ndx-microscopy: NWB Extension for Microscopy Data

The ndx-microscopy extension provides a standardized way to store and organize microscopy data in the Neurodata Without Borders (NWB) format. This extension integrates with ndx-ophys-devices to provide comprehensive optical component specifications.

Key Features

• Device components: MicroscopeModel, Microscope and MicroscopyRig, with optical components from ndx-ophys-devices

• Illumination patterns for line scanning, plane acquisition and random access scanning

• Planar and volumetric imaging spaces with the targeted anatomical region and pixel or voxel size

• Planar and volumetric series and static images, with multi-plane and multi-channel containers

• Segmentation, summary images and ROI response series

Documentation

Contents:

• Overview
  • Key Features
  • Dimension Order
  • Data Structure
  • For Developers
• Getting Started
  • Prerequisites
  • Installation
  • Basic Concepts
  • Quick Start Example
  • Next Steps
• User Guide
  • Two-Photon Imaging Session
  • One-Photon Miniscope Session with a GRIN Lens
• Examples
  • Two-Photon Calcium Imaging Example
  • One-Photon Calcium Imaging Example
  • Volumetric Imaging Example
  • Multi-Plane Imaging Example
  • Multi-Plane Multi-Channel Imaging Example
• Format Specification
  • Format Overview
  • Type Specifications
  • Schema Sources
• API
  • Device Components
  • Illumination Pattern Components
  • Imaging Space Components
  • Microscopy Series Components
  • Static Image Components
  • Multi-Plane and Multi-Channel Containers
  • Segmentation Components
  • Response Series Components
• Release Notes
  • Version 0.4.0 (October 14, 2026)
  • Version 0.3.0 (Jun 3, 2025)
  • Version 0.2.0 (March 19, 2025)
  • Version 0.1.0 (March 10, 2025)
• Credits
  • Acknowledgments
  • Authors
• Legal
  • License

Installation

Python Installation

pip install ndx-microscopy

Contributing

Contributions are welcome! Please see our GitHub repository for:

• Source code and documentation

• Issue tracking and feature requests

• Development guidelines

• Contributing instructions

Indices and Tables

• Index

• Module Index

• Search Page