PhotoniX, Volume. 4, Issue 1, 34(2023)

Digital staining in optical microscopy using deep learning - a review

Lucas Kreiss1,2、*, Shaowei Jiang3, Xiang Li4, Shiqi Xu1, Kevin C. Zhou1,5, Kyung Chul Lee1,6, Alexander Mühlberg2, Kanghyun Kim1, Amey Chaware1, Michael Ando7, Laura Barisoni8, Seung Ah Lee6, Guoan Zheng3, Kyle J. Lafata4, Oliver Friedrich2, and Roarke Horstmeyer1
Author Affiliations
  • 1Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
  • 2Institute of Medical Biotechnology, Friedrich-Alexander University (FAU), Erlangen, Germany
  • 3Department of Biomedical Engineering, University of Connecticut, Mansfield Connecticut, USA
  • 4Department of Radiation Physics, Duke University, Durham, NC 27708, USA
  • 5Department of Electrical Engineering & Computer Sciences, University of California, Berkeley CA, USA
  • 6School of Electrical & Electronic Engineering, Yonsei University, Seoul 03722, Republic of Korea
  • 7Google, Inc., Mountain View, CA 94043, USA
  • 8Department of Pathology, Duke University, Durham, NC 27708, USA
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    Until recently, conventional biochemical staining had the undisputed status as well-established benchmark for most biomedical problems related to clinical diagnostics, fundamental research and biotechnology. Despite this role as gold-standard, staining protocols face several challenges, such as a need for extensive, manual processing of samples, substantial time delays, altered tissue homeostasis, limited choice of contrast agents, 2D imaging instead of 3D tomography and many more. Label-free optical technologies, on the other hand, do not rely on exogenous and artificial markers, by exploiting intrinsic optical contrast mechanisms, where the specificity is typically less obvious to the human observer. Over the past few years, digital staining has emerged as a promising concept to use modern deep learning for the translation from optical contrast to established biochemical contrast of actual stainings. In this review article, we provide an in-depth analysis of the current state-of-the-art in this field, suggest methods of good practice, identify pitfalls and challenges and postulate promising advances towards potential future implementations and applications.

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    Lucas Kreiss, Shaowei Jiang, Xiang Li, Shiqi Xu, Kevin C. Zhou, Kyung Chul Lee, Alexander Mühlberg, Kanghyun Kim, Amey Chaware, Michael Ando, Laura Barisoni, Seung Ah Lee, Guoan Zheng, Kyle J. Lafata, Oliver Friedrich, Roarke Horstmeyer. Digital staining in optical microscopy using deep learning - a review[J]. PhotoniX, 2023, 4(1): 34

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    Paper Information

    Category: Research Articles

    Received: Apr. 26, 2023

    Accepted: Sep. 27, 2023

    Published Online: Dec. 14, 2023

    The Author Email: Kreiss Lucas (lucas.kreiss@duke.edu)

    DOI:10.1186/s43074-023-00113-4

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