The Self-Driving Microscope

20-h imaging of a fruit fly embryo with the nervous system fluorescently labeled. AutoPilot automatically detects the onset of the expression of the marker and optimizes all parameters associated with this color channel in response to the emerging signal. (Source: MPI-CBG)

20-h imaging of a fruit fly embryo with the nervous system fluorescently labeled. AutoPilot automatically detects the onset of the expression of the marker and optimizes all parameters associated with this color channel in response to the emerging signal. (Source: MPI-CBG)

Light-sheet micro­scopy is one of the most powerful method for imaging the deve­lopment and function of whole living organisms. However, achieving high-reso­lution images with these microscopes requires manual adjustments during imaging. Researchers of the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden together with colleagues at Janelia Research Campus (HHMI) have developed a new kind of light-sheet micro­scope that can ‘drive’ itself automa­tically by adapting to the challenging and dynamic optical conditions of large living specimens. This new smart micro­scope combines a novel hardware design and a smart ‘AutoPilot’ system that can analyze images and automa­tically adjust and optimize the microscope. This framework enables for the first time long-term adaptive imaging of entire deve­loping embryos and improves the resolution of light-sheet micro­scopes up to five-fold.

Light sheet micro­scopy is a novel microscopy technique developed in the last ten years that is uniquely suited to image large living organisms. In a light-sheet micro­scope, a laser light sheet illu­minates the sample perpen­dicularly to the obser­vation along a thin plane within the sample. Out-of-focus and scattered light from other planes – which often impair image quality – is largely avoided because only the observed plane is illu­minated.

The long-standing goal of microscopy is to achieve ever-sharper images deep inside of living samples. For light-sheet microscopes this requires to perfectly maintain the careful alignments between imaging and light-sheet illu­mination planes. Mismatches between these planes arise from the optical variability of living tissues across different locations and over time. Tackling this challenge is essential to acquire the high-reso­lution images necessary to decipher the biology behind organism deve­lopment and morpho­genesis. “So far, researchers had to sit at their micro­scope and tweak things manually – our system puts an end to this: it is like a self-driving car: it functions auto­nomously”, says Loïc Royer. This smart auto­nomous micro­scope can in real-time analyze and optimize the spatial relation­ship between light-sheets and detection planes across the specimen volume.

The researchers demonstrated the performance of their smart micro­scope by imaging the development of zebrafish and fly embryos for more than 20 hours. They also performed adaptive whole-brain functional imaging in larval zebrafish – obtaining sharper images of a whole ‘thinking’ fish brain. In the study they show how their system recovers cellular and sub-cellular resolution in many regions of the sample and how it adapts to changes in the spatial distri­bution of fluores­cent markers. “We have been using our AutoPilot system on several micro­scopes for more than two years and it makes a big difference in terms of image quality.” says Philipp Keller one of the senior authors with Gene Myers. Making micro­scopes adaptive and auto­nomous is important as it will enable the future use of light-sheet microscopy for automated high-throughput drug screens, mutant screens and the construc­tion of anatomical and deve­lopmental atlases in various bio­logical model systems. (Source: MPG)

Reference: L. A. Royer et al.: Adaptive light-sheet microscopy for long-term, high-resolution imaging in living organisms, Nat. Biotech., online 31 October 2016; DOI: 10.1038/nbt.3708

Link: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany • Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, USA

 

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