A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture

TiQuant: software for tissue analysis, quantification and surface reconstruction: Fig. 1.

(2015) Adrian Friebel et al.   BIOINFORMATICS

Hybrid Periportal Hepatocytes Regenerate the Injured Liver without Giving Rise to Cancer

(2015) Joan Font-Burgada et al.   CELL

Maintaining liver mass

(2015) Kenneth S. Zaret   NATURE

Self-renewing diploid Axin2+ cells fuel homeostatic renewal of the liver

(2015) Bruce Wang et al.   NATURE

Ultrastructurally smooth thick partitioning and volume stitching for large-scale connectomics

(2015) Kenneth J Hayworth et al.   NATURE METHODS

In vivo cell-cycle profiling in xenograft tumors by quantitative intravital microscopy

(2015) Deepak R Chittajallu et al.   NATURE METHODS

On the origin of liver regeneration

(2015) Katrina Ray   Nature Reviews Gastroenterology & Hepatology

MorphoGraphX: A platform for quantifying morphogenesis in 4D

(2015) Pierre Barbier de Reuille et al.   eLife

Protocols for staining of bile canalicular and sinusoidal networks of human, mouse and pig livers, three-dimensional reconstruction and quantification of tissue microarchitecture by image processing and analysis

(2014) Seddik Hammad et al.   ARCHIVES OF TOXICOLOGY

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

(2014) Fernando Amat et al.   NATURE METHODS

Fast Segmentation of Stained Nuclei in Terabyte-Scale, Time Resolved 3D Microscopy Image Stacks

(2014) Johannes Stegmaier et al.   PLoS One

Polyploidization in Liver Tissue

(2013) Géraldine Gentric et al.   AMERICAN JOURNAL OF PATHOLOGY

Modeling and simulation of biological systems from image data

(2013) Ivo F. Sbalzarini   BIOESSAYS

Integrated profiling of three dimensional cell culture models and 3D microscopy

(2013) Cemal Cagatay Bilgin et al.   BIOINFORMATICS

TeraStitcher - A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images

(2013) Alessandro Bria et al.   BMC BIOINFORMATICS

CLARITY for mapping the nervous system

(2013) Kwanghun Chung et al.   NATURE METHODS

SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction

(2013) Meng-Tsen Ke et al.   NATURE NEUROSCIENCE

To divide or not to divide: revisiting liver regeneration

(2013) Yuichiro Miyaoka et al.   Cell Division

Quantitative Measurements in 3-Dimensional Datasets of Mouse Lymph Nodes Resolve Organ-Wide Functional Dependencies

(2012) Jürgen Mayer et al.   Computational and Mathematical Methods in Medicine

E2F8 is essential for polyploidization in mammalian cells

(2012) Shusil K. Pandit et al.   NATURE CELL BIOLOGY

Icy: an open bioimage informatics platform for extended reproducible research

(2012) Fabrice de Chaumont et al.   NATURE METHODS

Elastic volume reconstruction from series of ultra-thin microscopy sections

(2012) Stephan Saalfeld et al.   NATURE METHODS

ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes

(2012) Kishore R. Mosaliganti et al.   PLoS Computational Biology

Whole Animal Perfusion Fixation for Rodents

(2012) Gregory J. Gage et al.   Jove-Journal of Visualized Experiments

The Cardiac Atlas Project—an imaging database for computational modeling and statistical atlases of the heart

(2011) Carissa G. Fonseca et al.   BIOINFORMATICS

Comparison of segmentation algorithms for fluorescence microscopy images of cells

(2011) Alden A. Dima et al.   CYTOMETRY PART A

Single-Cell Analysis of Ploidy and Centrosomes Underscores the Peculiarity of Normal Hepatocytes

(2011) Francesca Faggioli et al.   PLoS One

DNA double-strand breaks induced by high NaCl occur predominantly in gene deserts

(2011) N. I. Dmitrieva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The cardiac physiome: Foundations and future prospects for mathematical modelling of the heart

(2011) Nic Smith et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Generalized Voronoi Tessellation as a Model of Two-dimensional Cell Tissue Dynamics

(2010) Martin Bock et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Realistic modeling of the illumination point spread function in confocal scanning optical microscopy

(2010) Michael J. Nasse et al.   JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION

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

(2010) Hanchuan Peng et al.   NATURE BIOTECHNOLOGY

Prediction and validation of cell alignment along microvessels as order principle to restore tissue architecture in liver regeneration

(2010) S. Hoehme et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Role of Spatially Controlled Cell Proliferation in Limb Bud Morphogenesis

(2010) Bernd Boehm et al.   PLOS BIOLOGY

Globally optimal stitching of tiled 3D microscopic image acquisitions

(2009) S. Preibisch et al.   BIOINFORMATICS

Cellular organization of normal mouse liver: a histological, quantitative immunocytochemical, and fine structural analysis

(2009) Janie L. Baratta et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Improved Automatic Detection and Segmentation of Cell Nuclei in Histopathology Images

(2009) Y. Al-Kofahi et al.   IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING

Fast Gradient-Based Algorithms for Constrained Total Variation Image Denoising and Deblurring Problems

(2009) A. Beck et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

XuvTools: free, fast and reliable stitching of large 3D datasets

(2009) M. EMMENLAUER et al.   JOURNAL OF MICROSCOPY

Fractal and multifractal analysis: A review

(2009) R. Lopes et al.   MEDICAL IMAGE ANALYSIS

Fast interscale wavelet denoising of Poisson-corrupted images

(2009) Florian Luisier et al.   SIGNAL PROCESSING

Lymph Circulation in the Liver

(2008) Osamu Ohtani et al.   Anatomical Record-Advances in Integrative Anatomy and Evolutionary Biology

The Hepatic Microvascular System in Health and Its Response to Toxicants

(2008) Robert S. Mccuskey   Anatomical Record-Advances in Integrative Anatomy and Evolutionary Biology

Bioinformatics, multiscale modeling and the IUPS Physiome Project

(2008) P. J. Hunter et al.   BRIEFINGS IN BIOINFORMATICS