Tools and services tutorials

1

(% class="box infomessage" id="HWelcometothesingleentrypointtotutorialsforEBRAINStoolsandservices.Here2CyoucanfindalistofEBRAINSofferings2Csortedbytopic2Candlinkstotheirtutorials." style="text-align: center;" %)

2

(((

3

Welcome to the single entry point to tutorials for EBRAINS tools and services. Here, you can find a list of EBRAINS offerings, sorted by topic, and links to their tutorials.

4

)))

5

6

Some of the tutorials can also be accessed via the [[EBRAINS YouTube channel>>https://www.youtube.com/channel/UC6E796cVVR5Xrs2A5jJmleQ]].

== Arbor ==

* [[A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel="noopener noreferrer" target="_blank"]] (beginner)

11

* [[A detailed single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed.html||rel="noopener noreferrer" target="_blank"]] (advanced)

12

* [[A detailed single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed_recipe.html||rel="noopener noreferrer" target="_blank"]] (advanced)

13

* [[A ring network>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring.html||rel="noopener noreferrer" target="_blank"]] (advanced)

14

* [[A simple dendrite>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_cable.html||rel="noopener noreferrer" target="_blank"]] (advanced)

15

* [[A simple single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_recipe.html||rel="noopener noreferrer" target="_blank"]] (advanced)

16

* [[A single cell model from the Allen Brain Atlas>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_allen.html||rel="noopener noreferrer" target="_blank"]] (advanced)

17

* [[A single cell model from the BluePyOpt Cell Optimisation Library>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_bluepyopt.html||rel="noopener noreferrer" target="_blank"]] (advanced)

18

* [[Distributed ring network (MPI)>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_mpi.html||rel="noopener noreferrer" target="_blank"]] (advanced)

19

* [[Extracellular signals (LFPykit)>>https://docs.arbor-sim.org/en/stable/tutorial/probe_lfpykit.html||rel="noopener noreferrer" target="_blank"]] (advanced)

20

* [[GPU and profiling>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_gpu.html||rel="noopener noreferrer" target="_blank"]] (advanced)

21

* [[Spike Timing-dependent Plasticity Curve>>https://docs.arbor-sim.org/en/stable/tutorial/calcium_stdp_curve.html||rel="noopener noreferrer" target="_blank"]] (advanced)

22

* [[Two cells connected via a gap junction>>https://docs.arbor-sim.org/en/stable/tutorial/network_two_cells_gap_junctions.html||rel="noopener noreferrer" target="_blank"]] (advanced)

23

24

== Bids Manager & Pipeline ==

25

26

* [[BIDS Manager>>https://github.com/Dynamap/BIDS_Manager/blob/master/Tutorial_BIDS_Manager.pdf||rel="noopener noreferrer" target="_blank"]] (advanced)

== BluePyMM ==

* [[BluePyMM>>https://github.com/BlueBrain/BluePyMM/blob/master/notebook/BluePyMM.ipynb||rel="noopener noreferrer" target="_blank"]] (beginner)

== BluePyOpt ==

* [[Creating a simple cell optimisation>>https://github.com/BlueBrain/BluePyOpt/blob/master/examples/simplecell/simplecell.ipynb||rel="noopener noreferrer" target="_blank"]] (beginner)

== Brainstorm ==

* [[Introduction tutorials>>https://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction||rel="noopener noreferrer" target="_blank"]] (beginner)

39

* [[Best: Brain Entropy in space and time>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutBEst||rel="noopener noreferrer" target="_blank"]] (advanced)

40

* [[Connectivity>>https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity||rel="noopener noreferrer" target="_blank"]] (advanced)

41

* [[Connectivity Graphs>>https://neuroimage.usc.edu/brainstorm/Tutorials/ConnectivityGraph||rel="noopener noreferrer" target="_blank"]] (advanced)

42

* [[Converting to Brainstorm Events>>https://neuroimage.usc.edu/brainstorm/e-phys/ConvertToBrainstormEvents||rel="noopener noreferrer" target="_blank"]] (advanced)

43

* [[Coordinate systems>>https://neuroimage.usc.edu/brainstorm/CoordinateSystems||rel="noopener noreferrer" target="_blank"]] (advanced)

