Challenges in long-term imaging and quantification of single-cell dynamics

LEVER: software tools for segmentation, tracking and lineaging of proliferating cells

(2016) Mark Winter et al.   BIOINFORMATICS

Identification of factors promoting ex vivo maintenance of mouse hematopoietic stem cells by long-term single-cell quantification

(2016) K. D. Kokkaliaris et al.   BLOOD

Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos

(2016) Johannes Stegmaier et al.   DEVELOPMENTAL CELL

Dissecting mechanisms of mouse embryonic stem cells heterogeneity through a model-based analysis of transcription factor dynamics

(2016) Maria Herberg et al.   Journal of the Royal Society Interface

The struggle with image glut

(2016) Jeffrey M. Perkel   NATURE

Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios

(2016) Philipp S. Hoppe et al.   NATURE

Resolving early mesoderm diversification through single-cell expression profiling

(2016) Antonio Scialdone et al.   NATURE

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Software tools for single-cell tracking and quantification of cellular and molecular properties

(2016) Oliver Hilsenbeck et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Quantitative assessment of fluorescent proteins

(2016) Paula J Cranfill et al.   NATURE METHODS

Schedule-dependent interaction between anticancer treatments

(2016) Sheng-hong Chen et al.   SCIENCE

Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy

(2015) Michael K. Strasser et al.   BMC Systems Biology

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

The Regulatory Landscape of Lineage Differentiation in a Metazoan Embryo

(2015) Zhuo Du et al.   DEVELOPMENTAL CELL

Index sorting resolves heterogeneous murine hematopoietic stem cell populations

(2015) Reiner Schulte et al.   EXPERIMENTAL HEMATOLOGY

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Unsupervised lineage-based characterization of primate precursors reveals high proliferative and morphological diversity in the OSVZ

(2015) Michael Pfeiffer et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Network plasticity of pluripotency transcription factors in embryonic stem cells

(2015) Adam Filipczyk et al.   NATURE CELL BIOLOGY

Human keratinocytes have two interconvertible modes of proliferation

(2015) Amit Roshan et al.   NATURE CELL BIOLOGY

Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments

(2015) Ning Leng et al.   NATURE METHODS

Whole-animal functional and developmental imaging with isotropic spatial resolution

(2015) Raghav K Chhetri et al.   NATURE METHODS

Efficient processing and analysis of large-scale light-sheet microscopy data

(2015) Fernando Amat et al.   Nature Protocols

Intravital imaging of hair follicle regeneration in the mouse

(2015) Cristiana M Pineda et al.   Nature Protocols

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method

(2015) Jia-Ren Lin et al.   Nature Communications

In vivo time-lapse imaging shows diverse niche engagement by quiescent and naturally activated hematopoietic stem cells

(2014) N. M. Rashidi et al.   BLOOD

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

De Novo Inference of Systems-Level Mechanistic Models of Development from Live-Imaging-Based Phenotype Analysis

(2014) Zhuo Du et al.   CELL

Quantitative Single-Cell Approaches to Stem Cell Research

(2014) Martin Etzrodt et al.   Cell Stem Cell

Transcription factor heterogeneity in pluripotent stem cells: a stochastic advantage

(2014) M.-E. Torres-Padilla et al.   DEVELOPMENT

Quantitative imaging of cell dynamics in mouse embryos using light-sheet microscopy

(2014) R. S. Udan et al.   DEVELOPMENT

Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

(2014) Zakary S. Singer et al.   MOLECULAR CELL

The present and future role of microfluidics in biomedical research

(2014) Eric K. Sackmann et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Advances in fluorescence labeling strategies for dynamic cellular imaging

(2014) Kevin M Dean et al.   Nature Chemical Biology

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data

(2014) Fernando Amat et al.   NATURE METHODS

High-throughput microfluidic single-cell analysis pipeline for studies of signaling dynamics

(2014) Ryan A Kellogg et al.   Nature Protocols

Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution

(2014) Bi-Chang Chen et al.   SCIENCE

BIOCAT: a pattern recognition platform for customizable biological image classification and annotation

(2013) Jie Zhou et al.   BMC BIOINFORMATICS

An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy

(2013) Felix Buggenthin et al.   BMC BIOINFORMATICS

Biallelic Expression of Nanog Protein in Mouse Embryonic Stem Cells

(2013) Adam Filipczyk et al.   Cell Stem Cell

Statistical study of asymmetry in cell lineage data

(2013) Benoîte de Saporta et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Probing cellular processes by long-term live imaging - historic problems and current solutions

