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Updated: May 22, 2026

Imaging Local Ca2+ Signals in Cultured Mammalian Cells

Imaging Local Ca²⁺ Signals in Cultured Mammalian Cells

Published on: March 3, 2015

Protocol for using the multi-cellular analysis toolbox in ImageJ for single-cell calcium imaging analysis.

John Hageter¹, Eric Horstick²

¹West Virginia University, Morgantown, WV 26505, USA.

|May 20, 2026

Summary

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This study introduces a protocol for analyzing zebrafish calcium imaging data using the multi-cellular analysis (MCA) toolbox. This method extracts neuronal activity signals for a better understanding of brain function.

Area of Science:

Neuroscience
Biophysics
Computational Biology

Background:

Genetically encoded indicators (GEIs) are crucial for functional brain imaging.
Understanding neuronal and circuit mechanisms requires advanced data analysis techniques.
Zebrafish are a key model organism for studying brain function.

Purpose of the Study:

To present a detailed protocol for analyzing zebrafish calcium imaging data.
To demonstrate the utility of the multi-cellular analysis (MCA) toolbox in ImageJ.
To provide a reproducible pipeline for extracting neuronal activity signals.

Main Methods:

Installation and utilization of the multi-cellular analysis (MCA) toolbox in ImageJ.
Extraction of calcium signals from zebrafish calcium imaging data.

Keywords:

Cell Biology Computer sciences Developmental biology Microscopy Model Organisms Neuroscience Single Cell

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Last Updated: May 22, 2026

Imaging Local Ca2+ Signals in Cultured Mammalian Cells

Imaging Local Ca²⁺ Signals in Cultured Mammalian Cells

Published on: March 3, 2015

Single-Cell Calcium Imaging for Studying the Activation of Calcium Ion Channels

Single-Cell Calcium Imaging for Studying the Activation of Calcium Ion Channels

Published on: December 13, 2024

TACI: An ImageJ Plugin for 3D Calcium Imaging Analysis

TACI: An ImageJ Plugin for 3D Calcium Imaging Analysis

Published on: December 16, 2022

Identification of significant changes in neuronal activity using MCA functions.

Main Results:

Successful implementation of the MCA toolbox for zebrafish data analysis.
Generation of interpretable plots of neuronal activity.
A standardized pipeline for processing functional imaging data.

Conclusions:

The presented protocol enables robust analysis of neuronal activity from calcium imaging.
The MCA toolbox offers a versatile tool for neuroscience research.
This pipeline is adaptable to various model systems for studying brain function.