Quantitating the cell: turning images into numbers with ImageJ

Light-sheet microscopy for everyone? Experience of building an OpenSPIM to study flatworm development

(2016) Johannes Girstmair et al.   BMC DEVELOPMENTAL BIOLOGY

3D correlative light and electron microscopy of cultured cells using serial blockface scanning electron microscopy

(2016) Matthew R. G. Russell et al.   JOURNAL OF CELL SCIENCE

Tissue segmentation of computed tomography images using a Random Forest algorithm: a feasibility study

(2016) Daniel F Polan et al.   PHYSICS IN MEDICINE AND BIOLOGY

Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development

(2016) Jaroslav Icha et al.   Jove-Journal of Visualized Experiments

Real-time multi-view deconvolution: Fig. 1.

(2015) Benjamin Schmid et al.   BIOINFORMATICS

Investigating the Regulation of Stem and Progenitor Cell Mitotic Progression by In Situ Imaging

(2015) Abigail R. Gerhold et al.   CURRENT BIOLOGY

Statistical analysis of molecule colocalization in bioimaging

(2015) Thibault Lagache et al.   CYTOMETRY PART A

The ImageJ ecosystem: An open platform for biomedical image analysis

(2015) Johannes Schindelin et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

ClearVolume: open-source live 3D visualization for light-sheet microscopy

(2015) Loic A Royer et al.   NATURE METHODS

BigDataViewer: visualization and processing for large image data sets

(2015) Tobias Pietzsch et al.   NATURE METHODS

Quantum dot/antibody conjugates for in vivo cytometric imaging in mice

(2015) Hee-Sun Han et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Untwisting the Caenorhabditis elegans embryo

(2015) Ryan Patrick Christensen et al.   eLife

In Vivo Autofluorescence Imaging of Tumor Heterogeneity in Response to Treatment

(2015) Amy T. Shah et al.   NEOPLASIA

Bioimage Informatics in the context of Drosophila research

(2014) Florian Jug et al.   METHODS

Objective comparison of particle tracking methods

(2014) Nicolas Chenouard et al.   NATURE METHODS

Efficient Bayesian-based multiview deconvolution

(2014) Stephan Preibisch et al.   NATURE METHODS

Synapse Location during Growth Depends on Glia Location

(2013) Zhiyong Shao et al.   CELL

Color Quantification of Stained Maize Stem Section Describes Lignin Spatial Distribution within the Whole Stem

(2013) Yu Zhang et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Oncogenic targeting of BRM drives malignancy through C/EBPβ-dependent induction of α5 integrin

(2013) L Damiano et al.   ONCOGENE

ImgLib2—generic image processing in Java

(2012) Tobias Pietzsch et al.   BIOINFORMATICS

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

(2012) Erik Meijering   IEEE SIGNAL PROCESSING MAGAZINE

Rab10 and myosin-Va mediate insulin-stimulated GLUT4 storage vesicle translocation in adipocytes

(2012) Yu Chen et al.   JOURNAL OF CELL BIOLOGY

2D protrusion but not motility predicts growth factor–induced cancer cell migration in 3D collagen

(2012) Aaron S. Meyer et al.   JOURNAL OF CELL BIOLOGY

A call for bioimaging software usability

(2012) Anne E Carpenter et al.   NATURE METHODS

Current challenges in open-source bioimage informatics

(2012) Albert Cardona 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

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

TrakEM2 Software for Neural Circuit Reconstruction

(2012) Albert Cardona et al.   PLoS One

Spatial coordination between cell and nuclear shape within micropatterned endothelial cells

(2012) Marie Versaevel et al.   Nature Communications

A practical guide to evaluating colocalization in biological microscopy

(2011) Kenneth W. Dunn et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets

(2010) S. Saalfeld et al.   BIOINFORMATICS

A high-level 3D visualization API for Java and ImageJ

(2010) Benjamin Schmid et al.   BMC BIOINFORMATICS

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

(2010) Stephan Preibisch et al.   NATURE METHODS

A Complete Developmental Sequence of a Drosophila Neuronal Lineage as Revealed by Twin-Spot MARCM

(2010) Hung-Hsiang Yu et al.   PLOS BIOLOGY

An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy

(2010) Albert Cardona et al.   PLOS BIOLOGY

Blind Source Separation Techniques for the Decomposition of Multiply Labeled Fluorescence Images

(2009) Richard A. Neher et al.   BIOPHYSICAL JOURNAL

Deterministic and probabilistic approaches for tracking virus particles in time-lapse fluorescence microscopy image sequences

(2009) W.J. Godinez et al.   MEDICAL IMAGE ANALYSIS

Microfluidics meet cell biology: bridging the gap by validation and application of microscale techniques for cell biological assays

(2008) Amy L. Paguirigan et al.   BIOESSAYS

Bioimage informatics: a new area of engineering biology

(2008) Hanchuan Peng   BIOINFORMATICS

Multiphoton microscopy and fluorescence lifetime imaging microscopy (FLIM) to monitor metastasis and the tumor microenvironment

(2008) Paolo P. Provenzano et al.   CLINICAL & EXPERIMENTAL METASTASIS

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

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

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

(2008) Khuloud Jaqaman et al.   NATURE METHODS

Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy

(2008) P. J. Keller et al.   SCIENCE

The Phasor Approach to Fluorescence Lifetime Imaging Analysis

(2007) Michelle A. Digman et al.   BIOPHYSICAL JOURNAL