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SynQuant: An Automatic Tool to Quantify Synapses from Microscopy Images

By Yizhi Wang, Congchao Wang, Petter Ranefall, Gerard Broussard, Yinxue Wang, Guilai Shi, Boyu Lyu, Yue Wang, Lin Tian, Guoqiang Yu

Posted 02 Feb 2019
bioRxiv DOI: 10.1101/538769

Motivation: Synapses are essential to neural signal transmission. Therefore, quantification of synapses and related neurites from images is vital to gain insights into the underlying pathways of brain functionality and diseases. Despite the wide availability of synaptic punctum imaging data, several issues are impeding satisfactory quantification of these structures by current tools. First, the antibodies used for labeling synapses are not perfectly specific to synapses. These antibodies may exist in neurites or other cell compartments. Second, the brightness for different neurites and synaptic puncta is heterogeneous due to the variation of antibody concentration and synapse-intrinsic differences. Third, images often have low signal to noise ratio due to constraints of experiment facilities and availability of sensitive antibodies. These issues make the detection of synapses challenging and necessitates developing a new tool to easily and accurately quantify synapses. Results: We present an automatic probability-principled synapse detection algorithm and integrate it into our synapse quantification tool SynQuant. Derived from the theory of order statistics, our method controls the false discovery rate and improves the power of detecting synapses. SynQuant is unsupervised, works for both 2D and 3D data, and can handle multiple staining channels. Through extensive experiments on one synthetic and three real data sets with ground truth annotation or manual labeling, SynQuant was demonstrated to outperform peer specialized synapse detection tools as well as generic spot detection methods, including 4 unsupervised and 11 variants of 3 supervised methods. Availability: Java source code, Fiji plug-in, and test data available at https://github.com/yu-lab-vt/SynQuant.

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