Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

Microscopy Image Browser: A Platform for Segmentation and Analysis of Multidimensional Datasets

(2016) Ilya Belevich et al.   PLOS BIOLOGY

Survey statistics of automated segmentations applied to optical imaging of mammalian cells

(2015) Peter Bajcsy et al.   BMC BIOINFORMATICS

Cell-Size Control and Homeostasis in Bacteria

(2015) Sattar Taheri-Araghi et al.   CURRENT BIOLOGY

Empirical gradient threshold technique for automated segmentation across image modalities and cell lines

(2015) J. CHALFOUN et al.   JOURNAL OF MICROSCOPY

A noisy linear map underlies oscillations in cell size and gene expression in bacteria

(2015) Yu Tanouchi et al.   NATURE

Metabolic co-dependence gives rise to collective oscillations within biofilms

(2015) Jintao Liu et al.   NATURE

Deep learning

(2015) Yann LeCun et al.   NATURE

High-Sensitivity Measurements of Multiple Kinase Activities in Live Single Cells

(2014) Sergi Regot et al.   CELL

A Constant Size Extension Drives Bacterial Cell Size Homeostasis

(2014) Manuel Campos et al.   CELL

Hierarchical Mergence Approach to Cell Detection in Phase Contrast Microscopy Images

(2014) Lei Chen et al.   Computational and Mathematical Methods in Medicine

Stochasticity of metabolism and growth at the single-cell level

(2014) Daniel J. Kiviet et al.   NATURE

Nanoparticle vesicle encoding for imaging and tracking cell populations

(2014) Paul Rees et al.   NATURE METHODS

Scaling of Gene Expression with Transcription-Factor Fugacity

(2014) Franz M. Weinert et al.   PHYSICAL REVIEW LETTERS

Accurate information transmission through dynamic biochemical signaling networks

(2014) J. Selimkhanov et al.   SCIENCE

Internalization of Salmonella by Macrophages Induces Formation of Nonreplicating Persisters

(2014) S. Helaine et al.   SCIENCE

scikit-image: image processing in Python

(2014) Stéfan van der Walt et al.   PeerJ

Automatic Cell Detection in Bright-Field Microscope Images Using SIFT, Random Forests, and Hierarchical Clustering

(2013) Firas Mualla et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

A Morphological Approach to Curvature-Based Evolution of Curves and Surfaces

(2013) Pablo Marquez-Neila et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Single-Cell Dynamics Reveals Sustained Growth during Diauxic Shifts

(2013) Sarah Boulineau et al.   PLoS One

Microfabricated Polyacrylamide Devices for the Controlled Culture of Growing Cells and Developing Organisms

(2013) Philippe Nghe et al.   PLoS One

Segmenting time-lapse phase contrast images of adjacent NIH 3T3 cells

(2012) J. CHALFOUN et al.   JOURNAL OF MICROSCOPY

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

High-throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatio-temporal dynamics

(2011) Oleksii Sliusarenko et al.   MOLECULAR MICROBIOLOGY

Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy

(2011) Jonathan W Young et al.   Nature Protocols

Information Transduction Capacity of Noisy Biochemical Signaling Networks

(2011) R. Cheong et al.   SCIENCE

Robust Growth of Escherichia coli

(2010) Ping Wang et al.   CURRENT BIOLOGY

High-throughput, single-cell NF-κB dynamics

(2010) Timothy K Lee et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Single-cell NF-κB dynamics reveal digital activation and analogue information processing

(2010) Savaş Tay et al.   NATURE

Machine vision-assisted analysis of structure-localization relationships in a combinatorial library of prospective bioimaging probes

(2009) Kerby Shedden et al.   CYTOMETRY PART A

A high-throughput system for segmenting nuclei using multiscale techniques

(2008) Prabhakar R. Gudla et al.   CYTOMETRY PART A

Robust single-particle tracking in live-cell time-lapse sequences

(2008) Khuloud Jaqaman et al.   NATURE METHODS