We use a variety of open-source tools for interacting with animals and brains and analyzing the results.


Software for controlling animal training and closed-loop neural feedback via real-time state machines. Developed by Carlos Brody’s lab.


Software for coordinating the stimulation and recording of diverse streams of neural and behavioral data. The software has been previously developed at Cold Spring Harbor LaboratoryNorthwestern University , and Janelia Farm Research Campus, with NIH grant support to Gordon Shepherd and Karel Svoboda

As of 2014, ScanImage and Ephus are developed and supported by Vidrio Technologies, LLC as an open-source research resource.

Janelia Whisker Tracker

Software for automated segmentation and tracking of mouse whiskers from high-speed video. GUI interface for manual editing. Cluster-based automation. The best solution for tracking 1-4 whiskers in a single row.Screen Shot 2014-02-05 at 10.10.09 PM

Clack NG, O’Connor DH, Huber D, Petreanu L, Hires A., Peron, S., Svoboda, K., and Myers, E.W. (2012) Automated Tracking of Whiskers in Videos of Head Fixed Rodents. PLoS Comput Biol 8(7):e1002591


A github repository of matlab classes and routines used to analyze and package behavior, whisker and physiology data.  Originally developed by Dan O’Connor in Karel Svoboda’s lab and extended by the Hires lab.

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