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 instances, and MicroscopyRig for organizing optical components

• Illumination Patterns: Support for various scanning and acquisition methods

• Imaging Spaces: Support for 2D/3D imaging with precise coordinate systems

• Data Series: Time series data with multi-plane and variable depth support

• ROI Management: Segmentation and response data storage

Documentation

Contents:

• Overview
  • Key Features
  • Data Structure
  • Common Applications
  • For Developers
• Getting Started
  • Prerequisites
  • Installation
  • Basic Concepts
  • Quick Start Example
  • Next Steps
• User Guide
  • Core Concepts
  • Common Workflows
  • Best Practices
• Examples
  • Two-Photon Calcium Imaging
  • Volumetric Imaging
  • Multi-Plane Imaging
• Format
  • Device Components
  • Microscopy Series Components
  • Illumination Pattern Components
  • Imaging Space Components
  • Segmentation Components
• API
  • Device Components
  • Illumination Pattern Components
  • Imaging Space Components
  • Microscopy Series Components
  • Segmentation Components
  • Response Series Components
• Release Notes
  • 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