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

Authors :
Li B
Nelson MS
Chacko JV
Cudworth N
Eliceiri KW
Source :
Journal of biomedical optics [J Biomed Opt] 2023 Feb; Vol. 28 (2), pp. 026501. Date of Electronic Publication: 2023 Feb 08.
Publication Year :
2023

Abstract

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.<br />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.<br />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.<br />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.<br />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.<br /> (© 2023 The Authors.)

Details

Language :
English
ISSN :
1560-2281
Volume :
28
Issue :
2
Database :
MEDLINE
Journal :
Journal of biomedical optics
Publication Type :
Academic Journal
Accession number :
36761254
Full Text :
https://doi.org/10.1117/1.JBO.28.2.026501