Overview

The ndx-microscopy extension for NWB provides a standardized way to store and organize microscopy data in neuroscience research. This extension integrates with ndx-ophys-devices to provide comprehensive optical component specifications and supports various microscopy techniques while maintaining detailed metadata about the imaging setup, experimental conditions, and acquired data.

Key Features

Device and Optical Components

  • MicroscopeModel for defining microscope models

  • Microscope instances with technique specifications

  • MicroscopyRig for organizing optical components

  • Integration with ndx-ophys-devices for:

    • Excitation sources (continuous and pulsed)

    • Optical filters (band and edge types)

    • Dichroic mirrors

    • Photodetectors

    • Fluorescent indicators

Illumination Pattern Support

  • Base illumination pattern class for general use cases

  • Line scanning for high-speed XY raster scanning acquisition

  • Plane acquisition for light sheet and widefield techniques

  • Random access scanning for targeted region imaging

  • Detailed scanning parameters (rates, directions, dwell times)

Imaging Space Management

  • 2D planar imaging spaces

  • 3D volumetric imaging spaces

  • Precise coordinate system handling

  • Reference frame management

  • Grid spacing and resolution tracking

  • Integration with illumination patterns

Data Organization

  • Time series data for both 2D and 3D imaging

  • Multi-plane imaging support

  • Variable depth imaging capabilities

  • Multi-channel data handling

  • ROI/segmentation organization

  • Response data storage

Data Structure

The extension organizes microscopy data hierarchically:

nwbfile
├── devices
│   ├── microscope_model: MicroscopeModel
│   └── microscope: Microscope
├── acquisition
│   └── MicroscopySeries
│       └── microscopy_rig: MicroscopyRig
└── processing
    └── ophys
        ├── MicroscopyResponseSeriesContainer
        └── SegmentationContainer

Common Applications

Calcium Imaging

  • GCaMP and other calcium indicator imaging

  • Both one-photon and multi-photon implementations

  • ROI segmentation

  • Fluorescence time series data

Voltage Imaging

  • Direct measurement of neural activity

  • Voltage-sensitive fluorescent proteins/dyes

  • High-speed imaging capabilities

  • High temporal resolution data

For Developers

The extension is open source and welcomes contributions:

  • Source code: GitHub Repository

  • Issue tracking and feature requests

  • Development guidelines

  • Contributing instructions

Extension Design: - Integration with ndx-ophys-devices - Comprehensive test suite - Extensible architecture