Computational Neuroscience

SqueakR: An Experiment Interface for 'DeepSqueak' Bioacoustics Research

SqueakR is an open-source R package, available on CRAN, which streamlines bioacoustics research through automated data processing and visualizations for rodent vocalizations exported from DeepSqueak. These functions are harnessed through the ‘SqueakR’ Shiny Dashboard, available as a function within the package, which can be used to visualize experimental results and analyses, as well as conduct statistical significance test between call features across groups.

An artificial neural network for automated behavioral state classification in rats

While accurate behavioral state classification is critical for many research applications, it is often done manually, which can be both tedious and inaccurate. Here we present a novel artificial neural network that uses electrophysiological features to automatically classify behavioral state in rats with high accuracy, sensitivity, and specificity.


GeNN is a GPU enhanced Neuronal Network simulation environment supporting multiple frontends and backends. Spiking neural network models can be specified directly in Python or C++ or through interfaces to Brian 2, SpineCreator (SpineML), or PyNN.

Diffusion MRI Q-ball CSA-ODF and Hough Tractography

This is a diffusion-weighted MRI processing Matlab toolbox (including binaries), which can be used to: • Compute the Q-Ball Imaging Orientation Distribution Function in Constant Solid Angle (CSA-ODF) (Aganj et al, MRM 2010).


Neuroimaging researchers require a diverse collection of bespoke command-line and graphical tools to analyse data and answer research questions. Installing and maintaining a neuroimaging software setup is challenging and often results in un-reproducible environments.


Understanding of how neurons encode and compute information is fundamental to our study of the brain, but opportunities for hands-on experience with neurophysiological techniques on live neurons are scarce in science education.


Clinica is a software platform for clinical research studies involving patients with neurological and psychiatric diseases and the acquisition of multimodal data (neuroimaging, clinical and cognitive evaluations, genetics…), most often with longitudinal follow-up.

The Virtual Macaque Brain

A whole-cortex macaque structural connectome constructed from a combination of axonal tract-tracing and diffusion-weighted imaging data. Created for modeling brain dynamics using TheVirtualBrain ( platform. A detailed description and example usage can be found in the paper here: https://www.


World Wide Series Seminar Kilosort is a software package for identifying neurons and their spikes in extracellular electrophysiology, a process known as “spike sorting”. Kilosort has been primarily developed and tested on the Neuropixels 1.


World Wide Series Seminar Suite2P is a very modular imaging processing pipeline written in Python which allows you to perform registration of raw data movies, automatic cell detection, extraction of calcium traces and infers spike times.