Toward deep biophysical cytometry: prospects and challenges

PARC: ultrafast and accurate clustering of phenotypic data of millions of single cells

(2020) Shobana V Stassen et al.   BIOINFORMATICS

Label‐Free Leukemia Monitoring by Computer Vision

(2020) Minh Doan et al.   CYTOMETRY PART A

Single-cell adhesion force kinetics of cell populations from combined label-free optical biosensor and robotic fluidic force microscopy

(2020) Milan Sztilkovics et al.   Scientific Reports

High-Speed Single-Cell Dielectric Spectroscopy

(2020) Daniel Spencer et al.   ACS Sensors

Microfluidic deformability-activated sorting of single particles

(2020) Gihoon Choi et al.   Microsystems & Nanoengineering

A comparison of microfluidic methods for high-throughput cell deformability measurements

(2020) Marta Urbanska et al.   NATURE METHODS

Intelligent image-based deformation-assisted cell sorting with molecular specificity

(2020) Ahmad Ahsan Nawaz et al.   NATURE METHODS

Intelligent classification of platelet aggregates by agonist type

(2020) Yuqi Zhou et al.   eLife

Deep phase decoder: self-calibrating phase microscopy with an untrained deep neural network

(2020) Emrah Bostan et al.   Optica

Sequentially addressable dielectrophoretic array for high-throughput sorting of large-volume biological compartments

(2020) A. Isozaki et al.   Science Advances

Image-guided cell sorting using fast scanning lasers

(2020) Xinyu Chen et al.   APL Photonics

Mass measurements during lymphocytic leukemia cell polyploidization decouple cell cycle- and cell size-dependent growth

(2020) Luye Mu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Raman image-activated cell sorting

(2020) Nao Nitta et al.   Nature Communications

High-throughput single-cell rheology in complex samples by dynamic real-time deformability cytometry

(2019) Bob Fregin et al.   Nature Communications

Reagent-Free and Rapid Assessment of T Cell Activation State Using Diffraction Phase Microscopy and Deep Learning

(2019) Sukrut Hemant Karandikar et al.   ANALYTICAL CHEMISTRY

Quantitative Phase Imaging Flow Cytometry for Ultra‐Large‐Scale Single‐Cell Biophysical Phenotyping

(2019) Kelvin C.M. Lee et al.   CYTOMETRY PART A

Machine Learning Based Real‐Time Image‐Guided Cell Sorting and Classification

(2019) Yi Gu et al.   CYTOMETRY PART A

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Mammalian cell growth dynamics in mitosis

(2019) Teemu P Miettinen et al.   eLife

A practical review on the measurement tools for cellular adhesion force

(2019) Rita Ungai-Salánki et al.   ADVANCES IN COLLOID AND INTERFACE SCIENCE

Label-free chemical imaging flow cytometry by high-speed multicolor stimulated Raman scattering

(2019) Yuta Suzuki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Angularly resolved, finely sampled elastic scattering measurements of single cells: requirements for robust organelle size extractions

(2019) Ashley E. Cannaday et al.   JOURNAL OF BIOMEDICAL OPTICS

A Microfluidic Device Integrating Impedance Flow Cytometry and Electric Impedance Spectroscopy for High-Efficiency Single-Cell Electrical Property Measurement

(2019) Yongxiang Feng et al.   ANALYTICAL CHEMISTRY

Image-based morphological profiling identifies a lysosomotropic, iron-sequestering autophagy inhibitor

(2019) Herbert Waldmann et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Classification of Human White Blood Cells Using Machine Learning for Stain‐Free Imaging Flow Cytometry

(2019) Maxim Lippeveld et al.   CYTOMETRY PART A

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

(2019) Andrea Cossarizza et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Profiling Cell–Matrix Adhesion Using Digitalized Acoustic Streaming

(2019) Hongwei Cai et al.   ANALYTICAL CHEMISTRY

Cell Adhesiveness Serves as a Biophysical Marker for Metastatic Potential

(2019) Pranjali Beri et al.   CANCER RESEARCH

Studying Stem Cell Organization using “Label-Free” Methods and a Novel Generative Adversarial Model

(2018) Gregory Johnson et al.   BIOPHYSICAL JOURNAL

Development of microfluidic impedance cytometry enabling the quantification of specific membrane capacitance and cytoplasm conductivity from 100,000 single cells

(2018) Yang Zhao et al.   BIOSENSORS & BIOELECTRONICS

Seeing More: A Future of Augmented Microscopy

(2018) Devin P. Sullivan et al.   CELL

In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images

(2018) Eric M. Christiansen et al.   CELL

Opportunities and obstacles for deep learning in biology and medicine

(2018) Travers Ching et al.   Journal of the Royal Society Interface

Real-time fluorescence and deformability cytometry

(2018) Philipp Rosendahl et al.   NATURE METHODS

A comparison of methods to assess cell mechanical properties

(2018) Pei-Hsun Wu et al.   NATURE METHODS

High-throughput imaging flow cytometry by optofluidic time-stretch microscopy

(2018) Cheng Lei et al.   Nature Protocols

Detection of human disease conditions by single-cell morpho-rheological phenotyping of blood

(2018) Nicole Toepfner et al.   eLife

Intelligent Image-Activated Cell Sorting

(2018) Nao Nitta et al.   CELL

Simultaneous cell traction and growth measurements using light

(2018) Shamira Sridharan et al.   Journal of Biophotonics

Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy

(2018) Chawin Ounkomol et al.   NATURE METHODS

Quantitative phase imaging in biomedicine

(2018) YongKeun Park et al.   Nature Photonics

Standardized microgel beads as elastic cell mechanical probes

(2018) S. Girardo et al.   Journal of Materials Chemistry B

Live-cell phenotypic-biomarker microfluidic assay for the risk stratification of cancer patients via machine learning