44

* [[Corticomuscular coherence (CTF MEG)>>https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence||rel="noopener noreferrer" target="_blank"]] (advanced)

45

* [[Deriving LFP signals from raw signals>>https://neuroimage.usc.edu/brainstorm/e-phys/RawToLFP||rel="noopener noreferrer" target="_blank"]] (advanced)

46

* [[Digitize EEG sensor locations and head shape>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutDigitize||rel="noopener noreferrer" target="_blank"]] (advanced)

47

* [[ECoG/sEEG tutorial>>https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG||rel="noopener noreferrer" target="_blank"]] (advanced)

48

* [[EEG and epilepsy>>https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy||rel="noopener noreferrer" target="_blank"]] (advanced)

49

* [[Elekta-Neuromag tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag||rel="noopener noreferrer" target="_blank"]] (advanced)

50

* [[Epileptogenic Zone Fingerprint>>https://neuroimage.usc.edu/brainstorm/Tutorials/EZFingerprint||rel="noopener noreferrer" target="_blank"]] (advanced)

51

* [[Export raw files in BIDS format>>https://neuroimage.usc.edu/brainstorm/ExportBids||rel="noopener noreferrer" target="_blank"]] (advanced)

52

* [[Export surface source maps to SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm12||rel="noopener noreferrer" target="_blank"]] (advanced)

53

* [[Export volume source maps to SPM8 / SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm8||rel="noopener noreferrer" target="_blank"]] (advanced)

54

* [[FEM advanced tutorial with MEG/EEG Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMedianNerve||rel="noopener noreferrer" target="_blank"]] (advanced)

55

* [[FEM mesh generation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMesh||rel="noopener noreferrer" target="_blank"]] (advanced)

56

* [[FEM tensors estimation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemTensors||rel="noopener noreferrer" target="_blank"]] (advanced)

57

* [[Fitting dipoles with FieldTrip>>https://neuroimage.usc.edu/brainstorm/Tutorials/DipoleFitting||rel="noopener noreferrer" target="_blank"]] (advanced)

58

* [[Fitting Oscillations and One-Over-F (FOOOF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/Fooof||rel="noopener noreferrer" target="_blank"]] (advanced)

59

* [[Functions for Basic e-phys>>https://neuroimage.usc.edu/brainstorm/e-phys/functions||rel="noopener noreferrer" target="_blank"]] (advanced)

60

* [[Granger causality>>https://neuroimage.usc.edu/brainstorm/GrangerCausality||rel="noopener noreferrer" target="_blank"]] (advanced)

61

* [[Group analysis: Subject coregistration>>https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects||rel="noopener noreferrer" target="_blank"]] (advanced)

62

* [[How to write your own process>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutUserProcess||rel="noopener noreferrer" target="_blank"]] (advanced)

63

* [[Human Connectome Project: Resting-state MEG>>https://neuroimage.usc.edu/brainstorm/Tutorials/HCP-MEG||rel="noopener noreferrer" target="_blank"]] (advanced)

64

* [[MEG current phantom (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomCtf||rel="noopener noreferrer" target="_blank"]] (advanced)

65

* [[MEG current phantom (Elekta-Neuromag)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomElekta||rel="noopener noreferrer" target="_blank"]] (advanced)

66

* [[MEG median nerve tutorial (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/MedianNerveCtf||rel="noopener noreferrer" target="_blank"]] (advanced)

67

* [[MEG visual tutorial: Group analysis (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup||rel="noopener noreferrer" target="_blank"]] (advanced)

68

* [[MEG visual tutorial: Single subject (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle||rel="noopener noreferrer" target="_blank"]] (advanced)

69

* [[Montage editor>>https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor||rel="noopener noreferrer" target="_blank"]] (advanced)

70

* [[MRI Segmentation with CAT12>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12||rel="noopener noreferrer" target="_blank"]] (advanced)

71

* [[MRI segmentation with CIVET>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCIVET||rel="noopener noreferrer" target="_blank"]] (advanced)

72

* [[MRI segmentation with FastSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegFastSurfer||rel="noopener noreferrer" target="_blank"]] (advanced)

