OptiNiSt - Calcium Imaging Pipeline Tool

OptiNiSt(Optical Neuroimage Studio) helps researchers try multiple data analysis methods, visualize the results, and construct the data analysis pipelines easily and quickly. 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.

Main Features

• Easy-To-Create Workflow: allows you to create analysis pipelines easily on the GUI.

• Visualizing analysis results: supports you visualize the analysis results.

• Managing Workflows: records and reproduces the workflow pipelines easily.

User Guide:

• Installation
  • Installation (Users)
  • Installation (Developers)
  • Appendix
• Tutorials
  • Loading Sample Data
  • Adding Nodes to your Workflow
  • Checking the Data
  • Selecting ROIs
  • Visualising Analysis Algorithms
  • Practice with Tutorial 2 & 3
• GUI Guide
  • Workflow
  • Visualize
  • Record
• Specifications
  • Architecture
  • Data Nodes
  • Algorithm Nodes
  • Add your algorithm
• Other
  • Multi-user Mode
  • CLI Usage
  • Debugging
• For Developers
  • Documentation
  • Style Guides
  • Pull Request
  • Test
  • DataClass
  • NWB File I/O

Explore Our GitHub Repository

We’re building in the open! You can explore the codebase, check out open issues, and contribute to the project on GitHub.

Visit the Optinist GitHub Repository

Citation

If you use this software, please cite our paper: Optical Neuroimage Studio (OptiNiSt): intuitive, scalable, extendable framework for optical neuroimage data analysis.

@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.