User Guide

NeuroConv allows you to easily build programs to convert data from neurophysiology experiments to NWB. The building blocks of these conversions are DataInterface classes. Each DataInterface is responsible for a specific format of data, and contains methods to read data and metadata from that format and write it to NWB. We have pre-built DataInterface classes for many common data formats available in our Conversion Gallery.

NWB files often combine data from multiple sources- neurophysiology raw and processed data, behavior video and extracted position, stimuli, etc. A full conversion can require handling all of these different data types at the same time. The NWBConverter class allows you to combine multiple DataInterface objects into a single conversion, and provides methods to aggregate and synchronize data across multiple sources.

• DataInterfaces
  • 1. Installation
  • 2. Construction
  • 3. Get and adjust metadata
  • 4a. Run conversion
  • 4b. Create an in-memory NWB file
• NWBConverter
• Metadata Templates
  • Fiber Photometry
  • Optical Physiology
  • Pose Estimation
• Adding Trials to NWB Files
  • Creating an NWBFile Object
  • Adding Trials to the NWBFile
  • Writing the NWBFile to Disk
• Temporal Alignment
  • Gross and fine alignment
  • Gross alignment
  • Fine alignment
  • Multiple time-bearing objects
  • Alignment in a converter
• Specifying metadata using tables
• Path Expansion
  • Local Path Expander
  • Specifying Metadata Format
  • Example Usage
  • Non-local Path Expansion
• Backend Configuration
  • Default configuration
  • Customization
  • Existing configuration
  • Interfaces and Converters
  • Global Compression Settings
  • Repacking
  • FAQ
• Using YAML to specify metadata
• Converting Multiple Sessions into a Dataset
  • Finding and Converting the Sessions
  • Organizing the Converted Files
• NeuroConv Docker Demo
• RClone With Config Docker Demo
• NeuroConv AWS Demo