73

* [[NIRS data importation, visualization and response estimate in the optode space>>https://neuroimage.usc.edu/brainstorm/Tutorials/NIRSFingerTapping||rel="noopener noreferrer" target="_blank"]] (advanced)

74

* [[Plugins>>https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins||rel="noopener noreferrer" target="_blank"]] (advanced)

75

* [[Real-time head-tracking for adjusting head position>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime||rel="noopener noreferrer" target="_blank"]] (advanced)

76

* [[Realistic head model: FEM with DUNEuro>>https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro||rel="noopener noreferrer" target="_blank"]] (advanced)

77

* [[Resting state recordings from the OMEGA database>>https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega||rel="noopener noreferrer" target="_blank"]] (advanced)

78

* [[Simulations>>https://neuroimage.usc.edu/brainstorm/Tutorials/Simulations||rel="noopener noreferrer" target="_blank"]] (advanced)

79

* [[Spectral Parameterization Resolved in Time (SPRiNT)>>https://neuroimage.usc.edu/brainstorm/Tutorials/SPRiNT||rel="noopener noreferrer" target="_blank"]] (advanced)

80

* [[Spike Sorting in Brainstorm>>https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting||rel="noopener noreferrer" target="_blank"]] (advanced)

81

* [[SSP Cookbook>>https://neuroimage.usc.edu/brainstorm/Tutorials/SSPCookbook||rel="noopener noreferrer" target="_blank"]] (advanced)

82

* [[Synchronization with eye tracker (event transfer)>>https://neuroimage.usc.edu/brainstorm/Tutorials/EyetrackSynchro||rel="noopener noreferrer" target="_blank"]] (advanced)

83

* [[T1-MRI Segmentation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite||rel="noopener noreferrer" target="_blank"]] (advanced)

84

* [[Tutorial - Head Motion>>https://neuroimage.usc.edu/brainstorm/Tutorials/HeadMotion||rel="noopener noreferrer" target="_blank"]] (advanced)

85

* [[Using BrainVISA>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainVisa||rel="noopener noreferrer" target="_blank"]] (advanced)

86

* [[Using FreeSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer||rel="noopener noreferrer" target="_blank"]] (advanced)

87

* [[Using the anatomy templates>>https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy||rel="noopener noreferrer" target="_blank"]] (advanced)

88

* [[Virtual Fiber Tracks for Connectivity Visualization>>https://neuroimage.usc.edu/brainstorm/Tutorials/FiberConnectivity||rel="noopener noreferrer" target="_blank"]] (advanced)

89

* [[Yokogawa/KIT tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/Yokogawa||rel="noopener noreferrer" target="_blank"]] (advanced)

90

91

== Electrophysiology Analysis Toolkit ==

92

93

* [[Statistics of spike trains>>https://elephant.readthedocs.io/en/latest/tutorials/statistics.html||rel="noopener noreferrer" target="_blank"]] (beginner)

94

* [[ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains>>https://elephant.readthedocs.io/en/latest/tutorials/asset.html||rel="noopener noreferrer" target="_blank"]] (advanced)

95

* [[Gaussian Process Factor Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/gpfa.html||rel="noopener noreferrer" target="_blank"]] (advanced)

96

* [[Parallel>>https://elephant.readthedocs.io/en/latest/tutorials/parallel.html||rel="noopener noreferrer" target="_blank"]] (advanced)

97

* [[Spike Pattern Detection and Evaluation (SPADE)>>https://elephant.readthedocs.io/en/latest/tutorials/spade.html||rel="noopener noreferrer" target="_blank"]] (advanced)

98

* [[The Unitary Events Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/unitary_event_analysis.html||rel="noopener noreferrer" target="_blank"]] (advanced)

99

* [[Time-domain Granger Causality>>https://elephant.readthedocs.io/en/latest/tutorials/granger_causality.html||rel="noopener noreferrer" target="_blank"]] (advanced)

100

101

== Hodgkin Huxley Neuron Builder ==

102

103

* [[Hodgkin-Huxley Neuron Builder>>https://object.cscs.ch/v1/AUTH_c0a333ecf7c045809321ce9d9ecdfdea/web-resources-bsp/bsp-video-tutorials/HodgkinHuxleyNeuronBuilder/index.html||rel="noopener noreferrer" target="_blank"]] (advanced)

