Towards comprehensive cell lineage reconstructions in complex organisms using light-sheet microscopy

Noninvasive Imaging beyond the Diffraction Limit of 3D Dynamics in Thickly Fluorescent Specimens

(2012) Liang Gao et al.   CELL

Quantitative semi-automated analysis of morphogenesis with single-cell resolution in complex embryos

(2012) C. A. Giurumescu et al.   DEVELOPMENT

Current challenges in open-source bioimage informatics

(2012) Albert Cardona et al.   NATURE METHODS

Icy: an open bioimage informatics platform for extended reproducible research

(2012) Fabrice de Chaumont et al.   NATURE METHODS

Biological imaging software tools

(2012) Kevin W Eliceiri et al.   NATURE METHODS

Multiview light-sheet microscope for rapid in toto imaging

(2012) Uros Krzic et al.   NATURE METHODS

Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy

(2012) Raju Tomer et al.   NATURE METHODS

Shedding light on the system: studying embryonic development with light sheet microscopy

(2011) Raju Tomer et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Light sheet microscopy of living or cleared specimens

(2011) Philipp J Keller et al.   CURRENT OPINION IN NEUROBIOLOGY

A Semi-Markov Model for Mitosis Segmentation in Time-Lapse Phase Contrast Microscopy Image Sequences of Stem Cell Populations

(2011) An-An Liu et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Network anatomy and in vivo physiology of visual cortical neurons

(2011) Davi D. Bock et al.   NATURE

Deep and fast live imaging with two-photon scanned light-sheet microscopy

(2011) Thai V Truong et al.   NATURE METHODS

Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination

(2011) Thomas A Planchon et al.   NATURE METHODS

Vertebrate neural stem cell segmentation, tracking and lineaging with validation and editing

(2011) Mark Winter et al.   Nature Protocols

Reconstructing embryonic development

(2010) Khaled Khairy et al.   GENESIS

4D retrospective lineage tracing using SPIM for zebrafish organogenesis studies

(2010) Jim Swoger et al.   Journal of Biophotonics

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

(2010) Hanchuan Peng et al.   NATURE BIOTECHNOLOGY

Software for bead-based registration of selective plane illumination microscopy data

(2010) Stephan Preibisch 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

Proof-editing is the Bottleneck Of 3D Neuron Reconstruction: The Problem and Solutions

(2010) Hanchuan Peng et al.   NEUROINFORMATICS

A simple scanless two-photon fluorescence microscope using selective plane illumination

(2010) Jonathan Palero et al.   OPTICS EXPRESS

Cell Lineage Reconstruction of Early Zebrafish Embryos Using Label-Free Nonlinear Microscopy

(2010) N. Olivier et al.   SCIENCE

CATMAID: collaborative annotation toolkit for massive amounts of image data

(2009) S. Saalfeld et al.   BIOINFORMATICS

A 3D digital atlas of C. elegans and its application to single-cell analyses

(2009) Fuhui Long et al.   NATURE METHODS

Multiple object tracking in molecular bioimaging by Rao-Blackwellized marginal particle filtering

(2008) I. Smal et al.   MEDICAL IMAGE ANALYSIS

Cell population tracking and lineage construction with spatiotemporal context

(2008) Kang Li et al.   MEDICAL IMAGE ANALYSIS

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

(2008) Khuloud Jaqaman et al.   NATURE METHODS

Dynamic Analyses of Drosophila Gastrulation Provide Insights into Collective Cell Migration

(2008) A. McMahon et al.   SCIENCE

Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy

(2008) P. J. Keller et al.   SCIENCE