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Fiji is just ImageJ: a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. The main focus of Fiji is to assist research in life sciences. It is a free, open-source, community-driven project.

PALMsiever is a MATLAB-based application that allows the filtering (sieving) and analysis of localization-microscopy data. It provides the ability to render the data using different visualization algorithms and perform simple measurements on the point-localization data. It is extensible using simple MATLAB scripts and a number of plugins is already provided with the software itself, including a clustering algorithm and 3D rendering.

Strengths: intuitive, easy navigation through the point-localization data

Limitations: no multi-color

This ImageJ plugin creates high resolution PSF images by averaging many bead im- ages as well as exploiting the assumption that the point spread function is rotationally symmetric with respect to the axial axis (z-direction).

Easy-to-use, computationally efficient, two- and three-dimensional, feature point-tracking tool for the automated detection and analysis of particle trajectories as recorded by video imaging in cell biology. 

The tracking process requires no apriori mathematical modelling of the motion, it is self-initialising, it discriminates spurious detections, and it can handle temporary occlusion as well as particle appearance and disappearance from the image region. 

Image segmentation based on the MOSAIC Discrete region competition algorithm. 

‘’’Squassh’’’ is a tool for 2D and 3D segmentation and quantification of subcellular shapes in fluorescence microscopy images. It provides globally optimal detection and segmentation of objects with constant internal intensity distribution, followed by object-based colocalization analysis. The segmentation computed by Region Competition can optionally correct for the PSF of the microscope, hence providing optimally deconvolved segmentations. Part of the mosaic suite

A function to perform morphological operation on binary and grayscale images.