Posts

Bonsai is a high-performance, easy to use, and flexible visual programming language for designing closed-loop neuroscience experiments combining physiology and behaviour data. Bonsai has allowed scientists with no previous programming experience to quickly develop their own experimental rigs and is also being increasingly used as a platform to integrate new open-source hardware and software from the experimental neuroscience community.

Ethoscopes are machines for high-throughput analysis of behavior in Drosophila and other animals. Ethoscopes provide a software and hardware solution that is reproducible and easily scalable. They perform, in real-time, tracking and profiling of behavior by using a supervised machine learning algorithm, are able to deliver behaviorally triggered stimuli to flies in a feedback-loop mode, and are highly customizable and open source.

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:

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 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.

World Wide Series Seminar 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.

We describe the “FishCam”, a low-cost (500 USD) autonomous camera package to record videos and images underwater. The system is composed of easily accessible components and can be programmed to turn ON and OFF on customizable schedules.

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.

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.

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.