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Here are a number of really great projects from other people in the community who are developing open-source projects for neuroscience.
mouse optokinetic reflex

Openetho is a project by Friedrich Kretschmer at the NEI/NIH for measuring the optokinetic reflex in mice. This involves separate code modules for measuring animal orientation on a small platform using a camera, and for modulating a bar-grating stimulus dynamically on four-wall LCD screens based upon the animal's movement. This project is well developed and has really helpful comments for setting this project up from scratch!

SIMA: sequential image analysis

SIMA ("Sequential IMage Analysis") is a Python-based software package from the lab of Attila Losonczy at Columbia University for the processing and analysis of two-photon imaging data. Developed by Patrick Kaifosh, Jeff Zaremba, and Nathan Danielson, this package provides a complete set of Python scripts for TIF stack motion correction and ROI extraction, among other tools.


Labrigger is a great blog from Spencer Smith at UNC Chapel Hill that gives numerous open-source designs and links, as well as brief summaries of other interesting developments in Spencer's lab and others (esp. mouse visual cortex imaging). is a really great new open source project out of the UCLA department of Neuroscience. Miniscope is a miniature head-mounted epifluorescence microscope that allows monitoring of population calcium activity in freely moving mice. Check out their wiki and learn how to build the scope, perform the surgeries, run experiments, and analyze the data. Total price is only several thousand dollars!!!! Wow...

Bonsai is an open-source behavioral tracking and data acquisition program that provides much of the functionality of commercial programs such as Ethovision and Anymaze.

Your project here!

Send us a brief description of your open-source neuroscience-related hardware/software project and a link to share your ideas with others in the field.

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