Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.10.291286v1?rss=1 Authors: Preusser, F., dos Santos, N., Contzen, J., Stachelscheid, H., Costa, E. T., Mergenthaler, P., Preibisch, S. Abstract: Three-dimensional stem-cell-derived organoids are a powerful tool for studying cellular processes in tissue-like structures, enabling in vitro experiments in an organ specific context. While organoid research has been closely linked to advances in fluorescent microscopy, capturing cellular structures within their global context in an organoid often remains challenging due to the dense structure and opacity of organoids. The development of optical clearing methods has provided a solution for fixed organoids but optimizing clearing protocols for a given sample type and staining can be challenging. Importantly, quantitative measures for assessing image quality throughout cleared fluorescent samples are missing. Here, we propose the Fourier ring correlation-based quality estimation (FRC-QE) as a new metric for automated 3D image quality estimation in cleared organoids. We show that FRC-QE robustly captures differences in clearing efficiency within an organoid, across replicates and clearing protocols, and also works for different microscopy modalities. FRC-QE is open-source, written in ImgLib2, and provided as an easy-to-use and macro-scriptable plugin for the popular Fiji software. We therefore envision FRC-QE to fill the gap of providing a reliable quality metric for testing, optimizing and comparing optical clearing methods. Copy rights belong to original authors. Visit the link for more info