Evaluating batch correction methods for image-based cell profiling

Abstract

High-throughput image-based profiling platforms are powerful technologies capable of collecting data from billions of cells exposed to thousands of perturbations in a time- and cost-effective manner. Therefore, image-based profiling data has been increasingly used for diverse biological applications, such as predicting drug mechanism of action or gene function. However, batch effects pose severe limitations to community-wide efforts to integrate and interpret image-based profiling data collected across different laboratories and equipment. To address this problem, we benchmarked seven high-performing scRNA-seq batch correction techniques, representing diverse approaches, using a newly released Cell Painting dataset, the largest publicly accessible image-based dataset. We focused on five different scenarios with varying complexity, and we found that Harmony, a mixture-model based method, consistently outperformed the other tested methods. Our proposed framework, benchmark, and metrics can additionally be used to assess new batch correction methods in the future. Overall, this work paves the way for improvements that allow the community to make best use of public Cell Painting data for scientific discovery.

Keywords: Batch correction; Cell Painting; Harmony; high-throughput phenotypic screening; image-based profiling; machine learning; morphological profiling; pseudo-bulk analysis.

Figure 1:

Evaluation pipeline. We evaluated five image-based profiling scenarios with different image acquisition equipment (high-throughput microscopes), laboratory, number of compounds and number of replicates. We used a state-of-the-art pipeline for image analysis. We compared seven batch correction methods using qualitative and quantitative metrics.

Figure 2.

Evaluation Scenario 4. A) Quantitative comparison of seven batch correction methods measuring batch effect removal (four batch correction metrics) and conservation of biological variance (six bio-metrics). Metrics are mean aggregated by category. Overall score is the weighted sum of aggregated batch correction and bio-metrics with 0.4 and 0.6 weights respectively. Visualization of integrated data colored by B) Compound, C) Laboratory, and D) Microscope. Left-to-right layout reflects the methods’ descending order of performance. We selected 18 out of 306 compounds with replicates in different well positions to account for position effects that may cause profiles to look similar. Alphanumeric IDs denote positive controls.