== NEST ==

* [[Introduction to NEST: Simulating a single neuron>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/videos/one_neuron.html||rel="noopener noreferrer" target="_blank"]] (beginner)

108

* [[Neurons and simple neural networks>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/pynest_tutorial/part_1_neurons_and_simple_neural_networks.html||rel="noopener noreferrer" target="_blank"]] (beginner)

109

* [[Populations of neurons>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/pynest_tutorial/part_2_populations_of_neurons.html||rel="noopener noreferrer" target="_blank"]] (beginner)

110

* [[Connect two NEST simulations using MUSIC>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_2.html||rel="noopener noreferrer" target="_blank"]] (advanced)

111

* [[Connecting networks with synapses>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/pynest_tutorial/part_3_connecting_networks_with_synapses.html||rel="noopener noreferrer" target="_blank"]] (advanced)

112

* [[Introduction to the MUSIC Interface>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_1.html||rel="noopener noreferrer" target="_blank"]] (advanced)

113

* [[MUSIC Connections in C++ and Python>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_3.html||rel="noopener noreferrer" target="_blank"]] (advanced)

114

* [[MUSIC with SLI>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_sli.html||rel="noopener noreferrer" target="_blank"]] (advanced)

115

* [[Practical tips>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_4.html||rel="noopener noreferrer" target="_blank"]] (advanced)

116

* [[Spatially structured networks>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/pynest_tutorial/part_4_spatially_structured_networks.html||rel="noopener noreferrer" target="_blank"]] (advanced)

117

* [[The pymusic interface>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_4.html||rel="noopener noreferrer" target="_blank"]] (advanced)

== NESTML ==

* [[Izhikevich tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/izhikevich/nestml_izhikevich_tutorial.html||rel="noopener noreferrer" target="_blank"]] (beginner)

122

* [[Active dendrite tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/active_dendrite/nestml_active_dendrite_tutorial.html||rel="noopener noreferrer" target="_blank"]] (advanced)

123

* [[Dopamine-modulated STDP synapse tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/stdp_dopa_synapse/stdp_dopa_synapse.html||rel="noopener noreferrer" target="_blank"]] (advanced)

124

* [[Ornstein-Uhlenbeck noise tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/ornstein_uhlenbeck_noise/nestml_ou_noise_tutorial.html||rel="noopener noreferrer" target="_blank"]] (advanced)

125

* [[STDP synapse tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/triplet_stdp_synapse/triplet_stdp_synapse.html||rel="noopener noreferrer" target="_blank"]] (advanced)

126

* [[STDP windows tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/stdp_windows/stdp_windows.html||rel="noopener noreferrer" target="_blank"]] (advanced)

== Neuron ==

* [[Construction and Use of Models: Part 1. Elementary tools>>https://neuron.yale.edu/neuron/static/docs/elementarytools/outline.htm||rel="noopener noreferrer" target="_blank"]] (beginner)

131

* [[The hoc programming language>>https://neuron.yale.edu/neuron/static/docs/programming/hoc_slides.pdf||rel="noopener noreferrer" target="_blank"]] (beginner)

132

* [[ Introduction to Network Construction>>https://neuron.yale.edu/neuron/static/docs/netbuild/intro.html||rel="noopener noreferrer" target="_blank"]] (advanced)

133

* [[1. Implement and test the computational model itself>>https://neuron.yale.edu/neuron/docs/1-implement-and-test-computational-model-itself-0||rel="noopener noreferrer" target="_blank"]] (advanced)

134

* [[2. Run a "complete" simulation and save its results>>https://neuron.yale.edu/neuron/docs/2-run-complete-simulation-and-save-its-results||rel="noopener noreferrer" target="_blank"]] (advanced)

135

* [[3. Run a segmented simulation and save its results>>https://neuron.yale.edu/neuron/docs/3-run-segmented-simulation-and-save-its-results||rel="noopener noreferrer" target="_blank"]] (advanced)

136

* [[3D/Hybrid Intracellular Tutorial>>https://neuron.yale.edu/neuron/docs/3dhybrid-intracellular-tutorial||rel="noopener noreferrer" target="_blank"]] (advanced)

