Functional analysis of high-content high-throughput imaging data

ABSTRACT

High-content automated imaging platforms allow the multiplexing of several targets simultaneously to generate multi-parametric single-cell data sets over extended periods of time. Typically, standard simple measures such as mean value of all cells at every time point are calculated to summarize the temporal process, resulting in loss of time dynamics of the single cells. Multiple experiments are performed but observation time points are not necessarily identical, leading to difficulties when integrating summary measures from different experiments. We used functional data analysis to analyze continuous curve data, where the temporal process of a response variable for each single cell can be described using a smooth curve. This allows analyses to be performed on continuous functions, rather than on original discrete data points. Functional regression models were applied to determine common temporal characteristics of a set of single cell curves and random effects were employed in the models to explain variation between experiments. The aim of the multiplexing approach is to simultaneously analyze the effect of a large number of compounds in comparison to control to discriminate between their mode of action. Functional principal component analysis based on T-statistic curves for pairwise comparison to control was used to study time-dependent compound effects.

KEYWORDS:

• Automated image analysis
• functional t-test
• functional regression model
• functional principal component analysis
• toxicology

Acknowledgments

We thank Dr Joost Beltman (Division of Toxicology, Leiden Academic Centre for Drug Research,Leiden University, Leiden, The Netherlands) for providing valuable comments.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

The study was supported by European Union projects DETECTIVE ‘Detection of endpoints and biomarkers for repeated dose toxicity using in vitro systems’ under Grant agreement No. 266838.