Grid Screener: A Tool for Automated High-Throughput Screening on Biochemical and Biological Analysis Platforms

Abstract

Grid structures are common in high-throughput assays to parallelize experiments in biochemical or biological experiments. Manual analysis of grid images is laborious, time-consuming, expensive, and critical in terms of reproducibility. However, it is still common to do such analysis manually, as there is no standardized software for automated analysis. In this paper, we introduce a generic method to automatically detect grid structures in images and to perform flexible spot-wise analysis after successful grid detection. The deep learning-based approach of the grid structure detection allows being flexible concerning different grid types. The combination with a robust parameter estimation algorithm lowers the requirements of the detection quality and thus enhances robustness. Further, the method conducts semi-automated grid detection if a fully automated processing fails. An open-source software tool Grid Screener that implements the proposed methods is provided as a ready-for-use tool for researchers. The usability is demonstrated by taking different criteria into account, which are important for a successful application. We present the benefits of our proposed tool Grid Screener utilizing three different grid types in the context of high-throughput screening to show our contribution towards further lab automation. Our tool performs much faster than manual analysis, while maintaining or even enhancing accuracy.

Automated high-throughput image processing as part of the screening platform for personalized oncology

“…Therefore, only excerpts from the results are shown below. Please refer to 20 , 30 – 32 , 34 , 36 for further details.…”

“…Figure 5 shows the developed approach for automated high-throughput image processing based on the work of Schilling et al 32 . The method is composed of two components: (i) automated grid parameter estimation (macro level, cf.…”

“…In addition, our solutions consider a global data server for seamless data exchange between all computing systems. For further details, refer to the publications 20 , 32 , 34 .…”

“…We have developed an extensive open-source software portfolio with GUIs available as cross-platform Python pip packages. The tool Grid Screener 32 , available at https://git.scc.kit.edu/sc1357/grid-screener , covers the implementation of the proposed methods for automated high-throughput screening. The Karlsruhe Image Annotation Tool (KaIDA) 20 software package implements our proposal for assisted image annotation.…”

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Figure 8 Overview GUIs. The GUI of Grid Screener 32 ( a ) is shown. Besides, the usage of KaIDA 20 , integrated into a Lenovo x12 Detachable mobile touchscreen device ( b ) is visualized.

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