Monoclonalization refers to the isolation and expansion of a single cell derived from a cultured population. This is a valuable step in cell culture that serves to minimize a cell line’s technical variability downstream of cell-altering events, such as reprogramming or gene editing, as well as for processes such as monoclonal antibody development. However, traditional methods for verifying clonality do not scale well, posing a critical obstacle to studies involving large cohorts. Without automated, standardized methods for assessing clonality post hoc, methods involving monoclonalization cannot be reliably upscaled without exacerbating the technical variability of cell lines. Here, we report the design of a deep learning workflow that automatically detects colony presence and identifies clonality from cellular imaging. The workflow, termed Monoqlo, integrates multiple convolutional neural networks and, critically, leverages the chronological directionality of the cell-culturing process. Our algorithm design provides a fully scalable, highly interpretable framework that is capable of analysing industrial data volumes in under an hour using commodity hardware. We focus here on monoclonalization of human induced pluripotent stem cells, but our method is generalizable. Monoqlo standardizes the monoclonalization process, enabling colony selection protocols to be infinitely upscaled while minimizing technical variability.

单克隆化是指从培养的群体中分离和扩增单个细胞。这是细胞培养中的一个有价值的步骤，用于最大限度地减少细胞改变事件下游的细胞系技术变异性，例如重编程或基因编辑，以及单克隆抗体开发等过程。然而，验证克隆性的传统方法不能很好地扩展，这对涉及大型队列的研究构成了严重障碍。如果没有自动化、标准化的方法来评估克隆性事后，涉及单克隆化的方法无法在不加剧细胞系技术变异性的情况下可靠地放大。在这里，我们报告了一种深度学习工作流程的设计，该工作流程自动检测菌落存在并从细胞成像中识别克隆性。工作流程，称为 Monoqlo，集成了多个卷积神经网络，并且至关重要的是，利用了细胞培养过程的时间方向性。我们的算法设计提供了一个完全可扩展、高度可解释的框架，能够使用商用硬件在一小时内分析工业数据量。我们在这里专注于人类诱导多能干细胞的单克隆化，但我们的方法是可推广的。Monoqlo 标准化了单克隆化过程，使菌落选择方案能够无限放大，同时最大限度地减少技术可变性。高度可解释的框架，能够使用商品硬件在一小时内分析工业数据量。我们在这里专注于人类诱导多能干细胞的单克隆化，但我们的方法是可推广的。Monoqlo 标准化了单克隆化过程，使菌落选择方案能够无限放大，同时最大限度地减少技术可变性。高度可解释的框架，能够使用商品硬件在一小时内分析工业数据量。我们在这里专注于人类诱导多能干细胞的单克隆化，但我们的方法是可推广的。Monoqlo 标准化了单克隆化过程，使菌落选择方案能够无限放大，同时最大限度地减少技术可变性。