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Recent advancements in the ability to construct three-dimensional (3D) tissues and organoids from stem cells and biomaterials have not only opened abundant new research avenues in disease modeling and regenerative medicine but also have…
Understanding how growth induces form is a longstanding biological question. Many studies concentrated on the shapes of plant cells, fungi or bacteria. Some others have shown the importance of the mechanical properties of bacterial walls…
Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in…
Brillouin microscopy is an emerging optical elastography technique that can be used to assess mechanical properties of biological samples in a 3D, all-optical and hence non-contact fashion. However, the low cross-section of spontaneous…
For over two decades, Flux Balance Analysis (FBA) has been successfully used for predicting growth rates and intracellular reaction rates in microbiological metabolism. An aspect that is often omitted from this analysis, is segregation or…
The computational imaging technique of Fourier Ptychographic Microscopy (FPM) enables high-resolution imaging with a wide field of view and can serve as an extremely valuable tool, e.g. in the classification of cells in medical…
Fluorescence microscopy is an essential tool for the analysis of 3D subcellular structures in tissue. An important step in the characterization of tissue involves nuclei segmentation. In this paper, a two-stage method for segmentation of…
We present feature finding and tracking algorithms in 3D in living cells, and demonstrate their utility to measure metrics important in cell biological processes. We developed a computational imaging hybrid approach that combines automated…
Transfer learning has gained attention in medical image analysis due to limited annotated 3D medical datasets for training data-driven deep learning models in the real world. Existing 3D-based methods have transferred the pre-trained models…
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.…
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…
In this article, we propose a general framework to study the dynamics and topology of cellular networks that capture the geometry of cell packings in two-dimensional tissues. Such epithelia undergo large-scale deformation during…
While three-dimensional imaging is essential for clinical diagnosis, its high cost and long wait times have motivated the use of image-to-3D foundation models to infer volume from two-dimensional modalities. However, because these models…
Data-driven cell tracking and segmentation methods in biomedical imaging require diverse and information-rich training data. In cases where the number of training samples is limited, synthetic computer-generated data sets can be used to…
Transformers have demonstrated remarkable performance in natural language processing and computer vision. However, existing vision Transformers struggle to learn from limited medical data and are unable to generalize on diverse medical…
Spatial transcriptomics methods capture cellular measurements such as gene expression and cell types at specific locations in a cell, helping provide a localized picture of tissue health. Traditional visualization techniques superimpose the…
This article presents a method to perform diffraction tomography in a standard microscope that includes an LED array for illumination. After acquiring a sequence of intensity-only images of a thick sample, a ptychography-based…
Comprehensive assessment of the various aspects of the brain's microstructure requires the use of complementary imaging techniques. This includes measuring the spatial distribution of cell bodies (cytoarchitecture) and nerve fibers…
Real-time 3D fluorescence microscopy is crucial for the spatiotemporal analysis of live organisms, such as neural activity monitoring. The eXtended field-of-view light field microscope (XLFM), also known as Fourier light field microscope,…
Background Analyzing images to accurately estimate the number of different cell types in the brain using automatic methods is a major objective in neuroscience. The automatic and selective detection and segmentation of neurons would be an…