Indexed in SCIE, Scopus, PubMed & PMC
pISSN 1226-4512 eISSN 2093-3827


home Article View

Review Article

Korean J Physiol Pharmacol 2019; 23(4): 237-249

Published online July 1, 2019

Copyright © Korean J Physiol Pharmacol.

Imaging and analysis of genetically encoded calcium indicators linking neural circuits and behaviors

Jihae Oh#, Chiwoo Lee#, and Bong-Kiun Kaang*

School of Biological Sciences, Seoul National University, Seoul 08826, Korea

Correspondence to:Bong-Kiun Kaang

Received: January 14, 2019; Revised: May 29, 2019; Accepted: May 29, 2019

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.


Confirming the direct link between neural circuit activity and animal behavior has been a principal aim of neuroscience. The genetically encoded calcium indicator (GECI), which binds to calcium ions and emits fluorescence visualizing intracellular calcium concentration, enables detection of in vivo neuronal firing activity. Various GECIs have been developed and can be chosen for diverse purposes. These GECI-based signals can be acquired by several tools including two-photon microscopy and microendoscopy for precise or wide imaging at cellular to synaptic levels. In addition, the images from GECI signals can be analyzed with open source codes including constrained non-negative matrix factorization for endoscopy data (CNMF_E) and miniscope 1-photon-based calcium imaging signal extraction pipeline (MIN1PIPE), and considering parameters of the imaged brain regions (e.g., diameter or shape of soma or the resolution of recorded images), the real-time activity of each cell can be acquired and linked with animal behaviors. As a result, GECI signal analysis can be a powerful tool for revealing the functions of neuronal circuits related to specific behaviors.

Keywords: Calcium channel, Calcium imaging, Data analysis, Miniscope, Neuronal calcium-sensor proteins