All-in-focus fine needle aspiration biopsy imaging based on Fourier ptychographic microscopy

Liang, Mingshu; Bernadt, Cory T.; Wong, Soon Boon Justin; Choi, Changsoon; Côté, Richard J.; Yang, Changhuei

doi:10.1016/j.jpi.2022.100119

Cited by 14 publications

(6 citation statements)

References 20 publications

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“…Four brightfield images [ I i , Figure 1d(i)] are captured to compute S i according to Equation (1). Although the recovered complex optical field [amplitude and phase, Figure 1d(ii)] is 2D, it enables us to digitally generate a z-stack by introducing a defocusing phase to the pupil (32, 33). For example, the sharpest focus of the top, middle, and bottom beads within the boxed sections in Figure 1d(ii) corresponds to axial positions of -26, -3, and 22 microns, respectively.…”

Section: Resultsmentioning

confidence: 99%

Investigating 3D microbial community dynamics in the rhizosphere using complex-field and fluorescence microscopy

Zhang,

Alcalde,

Zhou

et al. 2024

Preprint

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Microbial interactions in the rhizosphere contribute to soil health. Understanding these interactions thus has the potential to advance sustainable agriculture, ecosystem management, and environmental stewardship. Yet it is difficult to understand what we cannot see; amongst the limitations in rhizosphere imaging are challenges associated with rapidly and non-invasively imaging microbial cells over field depths relevant to plant roots. Here, we present a novel bimodal imaging technique called Complex-field and Fluorescence microscopy using the Aperture Scanning Technique (CFAST) that begins to address these limitations by integrating quantitative phase and 3D fluorescence imaging. We showcase CFAST's practicality and versatility in two ways. First, by harnessing its depth of field of more than 100 microns, we significantly reduce the number of captures required for 3D imaging of plant roots and bacteria in the rhizoplane, thereby minimizing potential photobleaching and phototoxicity. Second, by leveraging CFAST's phase sensitivity and fluorescence specificity, we track early bacterial aggregate development, bacterial competition, and gene expression under varying environmental conditions. Specifically, we resolve bacterial growth dynamics of mixed populations at the early stages of colonization without the need for genetically labeling environmental isolates. Moreover, we find that the expression of genes of interest to rhizosphere chemistry (e.g. representative genes involved in phosphorus-sensing and antibiotic production) varies spatiotemporally within microbial populations that are surface-attached and appears distinct from their expression in planktonic cultures. Together, CFAST's attributes overcome commercial imaging platform limitations and enable new insights to be gained into microbial behavioral dynamics in experimental systems of relevance to the rhizosphere.

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Section: Resultsmentioning

confidence: 99%

Investigating 3D microbial community dynamics in the rhizosphere using complex-field and fluorescence microscopy

Zhang,

Alcalde,

Zhou

et al. 2024

Preprint

Self Cite

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“…We first measured the slide using holotomography to obtain RI images. It is important to note that the resulting 3D RI images were all-in-focused to ensure that the cellular details from slightly different axial positions could be integrated into a single focal plane 28 (See Methods). Subsequently, the same slide was imaged using a whole slide scanner (WSS) to obtain the H&E-stained BF images.…”

Section: Resultsmentioning

confidence: 99%

“…We applied an all-in-focus algorithm only to the RI images obtained from a slide used for network training 27 . This algorithm ensures that the single focal plane includes most of the cellular structures.…”

Section: All-in-focusmentioning

confidence: 99%

Revealing 3D cancer tissue structures using holotomography and virtual hematoxylin and eosin staining via deep learning

park,

Shin,

Kim

et al. 2023

Preprint

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In standard histopathology, hematoxylin and eosin (H&E) staining stands as a pivotal tool for cancer tissue analysis. However, this method is limited to two-dimensional (2D) analysis or requires labor-intensive preparation for three-dimensional (3D) inspection of cancer tissues. In this study, we present a method for 3D virtual H&E staining of label-free colon cancer tissues, employing holotomography and deep learning. Holotomography is used to measure the 3D refractive index (RI) distribution of the label-free colon cancer slides. A deep learning-based image-to-image translation framework is integrated into the resulting 3D RI distribution, enabling virtual H&E staining in 3D. Our method has been applied to colon cancer tissue slides with thicknesses up to 20 µm, with conventional chemical H&E staining providing a direct validation for the method. This framework not only bypasses the conventional staining process but also provides 3D structures of glands, lumens, and individual nuclei. The results demonstrate enhancement in histopathological efficiency and the extension of the standard histopathology into the 3D realm.

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“…While both scanning microscopy and FP unlock the ability to obtain an extended DoF through time-sequential image capture, no moving parts are necessary in FP. The ability to maintain high-axial resolution within thick samples makes FP ideal for applications such as cytology, where cells tend to aggregate in large clusters, necessitating a wide DoF [4].…”

Section: Accurate Measurement Of Thick Specimensmentioning

confidence: 99%

Applications and Extensions of Fourier Ptychography

et al. 2022

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Abstract:This is the third article within a three-part series on Fourier ptychography, which is a computational microscopy technique for high-resolution, large field-of-view imaging. While the previous articles introduced the working principles of the technique, in this article we focus on the practical benefits that it brings to the imaging community. We present a didactic overview of the most important and well-established practical use-cases such as gigapixel imaging, quantitative phase contrast, thick sample imaging, and aberration metrology. We also discuss how Fourier ptychography can leave the visible light domain and venture into the realm of smaller wavelengths such as X-rays and electrons, among other topics.

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All-in-focus fine needle aspiration biopsy imaging based on Fourier ptychographic microscopy

Cited by 14 publications

References 20 publications

Investigating 3D microbial community dynamics in the rhizosphere using complex-field and fluorescence microscopy

Investigating 3D microbial community dynamics in the rhizosphere using complex-field and fluorescence microscopy

Revealing 3D cancer tissue structures using holotomography and virtual hematoxylin and eosin staining via deep learning

Applications and Extensions of Fourier Ptychography

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