The SilverLab has developed a wide range of software resources for building models and acquiring and analysing data. Modelling tools include a 3D reaction-diffusion simulator that implements either deterministic or stochastic simulations and can simulate the diffusion of small and finite sized objects within configurable 3D spaces. We have also developed a suite of tools for building biologically detailed models of neural systems in a standardised structured format (NeuroML2) that can be automatically validated and shared through Open Source Brain , making them Findable, Accessible, Interoperable and Reproducible (FAIR). In addition, we have developed software for acquisition and analysis of 3D two-photon imaging and electrophysiological data. Links to these resources are here:

Neuroinformatics and neural modelling

• Standardised models of neurons and networks are available at www.OpenSourceBrain.org
• Tools for building models and converting them into a standardised machine readable format are available at www.NeuroML.org
• NeuroConstruct, a software application for building 3D network models is available at www.NeuroConstruct.org
• D3D is a Java-based 3D reaction-diffusion simulator that uses either an explicit finite-difference or Monte Carlo excluded-volume algorithm. https://github.com/SilverLabUCL/D3D
• NWB Explorer is a web based visualiser and analysis tool for Neurophysiology data, available at http://nwbexplorer.opensourcebrain.org .

Microscopy

• LabView and MatLab versions of the user interface and data acquisition software for the Acousto-Optic Lens 3D two photon Microscope (AOLM) developed in the Silver Lab is available at https://github.com/SilverLabUCL/SilverLab-Microscope. The software can perform multiple random access imaging modes and protocols including Z-stacks, multi-plane, single-plane, sub-volume, patches, line scans and points, as well performing real time 3D movement correction. It comes with a variety of ready-to-use tools for visualising the data acquired with the system.
• A model of light transmission through an Acousto-optic lens is available at www.github.com/SilverLabUCL/aol_model

Electrophysiology

• NeuroMatic 3.0, an electrophysiological data acquisition and analysis package written in the IGOR Pro environment is available at https://github.com/SilverLabUCL/NeuroMatic