Hardware-software co-design of an open-source automatic multimodal whole slide histopathology imaging system.

Significance: Advanced digital control of microscopes and programmable data acquisition workflows have become increasingly important for improving the throughput and reproducibility of optical imaging experiments. Combinations of imaging modalities have enabled a more comprehensive understanding of tissue biology and tumor microenvironments in histopathological studies. However, insufficient imaging throughput and complicated workflows still limit the scalability of multimodal histopathology imaging. Aim: We present a hardware-software co-design of a whole slide scanning system for high-throughput multimodal tissue imaging, including brightfield (BF) and laser scanning microscopy. Approach: The system can automatically detect regions of interest using deep neural networks in a low-magnification rapid BF scan of the tissue slide and then conduct high-resolution BF scanning and laser scanning imaging on targeted regions with deep learning-based run-time denoising and resolution enhancement. The acquisition workflow is built using Pycro-Manager, a Python package that bridges hardware control libraries of the Java-based open-source microscopy software Micro-Manager in a Python environment. Results: The system can achieve optimized imaging settings for both modalities with minimized human intervention and speed up the laser scanning by an order of magnitude with run-time image processing. Conclusions: The system integrates the acquisition pipeline and data analysis pipeline into a single workflow that improves the throughput and reproducibility of multimodal histopathological imaging.