Automatic and adaptive heterogeneous refractive index compensation for light-sheet microscopy

Duncan P Ryan,Douglas P Shepherd,Sukumar Vijayaraghavan,Wendy B Macklin,Omid Masihzadeh,Steven H Abman,Elizabeth A Gould,Gregory J Seedorf,Diego Restrepo

doi:10.1038/s41467-017-00514-7

Abstract

Optical tissue clearing has revolutionized researchers’ ability to perform fluorescent measurements of molecules, cells, and structures within intact tissue. One common complication to all optically cleared tissue is a spatially heterogeneous refractive index, leading to light scattering and first-order defocus. We designed C-DSLM (cleared tissue digital scanned light-sheet microscopy) as a low-cost method intended to automatically generate in-focus images of cleared tissue. We demonstrate the flexibility and power of C-DSLM by quantifying fluorescent features in tissue from multiple animal models using refractive index matched and mismatched microscope objectives. This includes a unique measurement of myelin tracks within intact tissue using an endogenous fluorescent reporter where typical clearing approaches render such structures difficult to image. For all measurements, we provide independent verification using standard serial tissue sectioning and quantification methods. Paired with advancements in volumetric image processing, C-DSLM provides a robust methodology to quantify sub-micron features within large tissue sections.

Highlights

Optical tissue clearing has revolutionized researchers’ ability to perform fluorescent measurements of molecules, cells, and structures within intact tissue
We show that Cleared tissue digital scanned light-sheet microscopy (C-DSLM) enables volumetric quantification in tissue that is intentionally undercleared to retain a lipid-bound endogenous reporter of myelin
We demonstrate that C-DSLM provides first-order defocus correction for a range of microscope objectives

Summary

Introduction

Optical tissue clearing has revolutionized researchers’ ability to perform fluorescent measurements of molecules, cells, and structures within intact tissue. We demonstrate the flexibility and power of C-DSLM by quantifying fluorescent features in tissue from multiple animal models using refractive index matched and mismatched microscope objectives This includes a unique measurement of myelin tracks within intact tissue using an endogenous fluorescent reporter where typical clearing approaches render such structures difficult to image. Motivated by existing work on remote focusing and self-adapting LSFM designs[8, 10,11,12,13], we developed C-DSLM (cleared tissue digital scanned light-sheet microscopy) This design is optimized to automatically account for spatially heterogeneous RI in thick optically cleared samples without the need for user intervention or a heavy investment in specialized optical/optomechanical components such as piezo stages, adaptive optics, or microscope objectives. We independently verify each measurement using uncleared tissue, serial sectioning, and standard microscopy techniques that in contrast to C-DSLM, require a significant time investment to obtain a single measurement

Methods

Results

Conclusion