Recent Trends and Perspectives in Cerebral Organoids Imaging and Analysis

Abstract

Purpose: Since their first generation in 2013, the use of cerebral organoids has spread exponentially. Today, the amount of generated data is becoming challenging to analyze manually. This review aims to overview the current image acquisition methods and to subsequently identify the needs in image analysis tools for cerebral organoids.Methods: To address this question, we went through all recent articles published on the subject and annotated the protocols, acquisition methods, and algorithms used.Results: Over the investigated period of time, confocal microscopy and bright-field microscopy were the most used acquisition techniques. Cell counting, the most common task, is performed in 20% of the articles and area; around 12% of articles calculate morphological parameters. Image analysis on cerebral organoids is performed in majority using ImageJ software (around 52%) and Matlab language (4%). Treatments remain mostly semi-automatic. We highlight the limitations encountered in image analysis in the cerebral organoid field and suggest possible solutions and implementations to develop.Conclusions: In addition to providing an overview of cerebral organoids cultures and imaging, this work highlights the need to improve the existing image analysis methods for such images and the need for specific analysis tools. These solutions could specifically help to monitor the growth of future standardized cerebral organoids.

Recent Advances in Brain Organoid Technology for Human Brain Research

“…The most prevalent method in brain organoid analysis is microscopic observation (Figure 6B(i)). 110 Confocal microscopy is primarily used in organoid imaging to obtain fluorescent images showing expression of specific markers. However, the disadvantage of confocal microscopy is having to slice the brain organoid into thin sections to facilitate imaging of millimeter-scale brain organoids because the penetration depth is limited to <100 μm due to light scattering and absorption.…”

“…The most prevalent method in brain organoid analysis is microscopic observation (Figure B­(i)) . Confocal microscopy is primarily used in organoid imaging to obtain fluorescent images showing expression of specific markers.…”

CelltypeR: A flow cytometry pipeline to annotate, characterize and isolate single cells from brain organoids

“…However, sample preparation, image acquisition, and analysis are labour inten sive and limited in quantitative accuracy. Moreover, for 3D tissues, either only a small section can be analyzed or the entire tissue must be reconstructed and only a few cell types can be detected at once 10, 11 .…”

“…Moreover, for 3D tissues, either only a small section can be analyzed or the entire tissue must be reconstructed and only a few cell types can be detected at once. 11,12…”

“…Moreover, for 3D tissues, either only a small section can be analyzed or the entire tissue must be reconstructed and only a few cell types can be detected at once. 11,12 Here, we use flow cytometry (FC) to measure the protein expression levels of a panel of cell surface markers enriched in specific brain cell types. FC is a fast, quantitative, and robust method, used widely in immunology and cancer research [13][14][15] but to date only sparsely in neuroscience.…”