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We present Defocusing Microscopy (DM), a bright-field optical microscopy technique able to perform total 3D imaging of transparent objects. By total 3D imaging we mean the determination of the actual shapes of the upper and lower surfaces…

Biological Physics · Physics 2015-06-19 P. M. S. Roma , L. Siman , F. T. Amaral , U. Agero , O. N. Mesquita

Imaging of biological cells and tissues often relies on fluorescent labels, which offer high contrast with molecular specificity. The use of exogenous labeling agents, however, may alter the normal physiology of the bio-specimens.…

Instrumentation and Detectors · Physics 2019-10-01 Zichao Bian , Shaowei Jiang , Pengming Song , He Zhang , Pouria Hoveida , Kazunori Hoshino , Guoan Zheng

Traditional fluorescence staining is phototoxic to live cells, slow, and expensive; thus, the subcellular structure prediction (SSP) from transmitted light (TL) images is emerging as a label-free, faster, low-cost alternative. However,…

Computer Vision and Pattern Recognition · Computer Science 2024-07-04 Jintu Zheng , Yi Ding , Qizhe Liu , Yi Cao , Ying Hu , Zenan Wang

Automated cell segmentation in microscopy images is essential for biomedical research, yet conventional methods are labor-intensive and prone to error. While deep learning-based approaches have proven effective, they often require large…

Computer Vision and Pattern Recognition · Computer Science 2024-11-20 Rüveyda Yilmaz , Kaan Keven , Yuli Wu , Johannes Stegmaier

There is a clear need for developments in characterisation techniques that provide detailed information about structure-function relationships in biology. Using electron microscopy to achieve high resolution while maintaining a broad field…

Quantitative Methods · Quantitative Biology 2023-09-12 Chen Huang , Judy S. Kim , Angus I. Kirkland

Cell nuclei segmentation is one of the most important tasks in the analysis of biomedical images. With ever-growing sizes and amounts of three-dimensional images to be processed, there is a need for better and faster segmentation methods.…

Computer Vision and Pattern Recognition · Computer Science 2017-02-20 Julian Arz , Peter Sanders , Johannes Stegmaier , Ralf Mikut

Fluorescence microscopy has been a significant tool to observe long-term imaging of embryos (in vivo) growth over time. However, cumulative exposure is phototoxic to such sensitive live samples. While techniques like light-sheet…

Image and Video Processing · Electrical Eng. & Systems 2022-01-05 Varun Mannam , Jacob Brandt , Cody J. Smith , Scott Howard

Breast cancer is the most prevalent cancer type in women, and while its survival rate is generally high the aesthetic outcome is an increasingly important factor when evaluating different treatment alternatives. 3D scanning and…

Computer Vision and Pattern Recognition · Computer Science 2017-06-21 Rene Lacher , Francisco Vasconcelos , David Bishop , Norman Williams , Mohammed Keshtgar , David Hawkes , John Hipwell , Danail Stoyanov

We present an in-depth investigation of a fully automated Fourier-based analysis to determine the cell size and the width of its distribution in 3D biological tissues. The results are thoroughly tested using generated images, and we offer…

Biological Physics · Physics 2022-04-26 Tess Homan , Sylvain Monnier , Cécile Jebane , Alice Nicolas , Hélène Delanoe-Ayari

Accounting for 26% of all new cancer cases worldwide, breast cancer remains the most common form of cancer in women. Although early breast cancer has a favourable long-term prognosis, roughly a third of patients suffer from a suboptimal…

Computer Vision and Pattern Recognition · Computer Science 2019-01-17 Rene Lacher , Francisco Vasconcelos , Norman Williams , Gerrit Rindermann , John Hipwell , David Hawkes , Danail Stoyanov

In tissue engineering, 3D scaffolds and chemical treatments are often used for providing a cell-friendly surface for improving cell adhesion and tissue growth. Indeed, the cell adhesion degree can be controlled by physical-chemical changes…

Highly multiplexed microscopy enables rich spatial characterization of tissues at single-cell resolution, yet most analyses rely on two-dimensional sections despite inherently three-dimensional tissue organization. Acquiring dense…

Computer Vision and Pattern Recognition · Computer Science 2026-04-10 Ido Harlev , Tamar Oukhanov , Raz Ben-Uri , Leeat Keren , Shai Bagon

3D printing has revolutionized numerous scientific fields and industries, with printing in biological systems emerging as a rapidly advancing area of research. However, its application to the subcellular level remains largely unexplored.…

Soft Condensed Matter · Physics 2025-06-17 Marusa Mur , Aljaz Kavcic , Uros Jagodic , Rok Podlipec , Matjaz Humar

Imaging dynamics of cellular morphogenesis with high spatial-temporal resolution in 3D is challenging, due to the low spatial resolution along the optical axis and photo-toxicity. However, some cellular structures are planar and hence 2D…

Quantitative Methods · Quantitative Biology 2020-07-14 Alka Bhat , Linjie Lu , Chen-Ho Wang , Simon Lo Vecchio , Riccardo Maraspini , Alf Honigmann , Daniel Riveline

A software for processing sets of full-color images of biological tissue histological sections is developed. We used histological sections obtained by the method of high-precision layer-by-layer grinding of frozen biological tissues. The…

The utilization of computational photography becomes increasingly essential in the medical field. Today, imaging techniques for dermatology range from two-dimensional (2D) color imagery with a mobile device to professional clinical imaging…

Image and Video Processing · Electrical Eng. & Systems 2021-09-06 Merlin A. Nau , Florian Schiffers , Yunhao Li , Bingjie Xu , Andreas Maier , Jack Tumblin , Marc Walton , Aggelos K. Katsaggelos , Florian Willomitzer , Oliver Cossairt

Photoemission orbital tomography provides direct access from laboratory measurements to the real-space molecular orbitals of well-ordered organic semiconductor layers. Specifically, the application of phase retrieval algorithms to…

Materials Science · Physics 2024-04-29 Thi Lan Dinh , G. S. Matthijs Jansen , D. Russell Luke , Wiebke Bennecke , Stefan Mathias

Accurate segmentation of 3-D cell nuclei in microscopy images is essential for the study of nuclear organization, gene expression, and cell morphodynamics. Current image segmentation methods are challenged by the complexity and variability…

Image and Video Processing · Electrical Eng. & Systems 2022-03-18 Sundaresh Ram , Jeffrey J. Rodriguez

We report on the 3-dimensional imaging of biological cells including living neurons by a recently developed fibered interferometric Scanning Optical Microscope. The topography and surface structure of mouse fibroblasts and hippocampal…

Three-dimensional (3D) imaging of the subcellular organisation and morphology of cells and tissues is essential for understanding biological function. Although staining is the most widely used approach for visualising biological samples…