Extraction of Activity Time Series from Volumetric Microscopy

Live volumetric microscopy of model organisms engineered to neuronally express genetically encoded calcium indicators is a widespread technique for recording neural activity at single-cell resolution. Extraction of the fluorescence time series associated with these recordings typically requires a combination of automated analysis tools and human oversight and correction. The software landscape for these sorts of tools is fragmented, and no robust and easily interpretable standard currently exists.

This project will create a pipeline for quantifying whole-brain neural activity from volumetric video microscopy of C. elegans and other organisms, including an interactive app for visualization and curation.