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01-01-2018 | Methods Paper

NeuroSeg: automated cell detection and segmentation for in vivo two-photon Ca²⁺ imaging data

Authors: Jiangheng Guan, Jingcheng Li, Shanshan Liang, Ruijie Li, Xingyi Li, Xiaozhe Shi, Ciyu Huang, Jianxiong Zhang, Junxia Pan, Hongbo Jia, Le Zhang, Xiaowei Chen, Xiang Liao

Published in: Brain Structure and Function | Issue 1/2018

Abstract

Two-photon Ca²⁺ imaging has become a popular approach for monitoring neuronal population activity with cellular or subcellular resolution in vivo. This approach allows for the recording of hundreds to thousands of neurons per animal and thus leads to a large amount of data to be processed. In particular, manually drawing regions of interest is the most time-consuming aspect of data analysis. However, the development of automated image analysis pipelines, which will be essential for dealing with the likely future deluge of imaging data, remains a major challenge. To address this issue, we developed NeuroSeg, an open-source MATLAB program that can facilitate the accurate and efficient segmentation of neurons in two-photon Ca²⁺ imaging data. We proposed an approach using a generalized Laplacian of Gaussian filter to detect cells and weighting-based segmentation to separate individual cells from the background. We tested this approach on an in vivo two-photon Ca²⁺ imaging dataset obtained from mouse cortical neurons with differently sized view fields. We show that this approach exhibits superior performance for cell detection and segmentation compared with the existing published tools. In addition, we integrated the previously reported, activity-based segmentation into our approach and found that this combined method was even more promising. The NeuroSeg software, including source code and graphical user interface, is freely available and will be a useful tool for in vivo brain activity mapping.

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Title: NeuroSeg: automated cell detection and segmentation for in vivo two-photon Ca2+ imaging data
Authors: Jiangheng Guan
Jingcheng Li
Shanshan Liang
Ruijie Li
Xingyi Li
Xiaozhe Shi
Ciyu Huang
Jianxiong Zhang
Junxia Pan
Hongbo Jia
Le Zhang
Xiaowei Chen
Xiang Liao
Publication date: 01-01-2018
Publisher: Springer Berlin Heidelberg
Published in: Brain Structure and Function / Issue 1/2018
Print ISSN: 1863-2653
Electronic ISSN: 1863-2661
DOI: https://doi.org/10.1007/s00429-017-1545-5

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NeuroSeg: automated cell detection and segmentation for in vivo two-photon Ca²⁺ imaging data

Abstract

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