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CALIMA: The semi-automated open-source calcium imaging analyzer.

F D W Radstake1, E A L Raaijmakers2, R Luttge3

  • 1Department of Electrical Engineering, Signal Processing Systems Group, Eindhoven University of Technology, Eindhoven, the Netherlands.

Computer Methods and Programs in Biomedicine
|August 25, 2019
PubMed
Summary

CALIMA is a new free software tool that automates calcium imaging analysis for neuronal cell cultures. It quickly detects cells, calcium spikes, and reconstructs neuronal networks, saving researchers valuable time.

Keywords:
Ca-spike detectionCalcium imagingNeuronal network reconstructionSegmentation

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Area of Science:

  • Neuroscience
  • Cell Biology
  • Bioinformatics

Background:

  • Calcium imaging is crucial for studying cellular communication.
  • Analyzing calcium imaging data is time-consuming for researchers.
  • Existing automated tools offer only partial data analysis solutions.

Purpose of the Study:

  • To develop CALIMA, a free, open-source software for automated calcium imaging data analysis.
  • To enable rapid cell detection, calcium spike identification, and neuronal network reconstruction.
  • To reduce the manual workload in analyzing neuronal cell culture experiments.

Main Methods:

  • Utilized the difference of Gaussians algorithm for rapid region of interest (ROI) detection.
  • Employed the z-scoring algorithm for setting calcium spike detection parameters.
  • Reconstructed neuronal connections by analyzing cross-correlations in cellular activity.
  • Evaluated performance using real-life datasets of primary rat cortical neurons and SH-SY5Y neuroblastoma cultures.

Main Results:

  • CALIMA detected cells within seconds, achieving an average sensitivity of 82%.
  • Calcium spike detection sensitivity reached 96% with optimized parameters.
  • Neuronal networks were successfully reconstructed by integrating ROI activity and cell positions.
  • Performance favorably compared to alternative software solutions and manual analysis.

Conclusions:

  • CALIMA is a robust and fast tool for analyzing calcium imaging data.
  • It facilitates the digital reconstruction of neuronal cellular networks.
  • The software requires minimal user input and offers time-efficient analysis.