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

By Karl Johnson, Guy M Hagen

Posted 11 Sep 2019
bioRxiv DOI: 10.1101/765396 (published DOI: 10.1093/gigascience/giaa035)

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. Keywords: Structured illumination microscopy, SIM, image stitching, Bayesian methods, MAP-SIM, SIMToolbox, histopathology, cancer.

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