Software

CaImAn: open source scalable algorithms for calcium and voltage imaging data

Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months.

COGAIN Association (COmmunication by GAze INteraction)

The COGAIN Association aims to promote research and development in the field of gaze-based interaction in computer-aided communication and control. Computer applications can be controlled by gazing at the computer screen.

PyControl

Open source, Python based, behavioural experiment control. pyControl is a system of open source hardware and software for controlling behavioural experiments, built around the Micropython microcontroller. pyControl makes it easy to program complex behavioural tasks using a clean, intuitive, and flexible syntax for specifying tasks as state machines.

CASCADE: Calibrated inference of spiking from calcium ΔF/F data using deep networks

CASCADE translates calcium imaging ΔF/F traces into spiking probabilities or discrete spikes. CASCADE is based on deep networks and runs on Python (Linux/Windows/Mac); it can be used either as a web application (Colaboratory notebook), or locally on a CPU or GPU.

DANNCE

DANNCE (3-Dimensional Aligned Neural Network for Computational Ethology) is a convolutional neural network (CNN) that calculates the 3D positions of user-defined anatomical landmarks on behaving animals from videos taken at multiple angles.

Building a Simple and Versatile Illumination System for Optogenetic Experiments

Controlling biological processes using light has increased the accuracy and speed with which researchers can manipulate many biological processes. Optical control allows for an unprecedented ability to dissect function and holds the potential for enabling novel genetic therapies.

GeNN

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.

Pingouin

Pingouin is an open-source statistical package written in Python 3 and based mostly on Pandas and NumPy. Some of its main features are listed below. For a full list of available functions, please refer to the API documentation.

YASA

YASA (Yet Another Spindle Algorithm) is a command-line sleep analysis toolbox in Python. The main functions of YASA are: Automatic sleep staging of polysomnography data (see preprint article). Event detection: sleep spindles, slow-waves and rapid eye movements, on single or multi-channel EEG data.

GuPPy, a Python toolbox for the analysis of fiber photometry data

Fiber photometry (FP) is an adaptable method for recording in vivo neural activity in freely behaving animals. It has become a popular tool in neuroscience due to its ease of use, low cost, the ability to combine FP with freely moving behavior, among other advantages.