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 in arbitrary orders to create custom acquisition protocols. navigate is designed to accommodate the needs of a diverse user base, from biologists with no programming experience to advanced technology developers.

Project Philosophy

• Prioritize standard library imports for maximum stability, and minimize external dependencies.

• Abstraction layer to drive different camera types, etc.

• Plugin architecture for extensibility.

• Maximize productivity for biological users through robust graphical user interface-based workflows.

• Performant and responsive.

• Brutally obvious, well-documented, clean code organized in an industry standard Model-View-Controller architecture.

Note

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 numerous individuals, both past and present, in The Dean Lab. Please see the accompanying manuscript for a full list of contributors. Outside contributors are welcome.

Funding

navigate is supported by the

• 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