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Volume electron microscopy is the method of choice for the in-situ interrogation of cellular ultrastructure at the nanometer scale. Recent technical advances have led to a rapid increase in large raw image datasets that require…
Accurate instance-level segmentation of organelles in electron microscopy (EM) is critical for quantitative analysis of subcellular morphology and inter-organelle interactions. However, current benchmarks, based on small, curated datasets,…
Modeling the 3D structures of cells and tissues is crucial in biology. Sequential cross-sectional images from electron microscopy provide high-resolution intracellular structure information. The segmentation of complex cell structures…
The analysis of dynamic organelles remains a formidable challenge, though key to understanding biological processes. We introduce Nellie, an automated and unbiased user-friendly pipeline for segmentation, tracking, and feature extraction of…
Automated and semi-automated techniques in biomedical electron microscopy (EM) enable the acquisition of large datasets at a high rate. Segmentation methods are therefore essential to analyze and interpret these large volumes of data, which…
The living body is composed of innumerable fine and complex structures and although these structures have been studied in the past, a vast amount of information pertaining to them still remains unknown. When attempting to observe these…
Metabolism unfolds within specific organelles in eukaryotic cells. Lysosomes are highly metabolically active organelles, and their metabolic states dynamically influence signal transduction, cellular homeostasis, and organismal…
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…
The task of labeling multiple organs for segmentation is a complex and time-consuming process, resulting in a scarcity of comprehensively labeled multi-organ datasets while the emergence of numerous partially labeled datasets. Current…
The measurement of three-dimensional (3D) images and the analysis of subcellular organelles are crucial for the study of the pathophysiology of cells and tissues. Optical diffraction tomography (ODT) facilitates label-free and quantitative…
Organoids are self-organized 3D cell clusters that closely mimic the architecture and function of in vivo tissues and organs. Quantification of organoid morphology helps in studying organ development, drug discovery, and toxicity…
With the growth of artificial intelligence (AI), there has been an increase in the adoption of computer vision and deep learning (DL) techniques for the evaluation of microscopy images and movies. This adoption has not only addressed…
In computer-assisted surgery, automatically recognizing anatomical organs is crucial for understanding the surgical scene and providing intraoperative assistance. While machine learning models can identify such structures, their deployment…
Multi-organ segmentation, which identifies and separates different organs in medical images, is a fundamental task in medical image analysis. Recently, the immense success of deep learning motivated its wide adoption in multi-organ…
Histopathology, the microscopic study of diseased tissue, is increasingly digitized, enabling improved visualization and streamlined workflows. An important task in histopathology is the segmentation of cells and glands, essential for…
Deep learning segmentation and fluorescence imaging techniques allow the cellular morphology of living embryos to be constructed spatiotemporally. These development processes involve numerous molecules distributed at the subcellular scale,…
Deep learning has revolutionized medical and biological imaging, particularly in segmentation tasks. However, segmenting biological cells remains challenging due to the high variability and complexity of cell shapes. Addressing this…
Modern spatial microscopy has provided developmental biology with powerful research tools. However, the recent significant technological breakthroughs have inevitably led to technical "bottlenecks" for the application of the new procedures…
Image segmentation plays an essential role in medicine for both diagnostic and interventional tasks. Segmentation approaches are either manual, semi-automated or fully-automated. Manual segmentation offers full control over the quality of…
Microelectronic morphogenesis is the creation and maintenance of complex functional structures by microelectronic information within shape-changing materials. Only recently has in-built information technology begun to be used to reshape…