Optical Neuroimage Studio (OptiNiSt): Intuitive, scalable, extendable framework for optical neuroimage data analysis

Area of Science:

• Neuroscience
• Optical Imaging
• Data Analysis

Background:

• Optical neural recording is increasingly common in neuroscience due to advancements in calcium indicators and imaging techniques.
• Growing data volumes necessitate streamlined analysis pipelines for image preprocessing, signal extraction, and neural activity analysis.
• Current challenges include ensuring data quality, selecting optimal algorithms, maintaining reproducibility, and adopting standard data formats.

Purpose of the Study:

• To develop a scalable, extendable, and reproducible framework for creating calcium data analysis pipelines.
• To address the challenges in optical neural data analysis, including data quality, algorithm selection, reproducibility, and data sharing.
• To facilitate the standardization of optical neural data analysis protocols.

Main Methods:

• Developed Optical Neuroimage Studio (OptiNiSt), a framework with a graphical user interface for creating analysis pipelines.
• OptiNiSt allows users to select processing modules, tune parameters, and visualize results.
• The framework supports adding new analysis algorithms, stores pipelines in YAML files for reproducibility, and integrates with high-performance computing clusters.
• OptiNiSt reads various image formats and saves results in the Neurodata Without Borders (NWB) standard format.

Main Results:

• OptiNiSt provides a user-friendly interface for building complex calcium data analysis workflows.
• Pipelines created with OptiNiSt are reproducible and can be deployed on high-performance computing clusters.
• The framework ensures compatibility with multiple data formats and promotes the use of the NWB standard for data sharing.

Conclusions:

• Optical Neuroimage Studio (OptiNiSt) offers a robust solution for standardizing and simplifying optical neural data analysis.
• The framework enhances reproducibility and data sharing in neuroscience research.
• OptiNiSt is expected to significantly aid researchers in managing and analyzing large-scale optical neural recording datasets.