plugin

Manual tracking using Trackmate plugin (comes with FIji, so no installation required if you are using Fiji). 

The freely available software module below is a 3D LoG filter. It applies a LoG (Laplacian of Gaussian or Mexican Hat) filter to a 2D image or to 3D volume. Here, we have a fast implementation. It is a perfect tool to enhance spots, like spherical particles, in noisy images. This module is easy to tune, only by selecting the standard deviations in X, Y and Z directions.

run("LoG 3D", "sigmax=1 sigmay=1 sigmaz=13 displaykernel=0 volume=1");

This method was originally designed to track objects (not necessarily spots) already identified in 2D 
frames and has been applied previously to particle tracking and analysis in high-speed atomic force microscopy image series.

The phase contrast microscopy segmentation toolbox (PHANTAST) is a collection of open-source algorithms and tools for the processing of phase contrast microscopy (PCM) images. It was developed at University College London's department of Biochemical Engineering and CoMPLEX.

An ImageJ plugin for DEFCoN, the fluorescence spot counter based on fully convolutional neural networks