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Artifact-free whole-slide imaging with structured illumination microscopy and Bayesian image reconstruction

Karl Johnson, View ORCID ProfileGuy M. Hagen
doi: https://doi.org/10.1101/765396
Karl Johnson
1UCCS center for the Biofrontiers Institute, University of Colorado at Colorado Springs 1420 Austin Bluffs Parkway, Colorado Springs, Colorado, 80918, USA
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Guy M. Hagen
1UCCS center for the Biofrontiers Institute, University of Colorado at Colorado Springs 1420 Austin Bluffs Parkway, Colorado Springs, Colorado, 80918, USA
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  • ORCID record for Guy M. Hagen
  • For correspondence: ghagen@uccs.edu
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Abstract

Background Structured illumination microscopy (SIM) is a method which can be used to image biological samples and can achieve both optical sectioning and super-resolution effects. Optimization of the imaging setup and data processing methods results in high quality images without artifacts due to mosaicking or due to the use of SIM methods. Reconstruction methods based on Bayesian estimation can be used to produce images with a resolution beyond that dictated by the optical system.

Findings Five complete datasets are presented including large panoramic SIM images of human tissues in pathophysiological conditions. Cancers of the prostate, skin, ovary, and breast, as well as tuberculosis of the lung, were imaged using SIM. The samples are available commercially and are standard histological preparations stained with hematoxylin and eosin.

Conclusion The use of fluorescence microscopy is increasing in histopathology. There is a need for methods which reduce artifacts when employing image stitching methods or optical sectioning methods such as SIM. Stitched SIM images produce results which may be useful for intraoperative histology. Releasing high quality, full slide images and related data will aid researchers in furthering the field of fluorescent histopathology.

  • Abbreviations

    Av Int Proj
    average intensity projection;
    FOV
    field of view;
    H&E
    hematoxylin and eosin;
    ICE
    Image Composite Editor;
    MAP-SIM
    maximum a posteriori probability SIM;
    NA
    numerical aperture;
    LCOS
    liquid crystal on silicon;
    PSDca
    circularly averaged power spectral density;
    SIM
    structured illumination microscopy;
    WF
    wide field.
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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    Posted September 11, 2019.
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    Artifact-free whole-slide imaging with structured illumination microscopy and Bayesian image reconstruction
    Karl Johnson, Guy M. Hagen
    bioRxiv 765396; doi: https://doi.org/10.1101/765396
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    Artifact-free whole-slide imaging with structured illumination microscopy and Bayesian image reconstruction
    Karl Johnson, Guy M. Hagen
    bioRxiv 765396; doi: https://doi.org/10.1101/765396

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