AutoPilot - Open Source Software Library for Real-Time Adaptive Light-Sheet Microscopy.

Light-sheet microscopy is a powerful method for imaging the development and function of biological systems. In order to successfully produce high-resolution images, these microscopes must achieve perfect overlap between the thin sheet of light used to illuminate the sample and the focal plane of the objective used to form an image. Whenever this co-planarity is violated, spatial resolution and image contrast immediately suffer.

Unfortunately, living specimens have complex optical properties that are not only heterogeneous in space but also dynamic in time, which typically leads to significant, spatiotemporally variable mismatches between light-sheet and detection planes. Achieving and maintaining high spatial resolution thus critically requires an automated framework capable of continuously analyzing and optimizing the spatial relationship between light-sheet and detection planes across the specimen volume and in real-time.

AutoPilot is the open source project that hosts the general algorithm for fast and robust assessment of local image quality, an automated computational method for image-based mapping of the three-dimensional light-sheet geometry inside a fluorescently labeled biological specimen, and a general algorithm for data-driven optimization of the system state of light-sheet microscopes capable of multi-color imaging with multiple illumination and detection arms.

Getting started

The main AutoPilot wiki is the place to start for in-depth installation instructions, documentation, examples, building guide, and more...

To get started even faster please go:


Real-Time Adaptive Light-Sheet Microscopy Recovers High Resolution in Large Living Organisms.
Loic A. Royer, William C. Lemon, Raghav K. Chhetri, Yinan Wan, Michael Coleman, Eugene Myers and Philipp J. Keller. Nature Biotechnology (2016)

Authors and Contributors

The AutoPilot core algorithms were written by Loic Royer (@royerloic) in collaboration with Mike Coleman and Philipp Keller.


The AutoPilot project is a collaboration between the Myers and Keller labs. The AutoPilot project was initiated by Loic Royer and Philipp Keller when the Myers Lab was still located at Janelia and then continued when Loic moved to the MPI-CBG.


If you have questions or comments, please do not hesitate to send us an email. We will get back to you as soon as we can.

Follow Loic Royer on Twitter: @loicaroyer