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