SynapCountJ --- a Tool for Analyzing Synaptic Densities in Neurons

TL;DR

SynapCountJ is an ImageJ plugin that automates the quantification of synaptic densities in neurons, reducing analysis time and increasing objectivity using a topology-inspired method.

Contribution

The paper introduces SynapCountJ, a novel ImageJ plugin that automates synapse quantification based on colocalization and topological methods, improving efficiency and consistency.

Findings

Reduces analysis time significantly

Provides semi-automatic quantification of synapses

Applicable for batch processing of neuron images

Abstract

The quantification of synapses is instrumental to measure the evolution of synaptic densities of neurons under the effect of some physiological conditions, neuronal diseases or even drug treatments. However, the manual quantification of synapses is a tedious, error-prone, time-consuming and subjective task; therefore, tools that might automate this process are desirable. In this paper, we present SynapCountJ, an ImageJ plugin, that can measure synaptic density of individual neurons obtained by immunofluorescence techniques, and also can be applied for batch processing of neurons that have been obtained in the same experiment or using the same setting. The procedure to quantify synapses implemented in SynapCountJ is based on the colocalization of three images of the same neuron (the neuron marked with two antibody markers and the structure of the neuron) and is inspired by methods coming from Computational Algebraic Topology. SynapCountJ provides a procedure to semi-automatically quantify the number of synapses of neuron cultures; as a result, the time required for such an analysis is greatly reduced.