RT Journal Article
SR Electronic
T1 Mesmerize: a dynamically adaptable user-friendly analysis platform for 2D & 3D calcium imaging data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 840488
DO 10.1101/840488
A1 Kushal Kolar
A1 Daniel Dondorp
A1 Jordi Cornelis Zwiggelaar
A1 Jørgen Høyer
A1 Marios Chatzigeorgiou
YR 2021
UL http://biorxiv.org/content/early/2021/06/10/840488.abstract
AB 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.Competing Interest StatementThe authors have declared no competing interest.