Cell lines and clearing approaches: a single-cell level 3D light-sheet fluorescence microscopy dataset of multicellular spheroids

Nowadays, three dimensional (3D) cell cultures are widely used in the biological laboratories and several optical clearing approaches have been proposed to visualize individual cells in the deepest layers of cancer multicellular spheroids. However, defining the most appropriate clearing approach for the different cell lines is an open issue due to the lack of a gold standard quantitative metric. In this article, we describe and share a single-cell resolution 3D image dataset of human carcinoma spheroids imaged using a light-sheet fluorescence microscope. The dataset contains 90 multicellular cancer spheroids derived from 3 cell lines (i.e. T-47D, 5-8F, and Huh-7D12) and cleared with 5 different protocols, precisely Clear(T) , Clear(T2) , CUBIC, ScaleA2, and Sucrose. To evaluate image quality and light penetration depth of the cleared 3D samples, all the spheroids have been imaged under the same experimental conditions, labelling the nuclei with the DRAQ(5) stain and using a Leica SP8 Digital LightSheet microscope. The clearing quality of this dataset was annotated by 10 independent experts and thus allows microscopy users to qualitatively compare the effects of different optical clearing protocols on different cell lines. It is also an optimal testbed to quantitatively assess different com putational metrics evaluating the image quality in the deepest layers of the spheroids. (C) 2021 The Author(s). Published by Elsevier Inc.

Automated summary

This article introduces a dataset of single-cell resolution 3D images of human carcinoma spheroids captured using a light-sheet fluorescence microscope, containing 90 multicellular cancer spheroids from 3 cell lines cleared with 5 different protocols. It can be used to qualitatively compare the effects of different optical clearing protocols on different cell lines and quantitatively assess computational metrics for image quality evaluation.