Large-scale Brain Imaging Analysis

Calcium imaging is a popular brain imaging technique that enables access to up to a million neurons with single-cell resolution and subsecond time resolution. In order to extract neural activity from raw data, multiple computationally intensive preprocessing steps are required. This project will develop a napari plugin to support the execution and visualization of the analysis pipelines provided by the CaImAn library, such as rigid and piecewise-rigid motion correction, neuron identification, and activity extraction from multiple imaging modalities, including volumetric datasets. The plugin will allow users to run the analyses of large datasets and analyze the results.

The project will also leverage napari’s efficient rendering capabilities to implement live online analysis with CaImAn. Crucially, the live real-time interpretation of neuronal activity enabled by napari will allow experimenters to simultaneously gather feedback during ongoing experiments and modify them in closed-loop setups. The ability to simultaneously perform manipulations based on real-time analysis will open the door to a plethora of novel biological questions in various neurobiological systems and behavioral paradigms. The project also aims to extend the number of users that can access the software pipeline. Building a user interface on a flexible and well-maintained package such as napari will enhance access to users and lower the software maintenance effort.