Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space

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

(2016) Johannes Stegmaier et al.   DEVELOPMENTAL CELL

Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition

(2015) B. Mathew et al.   BMC BIOINFORMATICS

Global Brain Dynamics Embed the Motor Command Sequence of Caenorhabditis elegans

(2015) Saul Kato et al.   CELL

GroupTracker: Video tracking system for multiple animals under severe occlusion

(2015) Tsukasa Fukunaga et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Whole-brain calcium imaging with cellular resolution in freely behavingCaenorhabditis elegans

(2015) Jeffrey P. Nguyen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-central nervous system functional imaging in larval Drosophila

(2015) William C. Lemon et al.   Nature Communications

Automated detection and tracking of many cells by using 4D live-cell imaging data

(2014) Terumasa Tokunaga et al.   BIOINFORMATICS

Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis

(2014) Etsuo A. Susaki et al.   CELL

Whole-Body Imaging with Single-Cell Resolution by Tissue Decolorization

(2014) Kazuki Tainaka et al.   CELL

Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy

(2014) Robert Prevedel et al.   NATURE METHODS

Improved and Robust Detection of Cell Nuclei from Four Dimensional Fluorescence Images

(2014) Md. Khayrul Bashar et al.   PLoS One

Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans

(2013) S. J. Aerni et al.   BIOINFORMATICS

TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization

(2013) Jean Ollion et al.   BIOINFORMATICS

Evaluation of the effectiveness of simple nuclei-segmentation methods on Caenorhabditis elegans embryogenesis images

(2013) Yusuke Azuma et al.   BMC BIOINFORMATICS

Region-based progressive localization of cell nuclei in microscopic images with data adaptive modeling

(2013) Yang Song et al.   BMC BIOINFORMATICS

Segmentation of neuronal nuclei based on clump splitting and a two-step binarization of images

(2013) A. LaTorre et al.   EXPERT SYSTEMS WITH APPLICATIONS

Structural and molecular interrogation of intact biological systems

(2013) Kwanghun Chung et al.   NATURE

Whole-brain functional imaging at cellular resolution using light-sheet microscopy

(2013) Misha B Ahrens et al.   NATURE METHODS

Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light

(2013) Tina Schrödel 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

Concentration memory-dependent synaptic plasticity of a taste circuit regulates salt concentration chemotaxis in Caenorhabditis elegans

(2013) Hirofumi Kunitomo et al.   Nature Communications

3D segmentations of neuronal nuclei from confocal microscope image stacks

(2013) Antonio LaTorre et al.   Frontiers in Neuroanatomy

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

(2012) Johannes Schindelin et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Automatic Extraction of Nuclei Centroids of Mouse Embryonic Cells from Fluorescence Microscopy Images

(2012) Md. Khayrul Bashar et al.   PLoS One

The Temporal Pattern of Stimulation Determines the Extent and Duration of MAPK Activation in a Caenorhabditis elegans Sensory Neuron

(2012) T. Tomida et al.   Science Signaling

Simultaneous recognition and segmentation of cells: application in C.elegans

(2011) L. Qu et al.   BIOINFORMATICS

An automatic segmentation algorithm for 3D cell cluster splitting using volumetric confocal images

(2011) C. INDHUMATHI et al.   JOURNAL OF MICROSCOPY

Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain

(2011) Hiroshi Hama et al.   NATURE NEUROSCIENCE

Improved Automatic Detection and Segmentation of Cell Nuclei in Histopathology Images

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

Automated three-dimensional detection and counting of neuron somata

(2009) Marcel Oberlaender et al.   JOURNAL OF NEUROSCIENCE METHODS

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

(2009) Fuhui Long et al.   NATURE METHODS

Splitting touching cells based on concave points and ellipse fitting

(2009) Xiangzhi Bai et al.   PATTERN RECOGNITION

Functional asymmetry in Caenorhabditis elegans taste neurons and its computational role in chemotaxis

(2008) Hiroshi Suzuki et al.   NATURE

Efficient subpixel image registration algorithms

(2008) Manuel Guizar-Sicairos et al.   OPTICS LETTERS