Software

Brainglobe atlas API

Many excellent brain atlases exist for different species. Some of them have an API (application programming interface) to allow users to interact with the data programmatically (e.g. the excellent Allen Mouse Brain Atlas), but many do not, and there is no consistent way to process data from multiple sources.

culture_shock

Culture Shock is an open-source electroporator that was developed through internet based collaboration, starting on the DIYbio Google Group. It is an evolution on the traditional capacitive discharge circuit topology, instead using pulsed induction to enable a programmable waveform as well as reduce the size, weight, and cost of the equipment.

brainrender

brainrender is a python package for the visualization of three dimensional neuro-anatomical data. It can be used to render data from publicly available data set (e.g. Allen Brain atlas) as well as user generated experimental data.

JASP

JASP is a cross-platform statistical software program with a state-of-the-art graphical user interface. The JASP interface allows you to conduct statistical analyses in seconds, and without having to learn programming or risking a programming mistake.

pyControl

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.

pyPhotometry

pyPhotometry is system of open source, Python based, hardware and software for neuroscience fiber photometry data acquisition, consisting of an acquisition board and graphical user interface. pyPhotometry supports data aquisition from two analog and two digital inputs, and control of two LEDs via built in LED drivers with an adjustable 0-100mA output.

SLEAP

SLEAP (Social LEAP Estimates Animal Poses) is a multi-animal pose tracker based on deep learning. It is the successor of LEAP (Pereira et al., Nature Methods, 2019) and was designed to deal with the problem of tracking body landmarks of multiple freely interacting animals.

Neuroimaging Informatics Tools and Resources Collaboratory (NITRC)

NeuroImaging Tools & Resources Collaboratory is an award-winning free web-based resource that offers comprehensive information on an ever expanding scope of neuroinformatics software and data. Since debuting in 2007, NITRC has helped the neuroscience community make further discoveries using software and data produced from research that used to end up lost or disregarded.

PiVR

PiVR is a system that allows experimenters to immerse small animals into virtual realities. The system tracks the position of the animal and presents light stimulation according to predefined rules, thus creating a virtual landscape in which the animal can behave.

ReproNim: A Center for Reproducible Neuroimaging Computation

ReproNim’s goal is to improve the reproducibility of neuroimaging science and extend the value of our national investment in neuroimaging research, while making the process easier and more efficient for investigators.