Automated pipeline for processing fluorescence calcium imaging microscopy data and electrophysiological measurements from 3D brain organoids

Abstract: Motivation: 3D brain organoids are biological models of human brain development from which a rich body of data can be extracted that allows for insights about neuronal dynamics. Several tools, such as fluorescence calcium imaging microscopy and electrophysiological recordings are being used to assess how 3D brain organoid dynamics recapitulate what is known from the human brain. In-silico automated workflows that process such datasets on a large scale in a robust and reproducible manner need to be developed. Results: An automated, modular and scalable workflow was written using Python 3.9. ImageJ, Inscopix API and Caiman/CNMFe that outputs neuronal cell traces and additional scripts were produced to enable large scale analysis of Axion multi-electrode array output.