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Modern single-cell flow and mass cytometry technologies measure the expression of several proteins of the individual cells within a blood or tissue sample. Each profiled biological sample is thus represented by a set of hundreds of…

Machine Learning · Computer Science 2022-06-29 Siyuan Shan , Vishal Baskaran , Haidong Yi , Jolene Ranek , Natalie Stanley , Junier Oliva

Single-cell technologies have revolutionized biomedical research by enabling scalable measurement of the genome, transcriptome, and proteome of multiple systems at single-cell resolution. Now widely applied to cancer models, these assays…

Genomics · Quantitative Biology 2020-05-05 Allen W Zhang , Kieran R Campbell

Nuclear magnetic resonance spectroscopy with solid-state spin sensors is a promising pathway for the detection of nuclear spins at the micro- and nanoscale. Although many nanoscale experiments rely on a single sensor spin for the detection…

The detection of single molecules has facilitated many advances in life- and material-sciences. Commonly, it founds on the fluorescence detection of single molecules, which are for example attached to the structures under study. For…

Single-cell technologies offer insights into molecular feature distributions, but comparing them poses challenges. We propose a kernel-testing framework for non-linear cell-wise distribution comparison, analyzing gene expression and…

Segmentation and classification of cell nuclei in histopathology images using deep neural networks (DNNs) can save pathologists' time for diagnosing various diseases, including cancers, by automating cell counting and morphometric…

Computer Vision and Pattern Recognition · Computer Science 2023-10-06 Amruta Parulekar , Utkarsh Kanwat , Ravi Kant Gupta , Medha Chippa , Thomas Jacob , Tripti Bameta , Swapnil Rane , Amit Sethi

Nitrogen-vacancy (NV) centers in diamond have emerged as quantum sensors capable of detecting nuclear magnetic resonance (NMR) signals at unprecedented length scales, ranging from picoliter sample volumes down to single spins at the diamond…

Chemical Physics · Physics 2025-01-07 Nick R. von Grafenstein , Karl D. Briegel , Jorge Casanova , Dominik B. Bucher

Cell imaging and analysis are fundamental to biomedical research because cells are the basic functional units of life. Among different cell-related analysis, cell counting and detection are widely used. In this paper, we focus on one common…

Computer Vision and Pattern Recognition · Computer Science 2019-04-19 Haoyi Liang , Aijaz Naik , Cedric L. Williams , Jaideep Kapur , Daniel S. Weller

Conventional nuclear magnetic resonance (NMR) spectroscopy relies on acquiring signal from a macroscopic ensemble of molecules to gain information about molecular structure and dynamics. Transferring this technique to nanoscale sample sizes…

Mesoscale and Nanoscale Physics · Physics 2019-02-06 Jeffrey Holzgrafe , Qiushi Gu , Jan Beitner , Dhiren Kara , Helena S. Knowles , Mete Atatüre

Nuclear magnetic resonance (NMR) at the single-molecule level with atomic resolution holds transformative potential for structural biology and surface chemistry. Near-surface solid-state spin sensors with optical readout ability offer a…

Quantum Physics · Physics 2025-12-12 Yu Chen , Qi Zhang , Yuanhong Teng , Chihang Luo , Zhijie Li , Jinpeng Liu , Ya Wang , Fazhan Shi , Jiangfeng Du

In recent years, the field of single-cell data analysis has seen a marked advancement in the development of clustering methods. Despite advancements, most of these algorithms still concentrate on analyzing the provided single-cell matrix…

Machine Learning · Computer Science 2023-12-18 Dayu Hu , Ke Liang , Hao Yu , Xinwang Liu

In this study, we propose a robust methodology for identification of myeloid blasts followed by prediction of genetic mutation in single-cell images of blasts, tackling challenges associated with label accuracy and data noise. We trained an…

Image and Video Processing · Electrical Eng. & Systems 2025-06-17 Garima Jain , Ravi Kant Gupta , Priyansh Jain , Abhijeet Patil , Ardhendu Sekhar , Gajendra Smeeta , Sanghamitra Pati , Amit Sethi

Nuclear magnetic resonance (NMR), conventionally detected in multi-tesla magnetic fields, is a powerful analytical tool for the determination of molecular identity, structure, and function. With the advent of prepolarization methods and…

One of the major challenges arising from single-cell transcriptomics experiments is the question of how to annotate the associated single-cell transcriptomic profiles. Because of the large size and the high dimensionality of the data,…

Genomics · Quantitative Biology 2024-09-11 Malek Senoussi , Thierry Artières , Paul Villoutreix

Extracellular vesicles (EVs) have drawn rapidly increasing attention as the next-generation diagnostic biomarkers and therapeutic agents. However, the heterogeneous nature of EVs necessitates advanced methods for profiling EVs at the…

Biomolecules · Quantitative Biology 2025-07-08 Yiting Liu , Anthony James El-helou , Bill Soderstrom , Juanfang Ruan , Ying Zhu

This study addresses the critical need for high signal-to-noise ratio in optical detection methods for biological sample discrimination under low-photon-flux conditions to ensure accuracy without compromising sample integrity. We explore…

Optics · Physics 2024-01-22 L. Zhang , V. R. Besaga , P. Rühl , C. Zou , S. H. Heinemann , Y. Wang , F. Setzpfandt

Nitrogen-vacancy (NV) centers show great potentials for nanoscale bio-sensing and bio-imaging. Nevertheless, their envisioned bio-applications suffer from intrinsic background noise due to unavoidable light scattering and autofluorescence…

Optics · Physics 2024-08-05 Yayin Tan , Xiaolu Wang , Feng Xu , Xinhao Hu , Yuan Lin , Bo Gao , Zhiqin Chu

We report on a nanoscale quantum-sensing protocol which tracks a free precession of a single nuclear spin and is capable of estimating an azimuthal angle---a parameter which standard multipulse protocols cannot determine---of the target…

Quantum Physics · Physics 2018-09-17 Kento Sasaki , Kohei M. Itoh , Eisuke Abe

We show that single walled carbon nanotubes with different isotope compositions exhibit distinct Raman Gband peaks and can be used for multiplexed multi-color Raman imaging of biological systems. Cancer cells with specific receptors are…

Materials Science · Physics 2008-09-16 Zhuang Liu , Xiaolin Li , Scott M. Tabakman , Kaili Jiang , Shoushan Fan , Hongjie Dai

Detecting individual spins--including stable and metastable states--represents a fundamental challenge in quantum sensing with broad applications across condensed matter physics, quantum chemistry, and single-molecule magnetic resonance…