Mesmerize is a dynamically adaptable user-friendly analysis platform for 2D and 3D calcium imaging data

Kushal Kolar (), Daniel Dondorp, Jordi Cornelis Zwiggelaar, Jørgen Høyer and Marios Chatzigeorgiou ()
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Kushal Kolar: University of Bergen
Daniel Dondorp: University of Bergen
Jordi Cornelis Zwiggelaar: University of Bergen
Jørgen Høyer: University of Bergen
Marios Chatzigeorgiou: University of Bergen

Nature Communications, 2021, vol. 12, issue 1, 1-15

Abstract: Abstract Calcium imaging is an increasingly valuable technique for understanding neural circuits, neuroethology, and cellular mechanisms. The analysis of calcium imaging data presents challenges in image processing, data organization, analysis, and accessibility. Tools have been created to address these problems independently, however a comprehensive user-friendly package does not exist. Here we present Mesmerize, an efficient, expandable and user-friendly analysis platform, which uses a Findable, Accessible, Interoperable and Reproducible (FAIR) system to encapsulate the entire analysis process, from raw data to interactive visualizations for publication. Mesmerize provides a user-friendly graphical interface to state-of-the-art analysis methods for signal extraction & downstream analysis. We demonstrate the broad scientific scope of Mesmerize’s applications by analyzing neuronal datasets from mouse and a volumetric zebrafish dataset. We also applied contemporary time-series analysis techniques to analyze a novel dataset comprising neuronal, epidermal, and migratory mesenchymal cells of the protochordate Ciona intestinalis.

Date: 2021
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DOI: 10.1038/s41467-021-26550-y

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