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

View ORCID ProfileKushal Kolar, Daniel Dondorp, Jordi Cornelis Zwiggelaar, Jørgen Høyer, View ORCID ProfileMarios Chatzigeorgiou
doi: https://doi.org/10.1101/840488
Kushal Kolar
Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5006 Bergen, Norway
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  • ORCID record for Kushal Kolar
  • For correspondence: kushalkolar@gmail.com Marios.Chatzigeorgiou@uib.no
Daniel Dondorp
Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5006 Bergen, Norway
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Jordi Cornelis Zwiggelaar
Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5006 Bergen, Norway
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Jørgen Høyer
Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5006 Bergen, Norway
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Marios Chatzigeorgiou
Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5006 Bergen, Norway
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  • ORCID record for Marios Chatzigeorgiou
  • For correspondence: kushalkolar@gmail.com Marios.Chatzigeorgiou@uib.no
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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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://doi.org/10.6084/m9.figshare.10289162

  • https://doi.org/10.6084/m9.figshare.10287113

  • https://doi.org/10.6084/m9.figshare.10293041

  • http://mesmerizelab.org/

  • https://github.com/kushalkolar/MESmerize

  • https://github.com/kushalkolar/mesmerize_manuscript_notebooks

  • https://doi.org/10.6084/m9.figshare.14748915

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted June 10, 2021.
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Mesmerize: a dynamically adaptable user-friendly analysis platform for 2D & 3D calcium imaging data
Kushal Kolar, Daniel Dondorp, Jordi Cornelis Zwiggelaar, Jørgen Høyer, Marios Chatzigeorgiou
bioRxiv 840488; doi: https://doi.org/10.1101/840488
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Mesmerize: a dynamically adaptable user-friendly analysis platform for 2D & 3D calcium imaging data
Kushal Kolar, Daniel Dondorp, Jordi Cornelis Zwiggelaar, Jørgen Høyer, Marios Chatzigeorgiou
bioRxiv 840488; doi: https://doi.org/10.1101/840488

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