PyZebrascope: An Open-Source Platform for Brain-Wide Neural Activity Imaging in Zebrafish

Area of Science:

• Neuroscience
• Biophysics
• Optical Engineering

Background:

• Understanding neural circuits controlling behavior is a key neuroscience challenge.
• Whole-brain imaging in zebrafish has advanced with new microscopy and calcium indicators.
• Previous whole-brain imaging methods relied on inaccessible custom software, limiting research dissemination.

Purpose of the Study:

• To introduce PyZebrascope, an open-source Python platform for light-sheet microscopy-based whole-brain neural activity imaging in zebrafish.
• To provide an accessible and user-friendly tool for the neuroscience community.
• To facilitate the development and dissemination of advanced light-sheet microscopy techniques.

Main Methods:

• Development of PyZebrascope, an open-source Python platform with intuitive user interfaces.
• Implementation of features for whole-brain imaging, including dual orthogonal excitation beams and eye protection.
• Integration of a high-throughput camera module (800 MB/s) and a modular architecture for advanced algorithms.
• Development of an automatic algorithm for optimizing image resolution via precise excitation beam alignment.

Main Results:

• PyZebrascope supports essential whole-brain imaging features and high data throughput.
• A novel algorithm was successfully implemented to automatically maximize image resolution.
• The platform enables whole-brain neural activity imaging in zebrafish within a virtual reality environment.

Conclusions:

• PyZebrascope provides an accessible, open-source solution for whole-brain neural imaging in zebrafish.
• The platform facilitates the dissemination and advancement of light-sheet microscopy techniques.
• PyZebrascope will contribute to a deeper understanding of whole-brain neural dynamics during behavior.