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.

FOCAL Clustering Algorithm for Localization Microscopy:
A rapid density based algorithm for detecting clusters in localization microscopy datasets. FOCAL is easily optimized to reduce artifacts that commonly degrade image reconstructions and minimize the detection of false or pseudo clusters. Details of the algorithm along with examples can be found in our Bioinformatics article.

Matlab Code: FOCAL.zip (with sample localization table)

Coming Soon: FOCAL 3D, our rapid 2D clustering software for 3D datasets.