Java

DeconvolutionLab2 includes a friendly user interface to run the following deconvolution algortihms: Regularized Inverse Filter, Tikhonov Inverse Filter, Naive Inverse Filter, Richardson-Lucy, Richardson-Lucy Total Variation, Landweber (Linear Least Squares), Non-negative Least Squares, Bounded-Variable Least Squares, Van Cittert, Tikhonov-Miller, Iterative Constraint Tikhonov-Miller, FISTA, ISTA.

The backbone of our software architecture is a library that contains the number-crunching elements of the deconvolution task. It includes the tool for a complete validation pipeline. Inquisitive minds inclined to peruse the code will find it fosters the understanding of deconvolution.

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GaussFit_OnSpot is an ImageJ plugin for fitting Gaussian profiles onto selected positions in diffraction-limited images (e.g. single molecules, protein clusters, vesicles, or stars).

The plugin performs a function fit in regions of interest (ROI) around spots marked by point selections in grayscale images. Single or multiple spots can be either selected manually with the Multi-point tool or automatically with the Find Maxima function.

There is a PDF with more information, and also an example image.

Quote " finding and/or analyzing colocalization of bright intensity spots (cells, particles, vesicles, comets, dots, etc) in images with heterogeneous background (microscopy, astronomy, engineering, etc). "

Uses Gaussian-Mexican hat convolution for preprocessing.

"PTA2 is an ImageJ1.x plugins that enable automatic particle tracking"

This plugin is developed specifically for single-molecule imaging, so it's good at tracking spots with noisy background. 

"The Microscope Image Analysis Toolbox MiToBo is an extension for the widely used image processing application ImageJ and its new release ImageJ 2.0.
MiToBo ships with a set of operators ready to be used as plugins in ImageJ. They focus on the analysis of biomedical images acquired by various types of microscopes."