navigate

navigate is an open-source Python software for light-sheet microscope control. It focuses on smart microscopy applications by providing reusable acquisition and analysis routines, termed features, that can be chained together arbitrarily to create custom acquisition protocols. navigate is accompanied by Altair, our open-source light-sheet microscope designs. navigate is designed to accommodate the needs of a diverse user base, from biologists with no programming experience to advanced technology developers.

Key Features

• Smart microscopy control with customizable acquisition protocols

• Hardware abstraction layer supporting multiple device vendors

• Intuitive GUI for biologists with no programming experience

• Extensible plugin architecture for developers

• Integration with open-source light-sheet microscope designs

See also

This project is under active development. See our GitHub repository for updates.

Warning

Please be advised that while the Dean Lab has implemented several safeguards in the automation of hardware, including but not limited to stage limits, voltage minimums, and maximums, are more, there are inherent risks associated with the use of such automated systems. Despite these precautions, the complexity and nature of automated hardware can lead to unpredictable outcomes. Therefore, the Dean Lab and UT Southwestern expressly disclaim any responsibility for any damages, losses, or injuries that may arise from or be related to the use of navigate. Users should be aware of these risks and agree to utilize navigate at their own risk.

Getting Started

• Quick Start Guide
• Software Installation
• I Want To…

User Guide

• Supported Hardware
• Supported File Formats
• User Interface Walkthrough
• Setting Up A Microscope
• Acquiring Data
• Case Studies

Development

• Contributing Guidelines
• Developer Install
• Software Architecture
• Feature Container
• REST-API
• Plugin Architecture

Troubleshooting & Known Issues

• Troubleshooting
• Known Issues

Plugins

• navigate Plugin Template
• navigate Confocal Projection
• navigate at Scale
• navigate Constant Velocity Acquisition
• navigate MMCore
• navigate ilastik Server
• navigate Photoactivation

Reference

• Implemented Microscopes
• Software API

Authors

navigate includes key contributions from individuals both inside and outside of The Dean Lab. Please see the GtiHub repository for a full list of contributors. We welcome community contributions - see our contributing guidelines for more information on how to get involved.

Funding

• Cancer Prevention and Research Institute of Texas (10068451).

• NIH National Institute of General Medical Science (RM1GM145399).

• NIH National Cancer Institute (1U54CA268072).

• Simmons Comprehensive Cancer Center Translational Seed Grant.

• UTSW President’s Research Council