Is Brightfield All You Need for MoA Prediction?

Abstract

Fluorescence staining techniques, such as Cell Painting, together with fluorescence microscopy have proven invaluable in visualizing and quantifying the effects that drugs and other perturbations have on cultured cells. However, fluorescence microscopy is expensive, time-consuming, and labour-intensive, and the stains applied can be cytotoxic, interfering with the activity under study. The simplest form of microscopy, brightfield microscopy, lacks these downsides, but the images produced have low contrast and the cellular compartments are difficult to discern. Nevertheless, harnessing deep learning for these brightfield images may still be sufficient for various predictive endeavours. In this study, we compare the predictive performance of models trained on fluorescence images to those trained on brightfield images for predicting the mechanism of action (MoA) of different drugs. We also extracted CellProfiler features from the fluorescence images and used them to benchmark the performance. Overall, we found comparable and correlated predictive performance for the two imaging modalities. This is promising for future studies of MoAs in time-lapse experiments.