Our lab has also developed various software related to bacterial dynamics and 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.
Agent Based Bacterial Competition within Microchannels:
This code provides an agent based simulation of competiting strains of bacterial cells confined within two-dimensional microchannels. This code was employed in our recent article on mechanics and microbial ecology in confined systems.
The code to run the simulations and analysis of the multispecies dynamics are available on GitHub at this link (courtesy of J. Rothschild ).
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.