Model-Based Estimators of Functional Connectivity for Calcium Imaging Data – Masters Project

Multiple measurement techniques, such as multi-fiber photometry and wide-field calcium imaging are used in our lab to acquire in vivo brainwide mesoscopic optical recordings in mice. This data can help to identify functional connections between different brain areas, and the relationship of individual brain area activity and behavioural variables such as paw or whisker movement. We are currently carrying out a study to compare the performance of most prominent model-based and model-free functional connectivity estimators using simulated and real data, with emphasis on calcium indicator-based optical imaging data. The student will help adapt a few model-based functional connectivity estimators to the calcium indicator forward model, test them against existing simulated benchmarks, as well as compare their performance to model-free estimators, which we have already implemented. Finally, the student will proceed to design fitness criteria for the above model-based estimators to evaluate and compare the feasibility of using the models to describe mesoscopic calcium imaging data.

Research Group:
Laboratory of Neural Circuit Dynamics (Prof. Fritjof Helmchen) at the Brain Research Institute, University of Zurich (Irchel Campus, building 55).


Experience in programming (Python/Matlab), statistics and/or machine learning.


Philipp Bethge (

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