Human Neuroscience

FastSurfer

FastSurfer is a fast and extensively validated deep-learning pipeline for the fully automated processing of structural human brain MRIs. As such, it provides FreeSurfer conform outputs, enables efficient big-data analysis for large cohort studies, and time-critical clinical applications such as structure localization during image acquisition or rapid extraction of quantitative measures for precision medicine.

YASA

YASA (Yet Another Spindle Algorithm) is a command-line sleep analysis toolbox in Python. The main functions of YASA are: Automatic sleep staging of polysomnography data (see preprint article). Event detection: sleep spindles, slow-waves and rapid eye movements, on single or multi-channel EEG data.

BioAmp EXG Pill

BioAmp EXG Pill is a small, powerful Analog Front End (AFE) biopotential signal acquisition board that can be paired with any 5 V Micro Controller Unit (MCU) with an ADC. It is capable of recording publication-quality biopotential signals like ECG, EMG, EOG, and EEG, without the inclusion of any dedicated hardware or software filters.

NeuroDesk

Neuroimaging researchers require a diverse collection of bespoke command-line and graphical tools to analyse data and answer research questions. Installing and maintaining a neuroimaging software setup is challenging and often results in un-reproducible environments.

Load confound

Load a sensible subset of the fMRI confounds generated with fMRIprep in python (Esteban et al., 2018). The predefined denoising strategies are all adapted from Ciric et al. 2017. Check the docstring of each strategy for more info and a list of parameters.

Collaborative Informatics and Neuroimaging Suite Toolkit for Anonymous Computation (COINSTAC)

COINSTAC provides a platform to analyze data stored locally across multiple organizations without the need for pooling the data at any point during the analysis. It is intended to be an ultimate one-stop shop by which researchers can build any statistical or machine learning model collaboratively in a decentralized fashion.

lab.js

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

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.

jsPsych

jsPsych is a JavaScript library for running behavioral experiments in a web browser. The library provides a flexible framework for building a wide range of laboratory-like experiments that can be run online.

Psygo

The easiest way to get started creating online behavioural experiments! psygo is a CLI tool that streamlines the development of custom jsPsych plugins, allowing you to create custom behavioural experiments that can be run online.