Experiments aiming to understand sensory-motor systems, cognition and behavior necessitate training animals to perform complex tasks. Traditional training protocols require lab personnel to move the animals between home cages and training chambers, to start and end training sessions, and in some cases, to hand-control each training trial.
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.
lab.js makes online experimentation easy. It’s a free, open, online study builder and data collection framework for the behavioral, neuro- and cognitive sciences. Studies built with lab.js run in the laboratory as well as online, across a wide variety of data collection platforms, and provide excellent performance for all modes of stimulus presentation.
MNE-Python is an open-source Python module for neuroscience data analysis. It implements many neuroscience-specific algorithms and statistical tools; has rich visualization capabilities that are both interactive and fully scriptable (for reproducibility); and integrates easily with general-purpose libraries like SciPy, Scikit-learn, and TensorFlow.
Napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing large multi-dimensional images. It’s built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (numpy, scipy).
Vision is one of the primary senses, and tracking eye gaze can offer insight into the cues that affect decision-making behavior. Thus, to study decision-making and other cognitive processes, it is fundamentally necessary to track eye position accurately.
Single cell electrophysiology remains one of the most widely used approaches of systems neuroscience. Decisions made by the experimenter during electrophysiology recording largely determine recording quality, duration of the project and value of the collected data.
pirecorder is a Python package, built on the picamera and OpenCV libraries, that provides a flexible solution for the collection of consistent image and video data with the raspberry pi. It was developed to overcome the need for a complete solution to help researchers, especially those with limited coding skills, to easily set up and configure their raspberry pi to run large numbers of controlled and automated image and video recordings using optimal settings.
The PocketPCR is a so called thermocycler used to activate biological reactions. To do so the device raises and lowers the temperature of the liquid in the small tubes. The polymerase chain reaction (PCR) is a method widely used in molecular biology to make copies of a specific DNA segment.
CLIJ2 is a GPU-accelerated image processing library for ImageJ/Fiji, Icy, Matlab and Java based on OpenCL. It comes with hundreds of operations for filtering, binarizing, labeling, measuring in images, projections, transformations and mathematical operations for images.