Software

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 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 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 (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.

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.

ACQ4 is a python-based platform for experimental neurophysiology developed at the Allen Institute for Brain Science and the University of North Carolina, Chapel Hill. It includes support for patch-clamp electrophysiology, multiphoton imaging, scanning laser photostimulation, and many other experimental techniques.

Nervous system development and plasticity involves changes in cellular morphology, making morphological analysis a valuable exercise in the study of nervous system development, function and disease. Morphological analysis is a time-consuming exercise requiring meticulous manual tracing of cellular contours and extensions.

PUMA is 3D printed open source portable modular microscope with augmented reality, fluorescence, phase contrast, epi-illumination, epi- and trans-polarisation and other features. You can either build it fully DIY or purchase the basic scope ready made and upgrade it as required (see below for details).

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).

Stalefish is a tool to analyse gene expression from ISH or other histology slice images. From your 2D brain slice images you can build a 3D expression surface from a brain structure such as the isocortex or the hippocampus.