Computational Neuroscience

napari

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).

morphologica

morphologica is a header-only C++ library which provides simulation support facilities for simulations of dynamical systems. It helps with: Configuration: morphologica allows you to easily set up a simulation parameter configuration system, using the JSON reading and writing abilities of morph::Config.

NetPyNE

NetPyNE (Networks using Python and NEURON) is a Python package to facilitate the development, simulation, parallelization, analysis, and optimization of biophysical neuronal networks using the NEURON simulator. For more details, installation instructions, documentation, tutorials, forums, videos and more, please visit: www.

Greedy

Greedy is a tool for fast medical image registration. It is a fast CPU-based deformable image registration tool that can be used in applications where many images have to be registered in parallel.

neurolib

Easy whole-brain modeling for computational neuroscientists πŸ‘©πŸΏβ€πŸ”¬πŸ’»πŸ§  In its essence, neurolib is a computational framework for simulating coupled neural mass models written in Python. It helps you to easily load structural brain scan data to construct brain networks where each node is a neural mass representing a single brain area.

YAPiC

World Wide Series Seminar With YAPiC you can make your own customized filter (also called model or classifier) to enhance a certain structure of your choice with a simple Python based command line interface, installable with pip.

Computational Cognitive Neuroscience 4th Ed

This is the 4th edition of the online, freely available textbook, providing a complete, self-contained introduction to the field of Computational Cognitive Neuroscience, where computer models of the brain are used to understand a wide range of cognitive functions, including perception, attention, motor control, learning, memory, language, and executive function.

Emergent Neural Network Simulation Software

Neural network simulation software written in Go and Python, for developing biologically-based but also computationally functional neural models. Features an interactive 3D interface for visualizing networks and data, and has many implemented models of a wide range of cognitive phenomena.

Uncertainpy A python toolbox for uncertainty quantification and sensitivity analysis tailored towards computational neuroscience

Uncertainpy is a python toolbox for uncertainty quantification and sensitivity analysis tailored towards computational neuroscience. Uncertainpy is model independent and treats the model as a black box where the model can be left unchanged.

PsychRNN: An Accessible and Flexible Python Package for Training Recurrent Neural Network Models on Cognitive Tasks

PsychRNN is designed for neuroscientists and psychologists who are interested in RNNs as models of cognitive function in the brain. Despite growing interest in RNNs as models of brain function, this approach poses relatively high barriers to entry to researchers, due to the technical know-how required for specialized deep learning software (e.