A novel data analysis pipeline for fiber-based in vivo calcium imaging

Catherine S. Thomas1, Xuejun Du2, Kai Wang1, Jayant Rai3, Kenichi Okamoto3, Miles Li1, Jian Zhao 2


In collaboration with computer scientists from the University of Waterloo, we have developed an analysis pipeline for calcium imaging analysis for data collected using the OASIS Implant. This pipeline addresses a major pain point for one photon calcium imaging by providing a code-free, user-friendly approach to extracting meaningful results from raw data. We are excited to present the pipeline at the upcoming IBRO conference and discuss its applications with the neuroscience community!


1 Mightex Systems, 111 Railside Road, Toronto, Canada, M3A 1B2

2 Cheriton School of Computer Science, University of Waterloo, 200 University Avenue West, Waterloo, N2L 3G1

3 Department of Molecular Genetics, Lunenfeld-Tanenbaum Research Institute, University of Toronto, 600 University Avenue, Toronto, Canada, M5G 1X5


Examining in vivo neural circuit dynamics in relation to behaviour is crucial to advances in understanding how the brain works. Two techniques that are often used to examine these dynamics are one photon calcium imaging and optogenetics. Fiber-based micro-endoscopy provides a versatile, modular, and lightweight option for combining in vivo calcium imaging and optogenetics in freely behaving animals. One challenge with this technique is that the data collected from such an approach are often complex and dense. Extraction of meaningful conclusions from these data can be computationally challenging and often requires coding experience…

As such, as a collaborative endeavour between behavioural neuroscientists, optical engineers, and computer science visual processing experts, we have developed a novel pipeline for extraction, examination, and visualization of calcium imaging data for fiber-based approaches. This pipeline offers a user-friendly, code-free interface with customizable features and parameters, capable of integrating imaging, optogenetics, and behavioural measures for holistic experimental visualization and analysis. This pipeline significantly expands the opportunities afforded to behavioural neuroscience researchers and shifts forward the possible research opportunities when examining circuit dynamics in freely behaving animals.