Software

Bonvision

BonVision is an open-source closed-loop visual environment generator developed by the Saleem Lab and Solomon Lab at the UCL Institute of Behavioural Neuroscience in collaboration with NeuroGEARS. BonVision’s key features include:

Poseidon

The Poseidon is an open-source syringe pump and microscope system. It uses 3D printed parts and common components that can be easily purchased. It can be used in microfluidics experiments or other applications.

DeepLabStream

DeepLabStream is a python based multi-purpose tool that enables the realtime tracking of animals and manipulation of experiments. Our toolbox is adapted from the previously published DeepLabCut (Mathis et al., 2018) and expands on its core capabilities.

SpikeInterface

SpikeInterface is a unified Python framework for spike sorting. With its high-level API, it is designed to be accessible and easy to use, allowing users to build full analysis pipelines for spike sorting (reading-writing (IO) / preprocessing / spike sorting / postprocessing / validation / curation / comparison / visualization) with a few lines of code.

neuTube

neuTube is an open source software for reconstructing neurons from fluorescence microscope images. It is easy to use and improves the efficiency of reconstructing neuron structures accurately. The framework combines 2D/3D visualization, semi-automated tracing algorithms, and flexible editing options that simplify the task of neuron reconstruction.

OpenTrons

Today, biologists spend too much time pipetting by hand. We think biologists should have robots to do pipetting for them. People doing science should be free of tedious benchwork and repetitive stress injuries.

Deep Cinac

Two-photon calcium imaging is now widely used to infer neuronal dynamics from changes in fluorescence of an indicator. However, state of the art computational tools are not optimized for the reliable detection of fluorescence transients from highly synchronous neurons located in densely packed regions such as the CA1 pyramidal layer of the hippocampus during early postnatal stages of development.

UC2

The open-source optical toolbox UC2 [YouSeeToo] simplifies the process of building optical setups, by combining 3D-printed cubes, each holding a specific component (e.g. lens, mirror) on a magnetic square-grid baseplate. The use of widely available consumables and 3D printing, together with documentation and software, offers an extremely low-cost and accessible alternative for both education and research areas.

Automated Operant Conditioning

Operant conditioning (OC) is a classical paradigm and a standard technique used in experimental psychology in which animals learn to perform an action to achieve a reward. By using this paradigm, it is possible to extract learning curves and measure accurately reaction times (RTs).

Heuristic Spike Sorting Tuner (HSST), a framework to determine optimal parameter selection for a generic spike sorting algorithm

Extracellular microelectrodes frequently record neural activity from more than one neuron in the vicinity of the electrode. The process of labeling each recorded spike waveform with the identity of its source neuron is called spike sorting and is often approached from an abstracted statistical perspective.