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Minian an Open-source Miniscope Analysis Pipeline

View ORCID ProfileZhe Dong, William Mau, Yu Feng, Zachary T. Pennington, Lingxuan Chen, Yosif Zaki, Kanaka Rajan, Tristan Shuman, View ORCID ProfileDaniel Aharoni, Denise J. Cai
doi: https://doi.org/10.1101/2021.05.03.442492
Zhe Dong
1Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai
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William Mau
1Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai
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Yu Feng
1Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai
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Zachary T. Pennington
1Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai
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Lingxuan Chen
1Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai
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Yosif Zaki
1Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai
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Kanaka Rajan
1Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai
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Tristan Shuman
1Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai
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Daniel Aharoni
2Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles
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  • For correspondence: denise.cai@mssm.edu
Denise J. Cai
1Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai
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  • For correspondence: denise.cai@mssm.edu
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Abstract

Miniature microscopes have gained considerable traction for in vivo calcium imaging in freely behaving animals. However, extracting calcium signals from raw videos is a computationally complex problem and remains a bottleneck for many researchers utilizing single-photon in vivo calcium imaging. Despite the existence of many powerful analysis packages designed to detect and extract calcium dynamics, most have either key parameters that are hard-coded or insufficient step-by-step guidance and validations to help the users choose the best parameters. This makes it difficult to know whether the output is reliable and meets the assumptions necessary for proper analysis. Moreover, large memory demand is often a constraint for setting up these pipelines since it limits the choice of hardware to specialized computers. Given these difficulties, there is a need for a low memory demand, user-friendly tool offering interactive visualizations of how altering parameters at each step of the analysis affects data output. Our open-source analysis pipeline, Minian (Miniscope Analysis), facilitates the transparency and accessibility of single-photon calcium imaging analysis, permitting users with little computational experience to extract the location of cells and their corresponding calcium traces and deconvolved neural activities. Minian contains interactive visualization tools for every step of the analysis, as well as detailed documentation and tips on parameter exploration. Furthermore, Minian has relatively small memory demands and can be run on a laptop, making it available to labs that do not have access to specialized computational hardware. Minian has been validated to reliably and robustly extract calcium events across different brain regions and from different cell types. In practice, Minian provides an open-source calcium imaging analysis pipeline with user-friendly interactive visualizations to explore parameters and validate results.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • This revised version includes updated validation and performance benchmark results, most notably the inclusion of performance results with and without visualization. This version also includes some minor clarification and correction of the manuscript. Figure 15, 16, 18, 19 were updated.

  • https://github.com/DeniseCaiLab/minian

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-ND 4.0 International license.
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Posted May 18, 2022.
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Minian an Open-source Miniscope Analysis Pipeline
Zhe Dong, William Mau, Yu Feng, Zachary T. Pennington, Lingxuan Chen, Yosif Zaki, Kanaka Rajan, Tristan Shuman, Daniel Aharoni, Denise J. Cai
bioRxiv 2021.05.03.442492; doi: https://doi.org/10.1101/2021.05.03.442492
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Minian an Open-source Miniscope Analysis Pipeline
Zhe Dong, William Mau, Yu Feng, Zachary T. Pennington, Lingxuan Chen, Yosif Zaki, Kanaka Rajan, Tristan Shuman, Daniel Aharoni, Denise J. Cai
bioRxiv 2021.05.03.442492; doi: https://doi.org/10.1101/2021.05.03.442492

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