Transfer learning for versatile and training free high content screening analyses

Abstract

High content screening (HCS) is a technology that automates cell biology experiments at large scale. A High Content Screen produces a high amount of microscopy images of cells under many conditions and requires that a dedicated image and data analysis workflow be designed for each assay to select hits. This heavy data analytic step remains challenging and has been recognized as one of the burdens hindering the adoption of HCS. In this work we propose a solution to hit selection by using transfer learning without additional training. A pretrained residual network is employed to encode each image of a screen into a discriminant representation. The deep features obtained are then corrected to account for well plate bias and misalignment. We then propose two training-free pipelines dedicated to the two main categories of HCS for compound selection: with or without positive control. When a positive control is available, it is used alongside the negative control to compute a linear discriminant axis, thus building a classifier without training. Once all samples are projected onto this axis, the conditions that best reproduce the positive control can be selected. When no positive control is available, the Mahalanobis distance is computed from each sample to the negative control distribution. The latter provides a metric to identify the conditions that alter the negative control’s cell phenotype. This metric is subsequently used to categorize hits through a clustering step. Given the lack of available ground truth in HCS, we provide a qualitative comparison of the results obtained using this approach with results obtained with handcrafted image analysis features for compounds and siRNA screens with or without control. Our results suggests that the fully automated and generic pipeline we propose offers a good alternative to handcrafted dedicated image analysis approaches. Furthermore, we demonstrate that this solution select conditions of interest that had not been identified using the primary dedicated analysis. Altogether, this approach provides a fully automated, reproducible, versatile and comprehensive alternative analysis solution for HCS encompassing compound-based or downregulation screens, with or without positive controls, without the need for training or cell detection, or the development of a dedicated image analysis workflow.