Calcium Imaging Data Analysis

Automatic detection of neurons and neuronal processes contained in the data streams generated by brains of test subjects. Here, the pink and yellow objects are active neurons or neuronal processes detected in the brain of a mouse engaged in a behavioral task

Calcium imaging is an increasingly popular experimental method that enables monitoring of large, targeted, neural populations in alive and behaving animals. This microscopy method offers an indirect signal that needs to be preprocessed for the extraction of the actual neural population activity.

Advances in microscopy techniques have enabled experiments with data rates that can reach hundreds of gigabytes in a single day, posing significant challenges in terms of handling and processing. We develop algorithms and open source software for dealing with the universal preprocessing problems in calcium imaging data analysis (motion correction, source extraction and neural activity deconvolution) in a large scale.