137

* [[4. Reconstitute and verify the "complete" simulation results>>https://neuron.yale.edu/neuron/docs/4-reconstitute-and-verify-complete-simulation-results||rel="noopener noreferrer" target="_blank"]] (advanced)

138

* [[A NEURON Programming Tutorial - Part A>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutA.html||rel="noopener noreferrer" target="_blank"]] (advanced)

139

* [[A NEURON Programming Tutorial - Part B>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutB.html||rel="noopener noreferrer" target="_blank"]] (advanced)

140

* [[A NEURON Programming Tutorial - part C>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutC.html||rel="noopener noreferrer" target="_blank"]] (advanced)

141

* [[A NEURON Programming Tutorial - Part E>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutE.html||rel="noopener noreferrer" target="_blank"]] (advanced)

142

* [[Ball and Stick model part 1>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-1||rel="noopener noreferrer" target="_blank"]] (advanced)

143

* [[Ball and Stick model part 2>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-2||rel="noopener noreferrer" target="_blank"]] (advanced)

144

* [[Ball and Stick model part 3>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-3||rel="noopener noreferrer" target="_blank"]] (advanced)

145

* [[Ball and Stick model part 4>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-4||rel="noopener noreferrer" target="_blank"]] (advanced)

146

* [[Creating a channel from a kinetic scheme specification>>https://neuron.yale.edu/neuron/static/docs/chanlbild/kinetic/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

147

* [[Creating a channel from an HH-style specification>>https://neuron.yale.edu/neuron/static/docs/chanlbild/hhstyle/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

148

* [[Creating a model of stochastic channel gating>>https://neuron.yale.edu/neuron/static/docs/chanlbild/stochastic/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

149

* [[Creating a stylized ("stick figure") model cell>>https://neuron.yale.edu/neuron/static/docs/cbtut/stylized/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

150

* [[Dealing with simulations that generate a lot of data>>https://neuron.yale.edu/neuron/docs/dealing-simulations-generate-lot-data||rel="noopener noreferrer" target="_blank"]] (advanced)

151

* [[Example: circadian rhythm>>https://neuron.yale.edu/neuron/docs/example-circadian-rhythm||rel="noopener noreferrer" target="_blank"]] (advanced)

152

* [[Example: restricting a reaction to part of a region>>https://neuron.yale.edu/neuron/docs/example-restricting-reaction-part-region||rel="noopener noreferrer" target="_blank"]] (advanced)

153

* [[Exploring morphometric data and fixing problems>>https://neuron.yale.edu/neuron/docs/import3d/fix_problems||rel="noopener noreferrer" target="_blank"]] (advanced)

154

* [[Extracellular Diffusion>>https://neuron.yale.edu/neuron/docs/extracellular-diffusion||rel="noopener noreferrer" target="_blank"]] (advanced)

155

* [[How to generate independent random spike streams>>https://neuron.yale.edu/neuron/docs/how-generate-independent-random-spike-streams||rel="noopener noreferrer" target="_blank"]] (advanced)

156

* [[Managing a model cell with complex anatomy>>https://neuron.yale.edu/neuron/static/docs/cbtut/pt3d/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

157

* [[mGluR example>>https://neuron.yale.edu/neuron/docs/mglur-example||rel="noopener noreferrer" target="_blank"]] (advanced)

158

* [[ModelView: Compact display of parameters for NEURON models.>>https://neuron.yale.edu/neuron/static/papers/mview/modelviewhbp2004.html||rel="noopener noreferrer" target="_blank"]] (advanced)

159

* [[Python introduction>>https://neuron.yale.edu/neuron/docs/python-introduction||rel="noopener noreferrer" target="_blank"]] (advanced)

160

* [[Randomness in NEURON models>>https://neuron.yale.edu/neuron/docs/randomness-neuron-models||rel="noopener noreferrer" target="_blank"]] (advanced)

161

* [[Reaction-Diffusion>>https://neuron.yale.edu/neuron/docs/reaction-diffusion||rel="noopener noreferrer" target="_blank"]] (advanced)

162

* [[Reaction-Diffusion: Calcium Wave>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-calcium-wave||rel="noopener noreferrer" target="_blank"]] (advanced)

