space for discussions and interaction among users.

Join the Optinist User Community on Slack

Feel free to use it as a space for casual conversations, product questions, requests, and feedback.

Owner

Name: Okinawa Institute of Science & Technology
Login: oist
Kind: organization
Email: webmaster@oist.jp
Location: Okinawa, Japan

Website: http://www.oist.jp/
Repositories: 48
Profile: https://github.com/oist

CodeMeta (codemeta.json)

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  "type": "SoftwareSourceCode",
  "applicationCategory": "Neuroscience",
  "author": [
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      "type": "Person",
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        "name": "Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University"
      },
      "email": "yukako.yamane@oist.jp",
      "familyName": "Yamane",
      "givenName": "Yukako"
    },
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      "id": "_:author_2",
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      },
      "familyName": "Desforges",
      "givenName": "Miles"
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      "affiliation": {
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        "name": "Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University"
      },
      "familyName": "Gutierrez",
      "givenName": "Carlos"
    },
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      "affiliation": {
        "type": "Organization",
        "name": "Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University"
      },
      "email": "doya@oist.jp",
      "familyName": "Doya",
      "givenName": "Kenji"
    }
  ],
  "codeRepository": "https://github.com/oist/optinist",
  "contributor": [
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      "type": "Person",
      "affiliation": {
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      "familyName": "Akiyama",
      "givenName": "Shogo "
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      "id": "_:contributor_2",
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  ],
  "dateCreated": "2022-02-21",
  "dateModified": "2025-05-26",
  "datePublished": "2022-06-22",
  "description": "OptiNiSt(Optical Neuroimage Studio) is a GUI based workflow pipeline tools for processing calcium imaging data. OptiNiSt helps researchers try multiple data analysis methods, visualize the results, and construct the data analysis pipelines easily and quickly on GUI. OptiNiSt's data-saving format follows NWB standards. OptiNiSt also supports reproducibility of scientific research, standardization of analysis protocols, and developments of novel analysis tools as plug-in.",
  "funder": {
    "type": "Organization",
    "name": "AMED"
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  "keywords": [
    "Calcium imaging",
    "cell detection",
    "population analysis"
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  "license": "https://spdx.org/licenses/GPL-3.0",
  "name": "OptiNiSt",
  "operatingSystem": [
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  "programmingLanguage": [
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  "runtimePlatform": [
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  "version": "2.2.3",
  "developmentStatus": "active",
  "funding": "Brain/MINDS",
  "issueTracker": "https://github.com/oist/optinist/issues",
  "referencePublication": "https://doi.org/10.1371/journal.pcbi.1013087"
}

GitHub Events

Total

Fork event: 1
Create event: 25
Release event: 7
Issues event: 27
Watch event: 11
Delete event: 12
Member event: 1
Issue comment event: 22
Push event: 49
Pull request review comment event: 17
Gollum event: 31
Pull request event: 84
Pull request review event: 49

Last Year

Fork event: 1
Create event: 25
Release event: 7
Issues event: 27
Watch event: 11
Delete event: 12
Member event: 1
Issue comment event: 22
Push event: 49
Pull request review comment event: 17
Gollum event: 31
Pull request event: 84
Pull request review event: 49

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 124
Total pull requests: 207
Average time to close issues: 8 months
Average time to close pull requests: 11 days
Total issue authors: 12
Total pull request authors: 13
Average comments per issue: 1.68
Average comments per pull request: 0.43
Merged pull requests: 156
Bot issues: 0
Bot pull requests: 12

Past Year

Issues: 2
Pull requests: 77
Average time to close issues: N/A
Average time to close pull requests: 3 days
Issue authors: 2
Pull request authors: 3
Average comments per issue: 0.0
Average comments per pull request: 0.13
Merged pull requests: 62
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

emuemuJP (35)
itutu-tienday (27)
milesOIST (19)
ReiHashimoto (13)
Miles-and-miles-away (5)
ShogoAkiyama (5)
ykyamane (2)
DeanTM (2)
milesAraya (2)
ethanbb (1)
kushalkolar (1)
ut29 (1)

Pull Request Authors

ReiHashimoto (65)
tsuchiyama-araya (45)
milesAraya (29)
itutu-tienday (24)
quanpython (16)
dependabot[bot] (12)
emuemuJP (10)
ykyamane (3)
sanglevinh (3)
josh-oloro (2)
kngwyu (2)
milesOIST (1)

Top Labels

Issue Labels

enhancement (55) backend (32) bug (30) frontend (29) question (3) documentation (2) dependencies (1) test (1) duplicate (1) testing (1)

Pull Request Labels

dependencies (12) python (10) documentation (7) github_actions (2)

Packages

Total packages: 1
Total downloads:
- pypi 238 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 26
Total maintainers: 1

pypi.org: optinist

Calcium Imaging Pipeline Tool

Homepage: https://github.com/oist/optinist
Documentation: https://optinist.readthedocs.io
License: GPL-3.0
Latest release: 2.2.3
published 7 months ago

Versions: 26
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 238 Last month

Rankings

Dependent packages count: 6.6%

Forks count: 13.6%

Stargazers count: 14.2%

Average: 20.6%

Dependent repos count: 30.6%

Downloads: 38.1%

Maintainers (1)

oistncu