Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification

Abstract

Current imaging approaches limit the ability to perform multiscale characterization of 3D organotypic cultures (organoids) in large numbers. Here, we present an automated multiscale 3D imaging platform synergizing high-density organoid cultures with 3D live single objective light-sheet imaging. It is composed of disposable microfabricated organoid culture chips embedding optical components and a custom laser beam steering unit coupled to a commercial inverted microscope. It streamlines organoid culture and high content 3D imaging on a single user-friendly instrument with minimal manipulations and unprecedented throughput of 300 organoids per hour in 3D. Collecting large number of 3D stacks allowed training deep learning-based algorithms to quantify the organoids morphogenetic organizations at multi-scales, ranging from the sub-cellular scale to the whole organoid level.We validated the versatility and robustness of our approach on intestine, hepatic, neuroectoderm organoids and oncospheres.

In-silicoandin-vitromorphometric analysis of intestinal organoids

“…Additionally, the versatility of the algorithm to be applied to agent-based simulations of organoids provides the opportunity to improve such models and make predictions of pattern or structure formations before experimentation, which has been tested before for pattern formation in 2D stem-cell cultures [65]. In the future, the code limitations could be improved by implementing deep learning and machine learning algorithms to aid in finding additional or better-fitted parameters to define crypt-like structures [57, 66, 67].…”

Advances in Microfluidics: Technical Innovations and Applications in Diagnostics and Therapeutics

“…The platform has 96 devices per standard plate, integrates TEER, flow, and oxygen sensors, and is compatible with high-throughput data collection tools. Another work showcases the streamlining of organoid culture and high-content 3D imaging on a single user-friendly instrument with minimal manipulations and a throughput of 300 organoids per hour . The microfluidic chip is composed of an array of individual culture chambers with 45° mirror walls enabling sequential light-sheet imaging via a single lens objective.…”

“…Another work showcases the streamlining of organoid culture and highcontent 3D imaging on a single user-friendly instrument with minimal manipulations and a throughput of 300 organoids per hour. 148 The microfluidic chip is composed of an array of individual culture chambers with 45°mirror walls enabling sequential light-sheet imaging via a single lens objective. Another industrial demand lies in the supply of 3D tumor models.…”

Digital Technologies: Advancing Individualized Treatments through Gene and Cell Therapies, Pharmacogenetics, and Disease Detection and Diagnostics

“…Another cell therapy platform is the organoid. Organoids are 3D multicellular tissue constructs that closely resemble functional organs, and their biological complexity provides new opportunities and challenges in data analytics [ 34 ], as well as chances to reduce the reliance on animal models [ 35 ], with higher physiological relevance [ 36 ] and automation [ 37 ].…”