Our lab has developed various software related to super-resolution localization microscopy. The programs are provided here free to use, just please credit us if you find any of them to be useful.

Fast Temporal Median Filter for ImageJ:
This filter is very useful at reducing background noise in STORM/PALM imaging, and should be used as a preprocessing step in image reconstructions. The plugin uses a variant of the Huang algorithm so is highly efficient. On our desktop workstation, for a stack of 50,000 frames (16-bit grayscale, 156x156 pixels), a variant using RapidSort took over 40 minutes compared to 3 minutes with the current plugin.

ImageJ Plugin: Fast_Temporal_Median.java ; Installation Instructions: README.txt
Now, thanks to Christophe Leterrier, with improved memory handling and image intensity normalization.

FOCAL3D: A 3-Dimensional Clustering Algorithm for Localization Microscopy
A rapid density based algorithm for detecting and quantifying clusters in 3-dimensional localization microscopy datasets. FOCAL3D is easily optimized to reduce artifacts that commonly degrade image reconstructions and cluster detection.

Program files, sample data, and a tutorial can be found at https://github.com/MilsteinLab/FOCAL3D.
Details of the algorithm can be found in our PLoS Computational Biology article.
Matlab code for our previous 2D only version : FOCAL.zip (with sample localization table)
Details of the algorithm along with examples can be found in our Bioinformatics article.