Romain Brette

Automatic Fitting of Spiking Neuron Models to Electrophysiological Recordings

Spiking models can accurately predict the spike trains produced by cortical neurons in response to somatically injected currents. Since the specific characteristics of the model depend on the neuron, a computational method is required to fit models to electrophysiological recordings. The fitting procedure can be very time consuming both in terms of computer simulations and in terms of code writing. We present algorithms to fit spiking models to electrophysiological data (time-varying input and spike trains) that can run in parallel on graphics processing units (GPUs). The model fitting library is interfaced with Brian, a neural network simulator in Python. If a GPU is present it uses just-in-time compilation to translate model equations into optimized code. Arbitrary models can then be defined at script level and run on the graphics card. This tool can be used to obtain empirically validated spiking models of neurons in various systems. We demonstrate its use on public data from the INCF Quantitative Single-Neuron Modeling 2009 competition by comparing the performance of a number of neuron spiking models.

Handbook of neural activity measurement

Neuroscientists employ many different techniques to observe the activity of the brain, from single-channel recording to functional imaging (fMRI). Many practical books explain how to use these techniques, but in order to extract meaningful information from the results it is necessary to understand the physical and mathematical principles underlying each measurement. This book covers an exhaustive range of techniques, with each chapter focusing on one in particular. Each author, a leading expert, explains exactly which quantity is being measured, the underlying principles at work, and most importantly the precise relationship between the signals measured and neural activity. The book is an important reference for neuroscientists who use these techniques in their own experimental protocols and need to interpret their results precisely; for computational neuroscientists who use such experimental results in their models; and for scientists who want to develop new measurement techniques or enhance existing ones.

On the design of script languages for neural simulation

In neural network simulators, models are specified according to a language, either specific or based on a general programming language (e.g. Python). There are also ongoing efforts to develop standardized languages, for example NeuroML. When designing these languages, efforts are often focused on expressivity, that is, on maximizing the number of model types than can be described and simulated. I argue that a complementary goal should be to minimize the cognitive effort required on the part of the user to use the language. I try to formalize this notion with the concept of “language entropy”, and I propose a few practical guidelines to minimize the entropy of languages for neural simulation.