(2018) Michael S. Manak et al.   Nature Biomedical Engineering

Computational modeling of cellular structures using conditional deep generative networks

(2018) Hao Yuan et al.   BIOINFORMATICS

Deep Learning in Image Cytometry: A Review

(2018) Anindya Gupta et al.   CYTOMETRY PART A

Label-Free High-Throughput Leukemia Detection by Holographic Microscopy

(2018) Matthias Ugele et al.   Advanced Science

Large-Scale Multi-Class Image-Based Cell Classification With Deep Learning

(2018) Nan Meng et al.   IEEE Journal of Biomedical and Health Informatics

Tomographic phase microscopy: principles and applications in bioimaging [Invited]

(2017) Di Jin et al.   JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS

The Human Cell Atlas: from vision to reality

(2017) Orit Rozenblatt-Rosen et al.   NATURE

Quantifying forces in cell biology

(2017) Pere Roca-Cusachs et al.   NATURE CELL BIOLOGY

Data-analysis strategies for image-based cell profiling

(2017) Juan C Caicedo et al.   NATURE METHODS

Image Data Resource: a bioimage data integration and publication platform

(2017) Eleanor Williams et al.   NATURE METHODS

Reconstructing cell cycle and disease progression using deep learning

(2017) Philipp Eulenberg et al.   Nature Communications

Genome-scale single-cell mechanical phenotyping reveals disease-related genes involved in mitotic rounding

(2017) Yusuke Toyoda et al.   Nature Communications

Multi-MHz laser-scanning single-cell fluorescence microscopy by spatiotemporally encoded virtual source array

(2017) Jianglai Wu et al.   Biomedical Optics Express

High accuracy label-free classification of single-cell kinetic states from holographic cytometry of human melanoma cells

(2017) Miroslav Hejna et al.   Scientific Reports

High-Throughput Multi-parametric Imaging Flow Cytometry

(2017) Anandkumar S. Rane et al.   Chem

Biophysical and biomolecular determination of cellular age in humans

(2017) Jude M. Phillip et al.   Nature Biomedical Engineering

Label-free detection of cellular drug responses by high-throughput bright-field imaging and machine learning

(2017) Hirofumi Kobayashi et al.   Scientific Reports

A review of impedance measurements of whole cells

(2016) Youchun Xu et al.   BIOSENSORS & BIOELECTRONICS

Optofluidic time-stretch imaging – an emerging tool for high-throughput imaging flow cytometry

(2016) Andy K. S. Lau et al.   LAB ON A CHIP

Cell refractive index for cell biology and disease diagnosis: past, present and future

(2016) P. Y. Liu et al.   LAB ON A CHIP

Drug sensitivity of single cancer cells is predicted by changes in mass accumulation rate

(2016) Mark M Stevens et al.   NATURE BIOTECHNOLOGY

High-throughput measurement of single-cell growth rates using serial microfluidic mass sensor arrays

(2016) Nathan Cermak et al.   NATURE BIOTECHNOLOGY

Confocal reference free traction force microscopy

(2016) Martin Bergert et al.   Nature Communications

Ultrafast laser-scanning time-stretch imaging at visible wavelengths

(2016) Jiang-Lai Wu et al.   Light-Science & Applications

Optical time-stretch imaging: Principles and applications

(2016) Cheng Lei et al.   Applied Physics Reviews

Deep Learning in Label-free Cell Classification

(2016) Claire Lifan Chen et al.   Scientific Reports

Multiparameter mechanical and morphometric screening of cells

(2016) Mahdokht Masaeli et al.   Scientific Reports

Three-dimensional label-free imaging and quantification of lipid droplets in live hepatocytes

(2016) Kyoohyun Kim et al.   Scientific Reports

High-Throughput Assessment of Cellular Mechanical Properties

(2015) Eric M. Darling et al.   Annual Review of Biomedical Engineering

Traction force microscopy on soft elastic substrates: A guide to recent computational advances

(2015) Ulrich S. Schwarz et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Microconstriction Arrays for High-Throughput Quantitative Measurements of Cell Mechanical Properties

(2015) Janina R. Lange et al.   BIOPHYSICAL JOURNAL

High-throughput screening for modulators of cellular contractile force

(2015) Chan Young Park et al.   Integrative Biology

Deep learning

(2015) Yann LeCun et al.   NATURE

Real-time deformability cytometry: on-the-fly cell mechanical phenotyping

(2015) Oliver Otto et al.   NATURE METHODS

Label-free identification of individual bacteria using Fourier transform light scattering

(2015) YoungJu Jo et al.   OPTICS EXPRESS

Significant correlation between refractive index and activity of mitochondria: single mitochondrion study

(2015) Keisuke Haseda et al.   Biomedical Optics Express

Evolution of cellular morpho-phenotypes in cancer metastasis

(2015) Pei-Hsun Wu et al.   Scientific Reports

Live-cell mass profiling: an emerging approach in quantitative biophysics

(2014) Thomas A Zangle et al.   NATURE METHODS

Quantitative Diagnosis of Malignant Pleural Effusions by Single-Cell Mechanophenotyping

(2013) H. T. K. Tse et al.   Science Translational Medicine

Hydrodynamic stretching of single cells for large population mechanical phenotyping

(2012) D. R. Gossett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput single-microparticle imaging flow analyzer

(2012) K. Goda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linear and Nonlinear Rheology of Living Cells

(2011) Philip Kollmannsberger et al.   Annual Review of Materials Research

Cell adhesion: integrating cytoskeletal dynamics and cellular tension

(2010) J. Thomas Parsons et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY