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OpenScope Databook

Basics

Background
Downloading an NWB File
Streaming an NWB File with remfile
Reading an NWB File
Getting Experimental Metadata from DANDI

Visualizing NWB Files

Visualizing Raw 2-Photon Images
Visualizing Unit Quality Metrics
Visualizing LFP Responses to Stimuli
Visualizing Neuronal Unit Responses
Visualizing 2P Responses to Stimulus
Visualizing Neuronal Unit Spikes
Visualizing Neuropixels Probe Locations
Visualizing Stimulus Templates

First-Order Analysis

Showing Receptive Fields
Identifying Optotagged Units
Current Source Density Analysis
Classifying Fast-Spiking and Regular-Spiking Neurons
Statistically Testing 2P Responses to Stimulus
Statistically Testing Spike Responses to Stimulus
Identifying Regions of Interest with Segmentation

Higher-Order Analysis

Using CEBRA-Time to Identify Latent Embeddings
Tensor Decomposition of Spiking Activity Through Trials
Introduction to Generalized Linear Models using Pynapple and NeMoS
Generalized Linear Models
Behavioral State from Trial Outcomes

Openscope Experimental Projects

Replicating OpenScope Credit Assignment project figures
OpenScope’s Global/Local Oddball Dataset
OpenScope’s Illusion Dataset
OpenScope’s Dendritic Coupling Dataset
OpenScope’s Sequence Learning Dataset
Introduction to the Temporal Barcode Dataset
OpenScope’s Vision2Hippocampus Dataset
OpenScope’s Vismo Dataset
OpenScope’s Texture Dataset
OpenScope’s LOOP Dataset
OpenScope’s Psycode Dataset

Embargoed Datasets

Aligning Data across Modalities
Visualizing Behavioral Data
Statistically Testing 2P Responses to Stimulus
Cell Matching Across Days

Methods

Jupyter/Jupyter Book
Git/GitHub
Managing Environments on Multiple Platforms

Appendix

Contributing to the Databook
Bibliography
Contributors
FAQ

Repository
Open issue

Index

By Carter Peene

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