SynQuant: An Automatic Tool to Quantify Synapses from Microscopy Images

Abstract

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.

Taurine Promotes Neurite Outgrowth and Synapse Development of Both Vertebrate and Invertebrate Central Neurons

“…To gain further insight into the effect of taurine on synaptic machinery, we next focused on analyzing neurites (cropped 50 μm × 20 μm section of neurites extending from pyramidal neurons; see “Materials and Methods” section for detailed description) using the SynQuant plugin in ImageJ (Wang et al, 2020 ). This method allows for the identification of puncta and the detailed quantification of the puncta intensity and area ( Figure 4A ).…”

“…It, therefore, remains unknown whether taurine affects the level of clustering of synaptic proteins at the single neuron-, neurite-, or network-levels. We took advantage of well-established methods such as SynQuant (Wang et al, 2020 ) and SynapCountJ (Mata et al, 2016 ) to analyze different synaptic parameters in entire images (networks) and primary neurites. We found that taurine not only regulated synaptic protein expression in networks but also their intensity in synaptic puncta along neurites.…”

“…The ImageJ plugin SynapCountJ was used to measure the number of synapses (colocalization of synaptophysin and PSD95) per area of traced neurite as previously described (Mata et al, 2016 ). Synaptic puncta parameters were measured with the ImageJ plugin SynQuant (Wang et al, 2020 ). To look at synaptophysin (presynaptic) and PSD95 (postsynaptic) puncta measurements in entire fields of view (many neuronal networks taken together), uncropped fluorescent images were analyzed by SynQuant, and the number of synaptophysin and PSD95 puncta was outputted.…”

Differential expression of tau species and the association with cognitive decline and synaptic loss in Alzheimer's disease

“…All statistical details of the experiments can be found in either the was quantified using the SynQuant plugin installed to Fiji software as described previously. 81 The following parameters were used to detect the puncta: 10 as a Z-score particle detection, 10 as a minimum particle size, 200 as a maximum particle size, 0.25 as a minimum fill, and 2 as a maximum width-height (WH) ratio. (4) We blindly counted the number of tau inclusion containing TauBiosensor cells.…”

Psilocybin Combines Rapid Synaptogenic And Anti-Inflammatory Effects In Vitro

“…Second order dendrites from ten individual cells per well were imaged and analyzed. To quantify synaptic puncta, we used SynQuant 45 . To optimize the settings for SynQuant we randomly chose 10 images distributed between the different treatments.…”