(2013) D. L. Coutu et al.   JOURNAL OF CELL SCIENCE

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy

(2013) Yicong Wu et al.   NATURE BIOTECHNOLOGY

Molecular live cell bioimaging in stem cell research

(2012) Max Endele et al.   Annals of the New York Academy of Sciences

Chemokine Guidance of Central Memory T Cells Is Critical for Antiviral Recall Responses in Lymph Nodes

(2012) Jung Hwan Sung et al.   CELL

Cell Segmentation: 50 Years Down the Road [Life Sciences]

(2012) Erik Meijering   IEEE SIGNAL PROCESSING MAGAZINE

A call for bioimaging software usability

(2012) Anne E Carpenter et al.   NATURE METHODS

Biological imaging software tools

(2012) Kevin W Eliceiri et al.   NATURE METHODS

OMERO: flexible, model-driven data management for experimental biology

(2012) Chris Allan et al.   NATURE METHODS

Computerized video analysis of social interactions in mice

(2012) Fabrice de Chaumont et al.   NATURE METHODS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Migration of cells in a social context

(2012) S. Vedel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An integrative clustering and modeling algorithm for dynamical gene expression data

(2011) J. Sivriver et al.   BIOINFORMATICS

openBIS: a flexible framework for managing and analyzing complex data in biology research

(2011) Angela Bauch et al.   BMC BIOINFORMATICS

Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers

(2011) Matt Thomson et al.   CELL

Gene expression heterogeneities in embryonic stem cell populations: origin and function

(2011) Alfonso Martinez Arias et al.   CURRENT OPINION IN CELL BIOLOGY

The role of Pax6 in regulating the orientation and mode of cell division of progenitors in the mouse cerebral cortex

(2011) M. Asami et al.   DEVELOPMENT

On the symmetry of siblings: automated single-cell tracking to quantify the behavior of hematopoietic stem cells in a biomimetic setup

(2011) Nico Scherf et al.   EXPERIMENTAL HEMATOLOGY

Automatic segmentation of adherent biological cell boundaries and nuclei from brightfield microscopy images

(2011) Rehan Ali et al.   MACHINE VISION AND APPLICATIONS

In vivo imaging of Treg cells providing immune privilege to the haematopoietic stem-cell niche

(2011) Joji Fujisaki et al.   NATURE

Self-organizing optic-cup morphogenesis in three-dimensional culture

(2011) Mototsugu Eiraku et al.   NATURE

Long-term single-cell imaging of mammalian stem cells

(2011) Timm Schroeder   NATURE METHODS

Proteins on the move: insights gained from fluorescent protein technologies

(2011) Atsushi Miyawaki   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNAi-based screening identifies the Mms22L–Nfkbil2 complex as a novel regulator of DNA replication in human cells

(2010) Wojciech Piwko et al.   EMBO JOURNAL

Haematopoietic stem cells derive directly from aortic endothelium during development

(2010) Julien Y. Bertrand et al.   NATURE

V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets

(2010) Hanchuan Peng et al.   NATURE BIOTECHNOLOGY

Computational prediction of neural progenitor cell fates

(2010) Andrew R Cohen et al.   NATURE METHODS

CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging

(2010) Michael Held et al.   NATURE METHODS

Fast, high-contrast imaging of animal development with scanned light sheet–based structured-illumination microscopy

(2010) Philipp J Keller et al.   NATURE METHODS

Fluorescent Proteins and Their Applications in Imaging Living Cells and Tissues

(2010) Dmitriy M. Chudakov et al.   PHYSIOLOGICAL REVIEWS

Late Origin of Glia-Restricted Progenitors in the Developing Mouse Cerebral Cortex

(2009) Marcos R. Costa et al.   CEREBRAL CORTEX

Timing of Gene Expression Responses to Environmental Changes

(2009) Gal Chechik et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Continuous single-cell imaging of blood generation from haemogenic endothelium

(2009) Hanna M. Eilken et al.   NATURE

Population context determines cell-to-cell variability in endocytosis and virus infection

(2009) Berend Snijder et al.   NATURE

Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche

(2009) Toshiro Sato et al.   NATURE

Hematopoietic Cytokines Can Instruct Lineage Choice

(2009) M. A. Rieger et al.   SCIENCE

Potency and Fate Specification in CNS Stem Cell Populations In Vitro

(2008) Rea Ravin et al.   Cell Stem Cell

Imaging stem-cell-driven regeneration in mammals

(2008) Timm Schroeder   NATURE

Mechanism of shape determination in motile cells

(2008) Kinneret Keren et al.   NATURE

LED Arrays as Cost Effective and Efficient Light Sources for Widefield Microscopy

(2008) Dinu F. Albeanu et al.   PLoS One