Software

Currently I an active maintainer and developer on a number of open-source Python packages, as part of the IOAM (It's only a model!) project. This primarily includes the Topographica neural simulator, the FeatureMapper pattern presentation and response measurement and analysis software, and finally the HoloViews data visualization software.

Topographica

Topographica is a general-purpose simulator for topographic neural maps. It forms the foundation for all of my research and during my PhD I have contributed a multi-threaded sparse implementation of the core algorithms, a Cython implementation of the core algorithms and numerous fixes to the API and functionality.

HoloViews

HoloViews is a multi-dimensional data visualization and visualization software that I developed as one of two core developers. It provides convenient data containers, for generating complex and interactive visualizations and animations in the IPython notebook. Most plots and animations on this website were generated using this package.

FeatureMapper

FeatureMapper, originally part of the Topographica package, allows you to analyze how a system responds to a protocol of parameterizable test patterns. By coordinating the presentation of ImaGen sine gratings with various parameter settings (orientation, phase, color, spatial frequency, etc.) to an external system, which returns responses in the form of a matrix of activity values. With this data, FeatureMapper can then calculate tuning curves, receptive fields, peri-stimulus time histograms, and feature maps that characterize the response of that system to the input patterns. These tools can be used to understand models implemented in any simulator, and can even be used with experimental data as long as the input patterns and their responses can be saved.