Authors
Liu Y, Müller G, Kowitz L, Chobola T, Weiss K, Maier P, Luo J, Roeßing M, Stenzel M, Grüneboom A, Paetzold J, Ertürk A, Navab N, Marr C, Chen J, Huisken J, Peng T
Journal
Research Square
Citation
Research Square 2025.
Abstract
Selective plane illumination microscopy (SPIM, also known as light sheet fluorescence microscopy) is the method of choice for studying organ morphogenesis and function, as it permits gentle and rapid volumetric imaging of biological specimens over days. In inhomogeneous samples, however, sample-induced aberrations, including light absorption, scattering, and refraction, can degrade the image, particularly as the focal plane gets deeper into the sample. Here, we present Leonardo, the first toolbox capable of resolving all sample-induced aberrations by using two modules: (1) DeStripe removes stripe artifacts in SPIM caused by light absorption; (2) Fuse reconstructs a single high-quality image from dual-sided illumination and/or dual-sided detection, while eliminating blur and optical distortions caused by light scattering and refraction. The efficacy of Leonardo is validated on a wide range of biological systems, from minimally invasive experiments on sensitive specimens (relatively translucent embryonic and optically opaque larval zebrafish) to immunolabeled mice up to 2 centimeters in size. We provide model code and a Napari-based graphical user interface, enabling the SPIM community to easily apply Leonardo to advance light sheet imaging of inhomogeneous and complex specimens.
