In Vivo Whole-Brain Imaging of Zebrafish Larvae Using Three-Dimensional Fluorescence Microscopy

We are developing optical immune systems and computational algorithms to record and analyze the neuroactivity of the entire brain with a high spatial and temporal resolution. Laboratory fish is an ideal model animal for research. Thanks to each optical transparency and the availability of diverse genetic tools The optical image quality may be degraded due to the aberration introduced by the Agarose gel used for sample mounting, and the fish may move during the recording causing motion artifacts in the images or impeding accuracy signal extraction from the images.

Publicly available protocols provide only a brief overview of the experimental procedure, living substantial parts of the details, such as agarose solidification precise mounting techniques, and simple positioning. Therefore, an effective and reproducible protocol is needed to acquire high quality image data. With minimal noise and motion.

Our protocol provides an optimized and reproducible experimental procedure. This protocol enables in vivo whole brain imaging over an extended period and visualizations of the acquired imaging data. The workflow focused on whole brain imaging but it can be easily applied to imaging other organs of lot of our zebra fish.

Our goal is to unravel the underlying principles of neural computation. For that we'll continue to work on a pipeline that involves large scale imaging of neural activity and structure and computational analysis of such for systematic brain mapping.