Some of the tutorials can also be accessed via the EBRAINS YouTube channel.
Arbor
- A simple single cell model (beginner)
- A detailed single cell model (advanced)
- A detailed single cell recipe (advanced)
- A ring network (advanced)
- A simple dendrite (advanced)
- A simple single cell recipe (advanced)
- A single cell model from the Allen Brain Atlas (advanced)
- A single cell model from the BluePyOpt Cell Optimisation Library (advanced)
- Distributed ring network (MPI) (advanced)
- Extracellular signals (LFPykit) (advanced)
- GPU and profiling (advanced)
- Spike Timing-dependent Plasticity Curve (advanced)
- Two cells connected via a gap junction (advanced)
Bids Manager & Pipeline
- BIDS Manager (advanced)
BluePyMM
- BluePyMM (beginner)
BluePyOpt
- Creating a simple cell optimisation (beginner)
Brainstorm
- Introduction tutorials (beginner)
- Best: Brain Entropy in space and time (advanced)
- Connectivity (advanced)
- Connectivity Graphs (advanced)
- Converting to Brainstorm Events (advanced)
- Coordinate systems (advanced)
- Corticomuscular coherence (CTF MEG) (advanced)
- Deriving LFP signals from raw signals (advanced)
- Digitize EEG sensor locations and head shape (advanced)
- ECoG/sEEG tutorial (advanced)
- EEG and epilepsy (advanced)
- Elekta-Neuromag tutorial: Median nerve stimulation (advanced)
- Epileptogenic Zone Fingerprint (advanced)
- Export raw files in BIDS format (advanced)
- Export surface source maps to SPM12 (advanced)
- Export volume source maps to SPM8 / SPM12 (advanced)
- FEM advanced tutorial with MEG/EEG Median nerve stimulation (advanced)
- FEM mesh generation (advanced)
- FEM tensors estimation with BrainSuite (advanced)
- Fitting dipoles with FieldTrip (advanced)
- Fitting Oscillations and One-Over-F (FOOOF) (advanced)
- Functions for Basic e-phys (advanced)
- Granger causality (advanced)
- Group analysis: Subject coregistration (advanced)
- How to write your own process (advanced)
- Human Connectome Project: Resting-state MEG (advanced)
- MEG current phantom (CTF) (advanced)
- MEG current phantom (Elekta-Neuromag) (advanced)
- MEG median nerve tutorial (CTF) (advanced)
- MEG visual tutorial: Group analysis (BIDS) (advanced)
- MEG visual tutorial: Single subject (BIDS) (advanced)
- Montage editor (advanced)
- MRI Segmentation with CAT12 (advanced)
- MRI segmentation with CIVET (advanced)
- MRI segmentation with FastSurfer (advanced)
- NIRS data importation, visualization and response estimate in the optode space (advanced)
- Plugins (advanced)
- Real-time head-tracking for adjusting head position (advanced)
- Realistic head model: FEM with DUNEuro (advanced)
- Resting state recordings from the OMEGA database (advanced)
- Simulations (advanced)
- Spectral Parameterization Resolved in Time (SPRiNT) (advanced)
- Spike Sorting in Brainstorm (advanced)
- SSP Cookbook (advanced)
- Synchronization with eye tracker (event transfer) (advanced)
- T1-MRI Segmentation with BrainSuite (advanced)
- Tutorial - Head Motion (advanced)
- Using BrainVISA (advanced)
- Using FreeSurfer (advanced)
- Using the anatomy templates (advanced)
- Virtual Fiber Tracks for Connectivity Visualization (advanced)
- Yokogawa/KIT tutorial: Median nerve stimulation (advanced)
Electrophysiology Analysis Toolkit
- Statistics of spike trains (beginner)
- ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains (advanced)
- Gaussian Process Factor Analysis (advanced)
- Parallel (advanced)
- Spike Pattern Detection and Evaluation (SPADE) (advanced)
- The Unitary Events Analysis (advanced)
- Time-domain Granger Causality (advanced)
Hodgkin Huxley Neuron Builder
- Hodgkin-Huxley Neuron Builder (advanced)
NEST
- Introduction to NEST: Simulating a single neuron (beginner)
- Neurons and simple neural networks (beginner)
- Populations of neurons (beginner)
- Connect two NEST simulations using MUSIC (advanced)
- Connecting networks with synapses (advanced)
- Introduction to the MUSIC Interface (advanced)
- MUSIC Connections in C++ and Python (advanced)
- MUSIC with SLI (advanced)
- Practical tips (advanced)
- Spatially structured networks (advanced)
- The pymusic interface (advanced)
NESTML
- Izhikevich tutorial (beginner)
- Active dendrite tutorial (advanced)
- Dopamine-modulated STDP synapse tutorial (advanced)
- Ornstein-Uhlenbeck noise tutorial (advanced)
- STDP synapse tutorial (advanced)
