High-Content Phenotypic Profiling with the Araceli Endeavor® Microscope
Fernanda Garcia Fóssa (1), Martin Theiß (2), Sonja Sievers (1)
(1)Max Planck Institute for Molecular Physiology, Dortmund, Germany
(2)Araceli Biosciences, Tigard, Oregon, USA
Introduction
High-content imaging has become an essential tool in modern biomedical research, particularly in the realms of drug discovery, toxicology, and functional genomics. Among the most widely adopted approaches is the Cell Painting Assay (CPA), which was originally conceived as a combination of fluorescent dyes to label eight organelles using five fluorescent channels (Bray et al., 2016). This method enables the extraction of thousands of morphological features per cell, allowing for comprehensive phenotypic profiling at scale. By capturing subtle changes in cell and organelle shape, texture, and intensity, CPA facilitates the unbiased identification of compound effects, mechanisms of action, and pathway perturbations.
However, the throughput and quality of data generated by CPA are tightly linked to the performance of the imaging platform used. Traditional high-content imaging systems are limited by acquisition speed, hardware scalability, or compatibility with modern analysis pipelines, making it challenging to meet the demands of large-scale screening efforts.
In this application note, we evaluate the performance of the Araceli Endeavor® imaging system for high-content phenotypic profiling using the CPA assay. We compare the morphological profiles generated by the Endeavor to those obtained from a well-established, prior imaging solution that has served as a standard in our workflow. Despite using one fewer imaging channel, the Endeavor platform demonstrates comparable, and in some cases superior, profiling performance. We further highlight its advantages in acquisition speed, data quality, and analytical robustness, demonstrating that the Endeavor microscope is a powerful and scalable tool for high-content phenotypic screening.