PyZebrascope

PyZebrascope provides control and data acquisition for brain-wide neural activity imaging in zebrafish using light-sheet fluorescence microscopy and genetically-encoded calcium indicators to investigate neuronal interactions during behavior.

Key Features:

• Light-sheet fluorescence microscopy support: Implements acquisition and control for whole-brain imaging using light-sheet fluorescence microscopy in zebrafish.
• Genetically-encoded calcium indicator compatibility: Supports recording neuronal activity using genetically-encoded calcium indicators.
• Two orthogonal excitation beams: Supports dual orthogonal excitation beams to enhance image quality and resolution.
• Eye damage prevention: Includes mechanisms to prevent illumination-induced damage to zebrafish eyes during imaging.
• High-performance data handling: Camera module manages data throughput up to 800 MB/s from acquisition to file writing while maintaining stable CPU and memory usage.
• Modular architecture: Modular design allows integration of advanced algorithms for microscope control and image processing.
• Automatic image resolution optimization: Includes an automatic algorithm that aligns excitation beams with the image focal plane to maximize image resolution.

Scientific Applications:

• Whole-brain neural activity imaging during behavior: Acquisition of brain-wide neural activity in zebrafish engaged in behavioral paradigms, including virtual reality environments.
• Investigation of neural dynamics across brain regions: Exploration of the dynamics of neural interactions across the entire brain during various behavioral states.

Methodology:

An automatic algorithm precisely aligns excitation beams with the image focal plane to maximize resolution; the camera module manages high-throughput data transfer up to 800 MB/s from acquisition to file writing while maintaining stable CPU and memory usage, and the modular architecture permits integration of advanced microscope-control and image-processing algorithms.