163

* [[Reaction-Diffusion: Thresholds>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-thresholds||rel="noopener noreferrer" target="_blank"]] (advanced)

164

* [[Reaction-Diffusion: varying initial concentrations and parameters>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-varying-initial-concentrations-and-parameters||rel="noopener noreferrer" target="_blank"]] (advanced)

165

* [[Reading a morphometric data file and converting it to a NEURON model>>https://neuron.yale.edu/neuron/docs/import3d/read_data||rel="noopener noreferrer" target="_blank"]] (advanced)

166

* [[RxD with MOD files>>https://neuron.yale.edu/neuron/docs/rxd-mod-files||rel="noopener noreferrer" target="_blank"]] (advanced)

167

* [[Scripting NEURON basics>>https://neuron.yale.edu/neuron/docs/scripting-neuron-basics||rel="noopener noreferrer" target="_blank"]] (advanced)

168

* [[Segmenting a simulation of a model cell>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-cell||rel="noopener noreferrer" target="_blank"]] (advanced)

169

* [[Segmenting a simulation of a model network>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-network||rel="noopener noreferrer" target="_blank"]] (advanced)

170

* [[Source code that demonstrates the solution>>https://neuron.yale.edu/neuron/docs/source-code-demonstrates-solution||rel="noopener noreferrer" target="_blank"]] (advanced)

171

* [[Specifying parameterized variation of biophysical properties>>https://neuron.yale.edu/neuron/static/docs/cbtut/parameterized/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

172

* [[The solution>>https://neuron.yale.edu/neuron/docs/solution||rel="noopener noreferrer" target="_blank"]] (advanced)

173

* [[Tutorial 1 : Fitting a function to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/func/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

174

* [[Tutorial 1: Making Networks of Artificial Neurons>>https://neuron.yale.edu/neuron/static/docs/netbuild/artnet/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

175

* [[Tutorial 2 : Fitting a model to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/model/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

176

* [[Tutorial 2: Making Hybrid Nets>>https://neuron.yale.edu/neuron/static/docs/netbuild/hybrid/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

177

* [[Using Import3D>>https://neuron.yale.edu/neuron/docs/import3d||rel="noopener noreferrer" target="_blank"]] (advanced)

178

* [[Using NEURON's Optimization Tools>>https://neuron.yale.edu/neuron/static/docs/optimiz/main.html||rel="noopener noreferrer" target="_blank"]] (advanced)

179

180

== Neurorobotics Platform ==

181

182

* [[Drag and drop experiment set up with multiple robots>>https://youtu.be/VF3xd3mXTqY||rel="noopener noreferrer" target="_blank"]] (beginner)

== PyNN ==

* [[Building and simulating a simple model>>https://youtu.be/zBLNfJiEvRc||rel="noopener noreferrer" target="_blank"]] (beginner)

187

* [[Installing PyNN on a Linux system>>https://youtu.be/BZB7xKUK8Vc||rel="noopener noreferrer" target="_blank"]] (beginner)

188

189

== The Virtual Brain ==

190

191

* [[Building Your Own Brain Network Model>>https://docs.thevirtualbrain.org/tutorials/tutorial_1_BuildingYourOwnBrainNetworkModel.html#tutorial-1-buildingyourownbrainnetworkmodel||rel="noopener noreferrer" target="_blank"]] (beginner)

192

* [[Getting Started>>https://docs.thevirtualbrain.org/tutorials/tutorial_0_GettingStarted.html#tutorial-0-gettingstarted||rel="noopener noreferrer" target="_blank"]] (beginner)

193

* [[My first simulation with The Virtual Brain>>https://youtu.be/326iA14UVzY||rel="noopener noreferrer" target="_blank"]] (beginner)

194

* [[Population Models in The Virtual Brain (TVB) and the Phase Plane>>https://youtu.be/Zo0HGwLHN3E||rel="noopener noreferrer" target="_blank"]] (beginner)

195

* [[Brain stimulation in The Virtual Brain>>https://youtu.be/mskxBYKoeq0||rel="noopener noreferrer" target="_blank"]] (advanced)

