Open Computational Neuroscience Resources

Computational neuroscience means one of two things:

Analysis of
neuroscientific data. Examples: analysis of MRI/fMRI imaging data, invasive intracranial electrode recordings from
a mouse running in a maze or performing a task, calcium-sensitive fluorescent dye imaging data, human EEG data, computer-vision analysis of post-mortem histology stains, statistical modeling of such data, and much more!
Simulation of neural systems. Examples: simulating (aka "modeling") many compartments of a
single neuron, large networks of model neurons with simple individual
behavior, dynamical systems analysis of simplified neurons, neural "mass" models where only groups of neurons (not individual cells) are modeled, and much more!

These endeavors initially require expensive data from wet-lab
experiments to inform parameters, but most of the computational work can be
accomplished using everyday, consumer-grade laptop and desktop computers!
Indeed, the biggest barrier to entry is not hardware, data, or expense, but
rather time and passion to learn the tools and underlying biology/mathematics
needed for such computational science. Coupled with the great tools coming out
of the modern Data Science movement, new Open Science and Open Data resources make it easier than
ever to learn or even contribute to the study of the brain! The resources
below should be more than enough to provide anyone with the means to begin
learning or working in computational neuroscience, at no cost other than time
and a modern personal computer.

Note: This is intended as a list of resources to help with neuroscientific
pursuits (trying to understand the brain as it exists), as opposed to artificial intelligence or machine learning pursuits (using brain-inspired mathematics and properties to engineer systems meant to accomplish a particular task). More broadly, I've
made a similar repo-list of general open science resources
here.

Contributions are VERY welcome!

Contents:

Meta-resources

Open Code

Analysis Software

Analysis Software For Electrophysiology

Note: "electrophysiology of neurons" (also called "ephys") is equivalent to the common term "neurophysiology". In neuroscience, unless it is mentioned explicitly, you can safely assume that "electrophysiology" is referring to that of neuron cells in particular, as opposed to electrophysiology of non-neuron brain cells like astrocytes, glia, etc.
Elephant - Software for common electrophysiological data analysis operations
- Elephant is the direct successor to Neurotools
- Elephant can consume electrophysiology data loaded by Neo
Neo - Python library for enabling interoperability of electrophysiological data, including conversion from proprietary file formats
- Note that Neo does not perform analysis or visualization, but instead is only for loading or converting between electrophysiology data types.
(deprecated) OpenElectrophy - Analysis software for electrophysiological data, built on Neo
- OpenElectrophy's README indicates that it is effectively abandoned, and you should use something else.
Pynapple - "PYthon Neural Analysis Package" for neurophysiological data analysis
SpykeViewer - Analysis software for electrophysiological spike data
- SpykeViewer can consume electrophysiology data loaded by Neo
Spike Sorting:

Analysis Software For Imaging