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.

Start Here

If you are new to navigate, begin with Software Installation.

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

Need Help?

• Start with Troubleshooting for common setup and runtime problems.

• Check Known Issues for current limitations and workarounds.

• If you cannot find a solution, open an issue on GitHub Issues.

Important

Operating system compatibility: navigate is primarily operated on Windows and has also been used on Linux in some environments. See Software Installation for setup recommendations.

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 and voltage minimums and maximums, 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 use navigate at their own risk.

Getting Started

• Computer Considerations
• Computer Power Configuration
• Software Installation
• Launching Navigate
• Configuring Navigate
• Acquiring Data
• Smart Acquisition Routines

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
• Developer Architecture Concepts
• Feature Container
• REST API
• Plugin Architecture
• Adding New Hardware

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

How to Cite

If navigate contributes to your research, please cite our publication on PubMed.

Marin Z, Wang X, Collison DW, McFadden C, Lin J, Borges HM, Chen B, Mehra D, Shen Q, Gałecki S, Daetwyler S, Sheppard SJ, Thien P, Porter BA, Conzen SD, Shepherd DP, Fiolka R, Dean KM. Navigate: an open-source platform for smart light-sheet microscopy. Nat Methods. 2024 Nov;21(11):1967-1969. doi: 10.1038/s41592-024-02413-4. PMID: 39261640; PMCID: PMC11540721.

Authors

navigate includes key contributions from individuals both inside and outside of The Dean Lab. Please see the GitHub 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