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Data Book for Summer Workshop on the Dynamic Brain
Experimental Data
Background
Mouse visual system
Transgenic tools
Behavioral apparatus
Extracellular electrophysiology
Neuropixels Probes
Unit Quality Metrics
Optotagging
Calcium imaging
Ophys ephys comparison
EM Connectomics
Common Coordinate Framework
Metadata
Physiology & Behavior
Optical Physiology
Visual Coding — 2-photon
Dataset
Getting data from a session
Visual stimuli
Exercise: Evoked response
Cross session data
Analysis files and cell specimens table
Visual Behavior Ophys
Visual Behavior Ophys Dataset
Behavior Session Data
Visual Behavior Ophys Experiment Data
Tutorial Comparing Trial Types
Tutorial Downloading Data
V1 Deep Dive
V1DD Dataset
Accessing V1DD data
Visual stimuli
Brain Computer Interface
Accessing BCI Data
BCI Stimuli
Electrophysiology
Visual Coding — Neuropixels
Quick start guide
Accessing Neuropixels Visual Coding Data
Units
Receptive fields
Local field potential (LFP)
Optotagging Analysis
Full example of accessing Visual Coding Neuropixels data
Visual Stimuli
Cheat sheet for visual coding Neuropixels
Other resources
Visual Behavior Neuropixels
Visual Behavior Neuropixels Dataset
Visual Behavior Neuropixels Session
Tutorial Aligning Neural Data to Stimuli
Tutorial Aligning Behavioral Data to Task Events
Tutorial Analyzing LFP data
Cell Type Look-up Table
Session data
Optotagging
Accessing cell type lookup table data
Identifying tagged neurons
Neuropixels Ultra & Psychedelics
NP Ultra & Psychedelics Stimuli and Optotagging protocol
Accessing NP Ultra & Psychedelics Data
Stimuli and Behavioral Tasks
Visual Stimuli
Visual Behavior Task
Dynamic Foraging
Anatomy
Electron Microscopy
Dataset Basics
Proofreading and Data Quality
Neuroglancer
Dash Apps
Setting up CAVEclient
Programmatic Access
Coordinate Systems
CAVE Annotation Tables
MICrONS Key Tables
V1DD Key Tables
Imagery and Segmentation
Skeletons
Meshes
MICrONS Functional Data
V1DD Functional Data
Ultrastructure Resources
Single Cell Morphology
ExaSPIM Image Processing
Single Cell Morphology Data Access
Computational Tools
Data Analysis Tutorials
Principal Component Analysis
Regression
Generalized Linear Model (GLM)
Classification Tutorial
Resources
Glossary
Practicalities
Creating a Code Ocean capsule synced to GitHub repo
Collaborating using Code Ocean
Using VS Code in Code Ocean
Allen SDK and pyNWB
Using Python to Access Neurodata Without Borders-type Files
Git
References
Contributors and Credits
Repository
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V1DD Functional Data
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Optical Physiology: V1DD
