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Minian, an open-source miniscope analysis pipeline.

Zhe Dong1, William Mau1, Yu Feng1

  • 1Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, United States.

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|June 1, 2022
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Summary
This summary is machine-generated.

Minian is an open-source tool that simplifies in vivo calcium imaging analysis for researchers. It offers user-friendly, interactive visualizations to extract neural activity from miniscope data with low memory demands.

Keywords:
Miniscopeanalysis pipelinecalcium imagingmouseneuroscience

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Area of Science:

  • Neuroscience
  • Computational Biology
  • Bioimaging

Background:

  • In vivo calcium imaging using miniature microscopes is crucial for studying freely behaving animals.
  • Extracting calcium signals from imaging data is computationally intensive and a bottleneck for many researchers.
  • Existing analysis tools often lack user-friendly parameter guidance and validation, hindering reliable data extraction.

Purpose of the Study:

  • To develop a low memory demand, user-friendly tool for analyzing single-photon in vivo calcium imaging data.
  • To provide interactive visualizations for parameter exploration and validation in calcium imaging analysis.
  • To enhance transparency and accessibility of calcium imaging data analysis for researchers with limited computational experience.

Main Methods:

  • Developed Minian, an open-source analysis pipeline for miniscope calcium imaging.
  • Integrated interactive visualization tools for each analysis step, aiding parameter selection.
  • Ensured low memory footprint for accessibility on standard hardware like laptops.

Main Results:

  • Minian enables users to extract cell locations, calcium traces, and deconvolved neural activity.
  • Interactive visualizations allow users to observe the impact of parameter choices on data output.
  • The pipeline has been validated for robust and reliable calcium event extraction across various brain regions and cell types.

Conclusions:

  • Minian addresses the need for accessible and transparent calcium imaging analysis.
  • The tool empowers researchers with limited computational resources to perform reliable in vivo calcium imaging analysis.
  • Minian facilitates the extraction and validation of neural activity, advancing neuroscience research.