- STDP windows tutorial (advanced)
Neuron
- Construction and Use of Models: Part 1. Elementary tools (beginner)
- The hoc programming language (beginner)
- Introduction to Network Construction (advanced)
- 1. Implement and test the computational model itself (advanced)
- 2. Run a "complete" simulation and save its results (advanced)
- 3. Run a segmented simulation and save its results (advanced)
- 3D/Hybrid Intracellular Tutorial (advanced)
- 4. Reconstitute and verify the "complete" simulation results (advanced)
- A NEURON Programming Tutorial - Part A (advanced)
- A NEURON Programming Tutorial - Part B (advanced)
- A NEURON Programming Tutorial - part C (advanced)
- A NEURON Programming Tutorial - Part E (advanced)
- Ball and Stick model part 1 (advanced)
- Ball and Stick model part 2 (advanced)
- Ball and Stick model part 3 (advanced)
- Ball and Stick model part 4 (advanced)
- Creating a channel from a kinetic scheme specification (advanced)
- Creating a channel from an HH-style specification (advanced)
- Creating a model of stochastic channel gating (advanced)
- Creating a stylized ("stick figure") model cell (advanced)
- Dealing with simulations that generate a lot of data (advanced)
- Example: circadian rhythm (advanced)
- Example: restricting a reaction to part of a region (advanced)
- Exploring morphometric data and fixing problems (advanced)
- Extracellular Diffusion (advanced)
- How to generate independent random spike streams (advanced)
- Managing a model cell with complex anatomy (advanced)
- mGluR example (advanced)
- ModelView: Compact display of parameters for NEURON models. (advanced)
- Python introduction (advanced)
- Randomness in NEURON models (advanced)
- Reaction-Diffusion (advanced)
- Reaction-Diffusion: Calcium Wave (advanced)
- Reaction-Diffusion: Thresholds (advanced)
- Reaction-Diffusion: varying initial concentrations and parameters (advanced)
- Reading a morphometric data file and converting it to a NEURON model (advanced)
- RxD with MOD files (advanced)
- Scripting NEURON basics (advanced)
- Segmenting a simulation of a model cell (advanced)
- Segmenting a simulation of a model network (advanced)
- Source code that demonstrates the solution (advanced)
- Specifying parameterized variation of biophysical properties (advanced)
- The solution (advanced)
- Tutorial 1 : Fitting a function to data (advanced)
- Tutorial 1: Making Networks of Artificial Neurons (advanced)
- Tutorial 2 : Fitting a model to data (advanced)
- Tutorial 2: Making Hybrid Nets (advanced)
- Using Import3D (advanced)
- Using NEURON's Optimization Tools (advanced)
Neurorobotics Platform
PyNN
- Building and simulating a simple model (beginner)
- Installing PyNN on a Linux system (beginner)
The Virtual Brain
- Building Your Own Brain Network Model (beginner)
- Getting Started (beginner)
- My first simulation with The Virtual Brain (beginner)
- Population Models in The Virtual Brain (TVB) and the Phase Plane (beginner)
- Brain stimulation in The Virtual Brain (advanced)
- Clinical Applications - Stroke Recovery & Dementia (advanced)
- Evoked Responses in the Visual Cortex (advanced)
- Exploring a model (advanced)
- Hands-On: Modeling stroke brain (advanced)
- Human Brain Project (HBP) TVB-NEST co-simulation (advanced)
- Import Virtual Brain ready data into TVB and create a brain model (advanced)
- Integrated workflows: Image processing pipeline (advanced)
- Modeling brain dynamics in brain tumor patients using The Virtual Brain (advanced)
- Modeling Epilepsy (advanced)
- Modelling Epilepsy with The Virtual Brain (advanced)
- Region simulation tutorial (advanced)
- Resting State Networks (advanced)
- Simulating The Virtual Mouse Brain (TVMB) (advanced)
- Simulating The Virtual Mouse Brain (TVMB) (Copy) (advanced)
- Surface simulation tutorial (advanced)
- Surface-based simulations and deep brain stimulations (advanced)
- The Bayesian Virtual Epileptic Patient (BVEP) (advanced)
- TVB to NEST multi-scale simulation (advanced)
VoluBA
ilastik
- Boundary-based segmentation with Multicut (advanced)
- Carving Workflow (advanced)
- Cell Density Counting Workflow (advanced)
- EBRAINS Atlases - QUINT workflow Tutorial (advanced)
- Object Classification (advanced)
- Pixel Classification workflow (advanced)
- Tracking MaMuT Export (advanced)
- Tracking workflow (advanced)