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EZcalcium: Open-Source Toolbox for Analysis of Calcium Imaging Data

Cantu, Daniel A. and Wang, Bo and Gongwer, Michael W. and He, Cynthia X. and Goel, Anubhuti and Suresh, Anand and Kourdougli, Nazim and Arroyo, Erica D. and Zeiger, William and Portera-Cailliau, Carlos (2020) EZcalcium: Open-Source Toolbox for Analysis of Calcium Imaging Data. Frontiers in Neural Circuits, 14 . Art. No. 25. ISSN 1662-5110. PMCID PMC7244005. https://resolver.caltech.edu/CaltechAUTHORS:20200609-074325707

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Abstract

Fluorescence calcium imaging using a range of microscopy approaches, such as two-photon excitation or head-mounted “miniscopes,” is one of the preferred methods to record neuronal activity and glial signals in various experimental settings, including acute brain slices, brain organoids, and behaving animals. Because changes in the fluorescence intensity of genetically encoded or chemical calcium indicators correlate with action potential firing in neurons, data analysis is based on inferring such spiking from changes in pixel intensity values across time within different regions of interest. However, the algorithms necessary to extract biologically relevant information from these fluorescent signals are complex and require significant expertise in programming to develop robust analysis pipelines. For decades, the only way to perform these analyses was for individual laboratories to write their custom code. These routines were typically not well annotated and lacked intuitive graphical user interfaces (GUIs), which made it difficult for scientists in other laboratories to adopt them. Although the panorama is changing with recent tools like CaImAn, Suite2P, and others, there is still a barrier for many laboratories to adopt these packages, especially for potential users without sophisticated programming skills. As two-photon microscopes are becoming increasingly affordable, the bottleneck is no longer the hardware, but the software used to analyze the calcium data optimally and consistently across different groups. We addressed this unmet need by incorporating recent software solutions, namely NoRMCorre and CaImAn, for motion correction, segmentation, signal extraction, and deconvolution of calcium imaging data into an open-source, easy to use, GUI-based, intuitive and automated data analysis software package, which we named EZcalcium.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.3389/fncir.2020.00025DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7244005PubMed CentralArticle
https://doi.org/10.1101/2020.01.02.893198DOIDiscussion Paper
ORCID:
AuthorORCID
Zeiger, William0000-0003-0567-2239
Additional Information:© 2020 Cantu, Wang, Gongwer, He, Goel, Suresh, Kourdougli, Arroyo, Zeiger and Portera-Cailliau. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Received: 20 December 2019; Accepted: 20 April 2020; Published: 15 May 2020. We thank Lauren Wierenga for her help in earlier stages of this project, Bryce Bajar, Orkun Akin, and Larry Zipursky for the Drosophila data, as well as Dean Buonomano and Dario Ringach for feedback on the manuscript. Some aspects of the EZcalcium code were described in Cantu (2019). Data Availability Statement: The datasets generated for this study are available on request to the corresponding author. Ethics Statement: The animal study was reviewed and approved by Chancellor’s Animal Research Committee and Office for Animal Research Oversight at the University of California, Los Angeles. Author Contributions: DC and CP-C designed the framework of the toolbox. DC, BW, and MG wrote the code of the toolbox. BW, CH, AG, AS, NK, EA, and WZ provided experimental data and tested the toolbox. DC, BW, MG, and CP-C wrote the manuscript. This research was supported by the UCLA Neural Microcircuits Training Grant (T32-NS058280) and the UCLA Eugene V. Cota-Robles Fellowship to DC, as well as grants W81XWH-17-1-0231 and W81XWH-14-1-0433 (USAMRMC, DOD), a Developmental Disabilities Translational Research Program grant #20160969 (The John Merck Fund), SFARI grants 295438 and 513155CP (Simons Foundation) and NIH NICHD grant R01 HD054453 to CP-C. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Funders:
Funding AgencyGrant Number
UCLAUNSPECIFIED
NIH Predoctoral FellowshipT32-NS058280
Army Medical Research and Materiel CommandW81XWH-17-1-0231
Army Medical Research and Materiel CommandW81XWH-14-1-0433
John Merck Fund20160969
Simons Foundation295438
Simons Foundation513155CP
NIHR01 HD054453
Subject Keywords:2-photon, CaImAn, deconvolution, neocortex, neural activity, software, two-photon
PubMed Central ID:PMC7244005
Record Number:CaltechAUTHORS:20200609-074325707
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200609-074325707
Official Citation:Cantu DA, Wang B, Gongwer MW, He CX, Goel A, Suresh A, Kourdougli N, Arroyo ED, Zeiger W and Portera-Cailliau C (2020) EZcalcium: Open-Source Toolbox for Analysis of Calcium Imaging Data. Front. Neural Circuits 14:25. doi: 10.3389/fncir.2020.00025
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:103784
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:09 Jun 2020 17:45
Last Modified:09 Jun 2020 17:45

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