196

* [[Clinical Applications - Stroke Recovery & Dementia>>https://youtu.be/ZA2UuHZiPnM||rel="noopener noreferrer" target="_blank"]] (advanced)

197

* [[Evoked Responses in the Visual Cortex>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s4_EvokedResponsesInTheVisualCortex.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced)

198

* [[Exploring a model>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s3_exploring_a_model.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced)

199

* [[Hands-On: Modeling stroke brain>>https://youtu.be/BDj9MLpt0io||rel="noopener noreferrer" target="_blank"]] (advanced)

200

* [[Human Brain Project (HBP) TVB-NEST co-simulation>>https://youtu.be/dUuQe_SI5lE||rel="noopener noreferrer" target="_blank"]] (advanced)

201

* [[Import Virtual Brain ready data into TVB and create a brain model>>https://youtu.be/OEOCFyiJgBM||rel="noopener noreferrer" target="_blank"]] (advanced)

202

* [[Integrated workflows: Image processing pipeline>>https://youtu.be/uUkq0K-xM0Q||rel="noopener noreferrer" target="_blank"]] (advanced)

203

* [[Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https://youtu.be/t9xyoHxTAmQ||rel="noopener noreferrer" target="_blank"]] (advanced)

204

* [[Modeling Epilepsy>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s6_ModelingEpilepsy.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced)

205

* [[Modelling Epilepsy with The Virtual Brain>>https://youtu.be/YrSxnMo6Lr8||rel="noopener noreferrer" target="_blank"]] (advanced)

206

* [[Region simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s1_region_simulation.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced)

207

* [[Resting State Networks>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s5_ModelingRestingStateNetworks.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced)

208

* [[Simulating The Virtual Mouse Brain (TVMB)>>https://youtu.be/gxhJku8KRYY||rel="noopener noreferrer" target="_blank"]] (advanced)

209

* [[Simulating The Virtual Mouse Brain (TVMB) (Copy)>>https://youtu.be/gxhJku8KRYY||rel="noopener noreferrer" target="_blank"]] (advanced)

210

* [[Surface simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s2_surface_simulation.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced)

211

* [[Surface-based simulations and deep brain stimulations>>https://youtu.be/ZXLrvHc24xE||rel="noopener noreferrer" target="_blank"]] (advanced)

212

* [[The Bayesian Virtual Epileptic Patient (BVEP)>>https://youtu.be/4XghviA_1Uk||rel="noopener noreferrer" target="_blank"]] (advanced)

213

* [[TVB to NEST multi-scale simulation>>https://youtu.be/PppyGzWUxuE||rel="noopener noreferrer" target="_blank"]] (advanced)

== VoluBA ==

* [[Anchoring partial volumetric data to BigBrain using VoluBA>>https://youtu.be/l_7ILe6_2Cs||rel="noopener noreferrer" target="_blank"]] (-)

== ilastik ==

* [[Boundary-based segmentation with Multicut>>https://youtu.be/leuTtIAmEwE||rel="noopener noreferrer" target="_blank"]] (advanced)

222

* [[Carving Workflow>>https://youtu.be/xGyTriPQXHI||rel="noopener noreferrer" target="_blank"]] (advanced)

223

* [[Cell Density Counting Workflow>>https://youtu.be/N-QhiTWVDmk||rel="noopener noreferrer" target="_blank"]] (advanced)

224

* [[EBRAINS Atlases - QUINT workflow Tutorial>>https://youtu.be/n-gQigcGMJ0||rel="noopener noreferrer" target="_blank"]] (advanced)

225

* [[Object Classification>>https://youtu.be/SQeRGvHeT3o||rel="noopener noreferrer" target="_blank"]] (advanced)

226

* [[Pixel Classification workflow>>https://youtu.be/5N0XYW9gRZY||rel="noopener noreferrer" target="_blank"]] (advanced)

227

* [[Tracking MaMuT Export>>https://youtu.be/kjVqWSSdDmU||rel="noopener noreferrer" target="_blank"]] (advanced)

228

* [[Tracking workflow>>https://youtu.be/bZoWx2FuT08||rel="noopener noreferrer" target="_blank"]] (advanced)

Wiki source code of Tools and services tutorials

EBRAINS Documentation