COMPASS

Biologists are increasingly transitioning towards more complex assays that require volumetric imaging with high spatiotemporal resolution. Whether it is a developing embryo, the formation of an immunological synapse, cancer migrating through a 3D collagen matrix, these biological processes can only be understood when non-invasively and quantitatively evaluated in their entirety through time.

To meet these growing demands, we aim to develop simplified optical systems that provide cutting-edge imaging performance while ensuring ease of assembly and accessibility. By leveraging precision-engineered, baseplate-mounted designs, we eliminate unnecessary degrees of freedom, making high-resolution light-sheet microscopy more robust, reproducible, and approachable for researchers across disciplines. Our goal is to create powerful yet modular imaging platforms that enable biologists to focus on discovery rather than instrument complexity, accelerating the adoption of advanced volumetric imaging techniques.

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Project Philosophy

• High-performance, easy-to-assemble light-sheet microscopes designed for broad accessibility.

• Seamless integration with navigate software for optimized operation and intelligent imaging workflows.

• Precision-engineered optomechanical design for ease of use, reproducibility, and low maintenance.

• Streamlined optoelectronics and control architecture for robust, reliable, and modular system operation.

• Modular, adaptable platforms that support future advancements in light-sheet microscopy.

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Warning

Please be advised that while the Dean Lab has implemented several safeguards, there are inherent risks associated with the use of such mechanical and optical systems. Despite these precautions, the complexity and nature of 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 COMPASS. Users should be aware of these risks and agree to utilize COMPASS at their own risk.

Warning

Licensing Note: These design materials are freely available to academic and non-profit users for research and educational purposes. Commercial or for-profit entities must obtain a license before use; please contact the Office of Technology Development for more information.

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Table of Contents

• Introduction
  • Why is Volumetric Imaging Important?
  • The Importance of Parallelization
  • Challenges with 3D Imaging
  • Why Build a Microscope?
• Overview of Subcellular Light-Sheet Microscope Technologies
  • Lattice Light-Sheet Microscopy (LLSM)
  • Field Synthesis
  • Dual Inverted Selective Plane Illumination Microscopy (diSPIM)
  • Axially Swept Light-Sheet Microscopy (ASLM)
  • Oblique Plane Microscopy (OPM)
• Software
  • Optical Simulations
  • Computer-Aided Design
  • Microscope Control Software: navigate
  • Post-Processing
• Room and Hardware Considerations
  • Preparation of the Imaging Room
  • Optical Table
  • Computer Specifications
  • Laser Sources
• Design Process
  • Initial Lens Selection
  • Zemax Simulation Setup Process
  • Zemax Simulation Analysis
  • Zemax Tolerance Analysis
  • Baseplate Design
  • Physical Coordinate Definitions
• Microscope Assembly
  • Parts List and Cost
  • Illumination Path
  • Detection Path
  • Optomechanics
  • Optoelectronics
• System Characterization
  • Beam Characterization and PSF Analysis
  • Sample Biological Images
• Imaging Process
  • Imaging Configurations
  • Visualization of Axes Mapping
  • Minimizing Spherical Aberrations
  • Sample Image Examples
  • Deskewing
  • Reslicing
  • Deconvolution
• Future Releases

Authors

Dr. John Haug performed all simulations, design, testing, and validation of COMPASS. Seweryn Gałecki provided cells for testing imaging performance and assisted in their visualization. Dr. Kevin Dean oversaw and provided feedback on all research operations. This project also benefited from valuable feedback from the Dean, Fiolka, and Danuser labs at UTSW.

Acknowledgements

The authors extend their gratitude to Calvin Jones and Dr. Sophia Theodossiou (Boise State University) for their assistance in designing and printing the custom sample chamber, as well as Melissa Glidewell for her initial evaluation of optical tolerances.

Funding

navigate is supported by the UT Southwestern and University of North Carolina Center for Cell Signaling, a Biomedical Technology Development and Dissemination (BTDD) Center funded by the NIH National Institute of General Medical Science (RM1GM145399), and the Center for Metastatic Tumor Imaging program, a Cellular Cancer Biology Imaging Research (CCBIR) program funded by the NIH National Cancer Institute (U54CA268072).