Collected by: Payman Roghani

Here, you'll find links to various tools, articles, datasets, and more, related to the field of Computational Cognitive Neuroscience.

• Brain Imaging Data Structure (BIDS) - A simple and intuitive way to organize and describe your neuroimaging and behavioral data.
• BrainMap - Database of published task and structural neuroimaging experiments with coordinate-based results.
• Cam-CAN - Large-scale collaborative research project from the University of Cambridge (MRI, MEG, cognitive data).
• Computational Psychiatry Data - Data resources curated by Dr. Eiko Fried.
• CRCNS - Collaborative Research in Computational Neuroscience - Data sharing.
• DANDI Archive - Archive for publishing and sharing neurophysiology data (electrophysiology, optophysiology, etc.).
• DRYAD - Open data publishing platform.
• EBRAINS - Platform to share models, tools, and data.
• Google Dataset Search
• Healthy Brain Network - Large-scale MRI dataset.
• Human Brain Project
• International Brain Laboratory (IBL) - Releases all data sets within 12 months of collection.
• Neuro Data Without Borders (NWB) - Data standard for neurophysiology.
• Neurosynth - Platform for large-scale, automated synthesis of fMRI data.
• NeuroVault - A public repository of unthresholded statistical maps, parcellations, and atlases.
• OpenNEURO - A free platform for sharing BIDS-compliant MRI, PET, MEG, EEG, and iEEG data.
• Poldracklab Software and Data
• The fMRI Data Center - A free database of fMRI data used in peer-reviewed studies.
• THINGS-data - Multimodal collection of large-scale datasets for investigating object representations.
• Zenodo - Open Science platform for data sharing.
• 3D Brain Atlas - Interactive brain atlas.

• Brain Connectivity Toolbox (MATLAB) - MATLAB toolbox for complex brain-network analysis.
• Brain Connectivity Toolbox (Python) - Python port of the BCT.
• CorticalParcellation - A novel 15-network parcellation of the cerebral cortex.
• DeepPrep - Accelerated, scalable, and robust pipeline for neuroimaging preprocessing.
• ENIGMA TOOLBOX - For accessing ENIGMA-derived statistical maps and visualizing cortical/subcortical data.
• fMRIPrep - A Robust Preprocessing Pipeline for fMRI Data.
• FreeSurfer - Toolkit for processing, analyzing, and visualizing human brain MR images.
• Functio-Structural Current (FSC) - Python code to combine functional and structural brain connectivity.
• JuSpace - Integration of imaging modalities with PET-derived neurophysiological measures.
• nemos - Statistical modeling framework for systems neuroscience (GLM for spikes).
• netneurotools - Functions for network neuroscience analysis.
• NetworkX - Python package for complex networks.
• neuromaps - Toolbox for making statistically-rigorous comparisons between brain maps.
• NLTools - Python package for analyzing neuroimaging data.
• pynapple - Lightweight Python library for neurophysiological data analysis.
• torch_brain - Python library for various deep learning models designed for neuroscience.

• Brain Dynamics Toolbox - MATLAB software for simulating bespoke dynamical systems.
• BrainPy - Flexible framework for computational neuroscience and brain-inspired computation.
• Human Neocortical Neurosolver (HNN) - Test hypotheses on circuit mechanisms underlying EEG/MEG data.
• NEST - Simulator for spiking neural network models.
• NeuroGym - Curated collection of neuroscience tasks for training neural networks.
• The Virtual Brain - Brain simulation platform.
• WhoBPyT - Whole-Brain Modelling in PyTorch.
• fast-slow brain network model - Code from Learning how network structure shapes decision-making.
• Heterogenous Neural Model (HNM) - For large scale modelling of brain activity.

• Connectome Workbench - Visualization and discovery tool for neuroimaging data.
• fastplotlib - High-performance GPU plotting library for scientific visualization.
• MRIcroGL - View 2D slices and renderings of brain imaging data.
• Neurodesk - A flexible and scalable data analysis environment (containerized).
• Subcortex visualization software - Generate two-dimensional subcortex images.
• brainlife - Open-source, secure reproducible neuroscience analysis platform.

• An Easy-to-Follow Handbook for EEG Data Analysis - Python-based guide.
• Behavioural Modelling - Reinforcement learning and Bayesian learning tutorial.
• Brain-Inspired Artificial Intelligence - Course offered at McGill.
• Brain Dynamics on the Connectome - Talks and tutorials from the University of Lausanne.
• Computational Models Course - Experimental Psychology, University of Oxford.
• EEG/ERP Analysis with Python and MNE - Introductory Udemy course.
• Gatsby Bridging Programme - Mathematics course for Theoretical Neuroscience.
• How to Build a Brain from Scratch - Christopher Summerfield's lab, Oxford University.
• Mathematical Tools for Neural and Cognitive Science - Graduate course offered by NYU.
• Mathematics of Neuroscience and AI - YouTube playlist (Rome 2024).
• Methods in Neuroimaging - Resources for PSY 6930, University of Florida.
• Neuronal Dynamics - Online book: From single neurons to networks and models of cognition.
• Neuromatch Academy - Computational neuroscience course materials.
• Neurons: Beyond the Textbook - Educational resources by the Allen Institute.
• Neuroscience for Machine Learners - Short course for ML backgrounds.
• Reinforcement Learning Course - David Silver (DeepMind) on YouTube.
• Short Courses and Summer Schools List - Spreadsheet of various Comp Neuro/MEEG courses.

• Awesome Computational Neuroscience - Curated list of resources.
• Awesome Vision Neuroscience - Resources on vision neuroscience.
• Cambridge University Imaging Wiki - Design and analysis of fMRI studies.
• National Neuroscience Curriculum Initiative (NNCI)
• Neural Strategies - Russ Poldrack's Substack on coding and data management.
• neuro_resources - Useful resources for neuroscientists.
• Neurohackademy - Summer school in neuroimaging and data science (recordings available).
• NeuroStars - Q&A forum for neuroscience researchers.
• The Routledge Handbook of the Computational Mind - Book: An overview of computational approaches.

• Babraham Bioinformatics - Stats, programming and plotting courses.
• Inkscape Tutorial - YouTube guide.
• Making Figures - Tips for scientific figures.
• Scientific Inkscape - Extensions for figure editing.
• ScientificFigures - Guide for figures in publications and posters.

• Computational Psychiatry Conference
• Cosyne - Computational and Systems Neuroscience.
• International Conference on Artificial Neural Networks (ICANN)
• NetSci - Network Science Conference.
• Organization for Computational Neurosciences (OCNS)
• Organization for Human Brain Mapping (OHBM)
• Society for Neuroscience (SfN)

• Nature Neuroscience
• Nature Reviews Neuroscience
• NeuroImage
• Neuron
• The Transmitter - Insights and tools for neuroscience.
• Trends in Neurosciences

• Advanced Research + Invention Agency (ARIA) - UK R&D funding agency.
• Blue Brain Portal - EPFL Simulation Neuroscience.
• BRAIN Initiative - NIH partnership for neurotechnologies.
• Computational Psychiatry Resources - Applied Computational Psychiatry Lab, UCL.
• Connectomics Lab - Prof. Patric Hagmann's lab.
• INCF - International Neuroinformatics Coordinating Facility.
• MKDocs - Static site generator for documentation.
• Neuroinformatics Unit (NIU) - Gatsby Unit software development.
• NeuroML - Standards for detailed models of neural systems.
• NeuroRSE - Flatiron Institute Center for Computational Neuroscience.