NIH Image to ImageJ: 25 years of image analysis.

PubWeight™: 84.41‹?› | Rank: Top 0.01% | All-Time Top 1000

🔗 View Article (PMID 22930834)

Published in Nat Methods on July 01, 2012


Caroline A Schneider1, Wayne S Rasband, Kevin W Eliceiri

Author Affiliations

1: Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, Wisconsin, USA.

Associated clinical trials:

Fitting of Commonly Available Face Masks for Late Preterm and Term Infants (CAFF) | NCT03369028

Semi-manual Vessel Density Analysis on Optical Coherence Tomography Angiography Images of Healthy Adults | NCT03590899

Short Dental Implants (5 mm) Versus Long Dental Implants (10 mm) | NCT04144322

Articles citing this

(truncated to the top 100)

Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat Biotechnol (2014) 3.72

CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell (2014) 3.68

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility. Cell (2016) 3.47

Signaling by IL-6 promotes alternative activation of macrophages to limit endotoxemia and obesity-associated resistance to insulin. Nat Immunol (2014) 3.12

Bi-directional interconversion of brite and white adipocytes. Nat Cell Biol (2013) 3.08

Asymmetric recognition of the HIV-1 trimer by broadly neutralizing antibody PG9. Proc Natl Acad Sci U S A (2013) 2.96

Mitophagy of damaged mitochondria occurs locally in distal neuronal axons and requires PINK1 and Parkin. J Cell Biol (2014) 2.95

Biological imaging software tools. Nat Methods (2012) 2.91

Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics. Front Mol Neurosci (2013) 2.79

Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo. Nat Biotechnol (2014) 2.75

Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement. Theor Appl Genet (2013) 2.75

Clinical Cerenkov luminescence imaging of (18)F-FDG. J Nucl Med (2013) 2.63

Inhibiting EGF receptor or SRC family kinase signaling overcomes BRAF inhibitor resistance in melanoma. Cancer Discov (2012) 2.56

Bufalin is a potent small-molecule inhibitor of the steroid receptor coactivators SRC-3 and SRC-1. Cancer Res (2014) 2.54

Interfollicular epidermal stem cells self-renew via autocrine Wnt signaling. Science (2013) 2.52

Conformational coupling across the plasma membrane in activation of the EGF receptor. Cell (2013) 2.49

Cellular mechanisms of brain state-dependent gain modulation in visual cortex. Nat Neurosci (2013) 2.36

Open data and digital morphology. Proc Biol Sci (2017) 2.24

The transition from meiotic to mitotic spindle assembly is gradual during early mammalian development. J Cell Biol (2012) 2.18

Ccl2, Cx3cr1 and Ccl2/Cx3cr1 chemokine deficiencies are not sufficient to cause age-related retinal degeneration. Exp Eye Res (2012) 2.18

Modeling recent human evolution in mice by expression of a selected EDAR variant. Cell (2013) 2.17

Transgenerational inheritance of increased fat depot size, stem cell reprogramming, and hepatic steatosis elicited by prenatal exposure to the obesogen tributyltin in mice. Environ Health Perspect (2013) 2.12

Retracted Experimental orthotopic transplantation of a tissue-engineered oesophagus in rats. Nat Commun (2014) 2.09

CRM1 blockade by selective inhibitors of nuclear export attenuates kidney cancer growth. J Urol (2012) 2.05

Membrane proteins bind lipids selectively to modulate their structure and function. Nature (2014) 2.05

A single subset of dendritic cells controls the cytokine bias of natural killer T cell responses to diverse glycolipid antigens. Immunity (2014) 2.02

Structure of a type IV secretion system. Nature (2014) 2.01

Quantitative assessment of antibody internalization with novel monoclonal antibodies against Alexa fluorophores. PLoS One (2015) 2.00

Provirophages and transpovirons as the diverse mobilome of giant viruses. Proc Natl Acad Sci U S A (2012) 1.96

Geometric catalysis of membrane fission driven by flexible dynamin rings. Science (2013) 1.95

Electron microscopy: Ultrastable gold substrates for electron cryomicroscopy. Science (2014) 1.95

Identification of functional cooperative mutations of SETD2 in human acute leukemia. Nat Genet (2014) 1.94

scikit-image: image processing in Python. PeerJ (2014) 1.93

Wapl is an essential regulator of chromatin structure and chromosome segregation. Nature (2013) 1.92

X-ray phase-contrast in vivo microtomography probes new aspects of Xenopus gastrulation. Nature (2013) 1.90

Simultaneous detection of hepatitis C virus and interferon stimulated gene expression in infected human liver. Hepatology (2014) 1.89

Septin assemblies form by diffusion-driven annealing on membranes. Proc Natl Acad Sci U S A (2014) 1.89

Imbalance of desmoplastic stromal cell numbers drives aggressive cancer processes. J Pathol (2013) 1.86

Synapse location during growth depends on glia location. Cell (2013) 1.80

Rapid fucosylation of intestinal epithelium sustains host-commensal symbiosis in sickness. Nature (2014) 1.78

A multilevel multimodal circuit enhances action selection in Drosophila. Nature (2015) 1.77

Global microRNA depletion suppresses tumor angiogenesis. Genes Dev (2014) 1.76

Lipid droplets: a new player in colorectal cancer stem cells unveiled by spectroscopic imaging. Stem Cells (2015) 1.75

Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex. Nature (2013) 1.74

Imaging of neutral lipids by oil red O for analyzing the metabolic status in health and disease. Nat Protoc (2013) 1.72

Polysulfides link H2S to protein thiol oxidation. Antioxid Redox Signal (2013) 1.70

Discovery of unconventional kinetochores in kinetoplastids. Cell (2014) 1.70

Preclinical comparison of near-infrared-labeled cetuximab and panitumumab for optical imaging of head and neck squamous cell carcinoma. Mol Imaging Biol (2013) 1.67

Endocrine remodelling of the adult intestine sustains reproduction in Drosophila. Elife (2015) 1.66

Biochar and microbial signaling: production conditions determine effects on microbial communication. Environ Sci Technol (2013) 1.65

Quantitative proteomics identifies NCOA4 as the cargo receptor mediating ferritinophagy. Nature (2014) 1.65

The metabolite α-ketoglutarate extends lifespan by inhibiting ATP synthase and TOR. Nature (2014) 1.63

Arrhythmia risk stratification of patients after myocardial infarction using personalized heart models. Nat Commun (2016) 1.62

Osterix marks distinct waves of primitive and definitive stromal progenitors during bone marrow development. Dev Cell (2014) 1.60

Genome-wide association mapping of root traits in a japonica rice panel. PLoS One (2013) 1.58

Characterization of the Newly Isolated Lytic Bacteriophages KTN6 and KT28 and Their Efficacy against Pseudomonas aeruginosa Biofilm. PLoS One (2015) 1.58

The Pseudomonas aeruginosa type III translocon is required for biofilm formation at the epithelial barrier. PLoS Pathog (2014) 1.57

Targeted chromosomal deletions and inversions in zebrafish. Genome Res (2013) 1.57

Sequence determinants of improved CRISPR sgRNA design. Genome Res (2015) 1.56

Evidence for sex and recombination in the choanoflagellate Salpingoeca rosetta. Curr Biol (2013) 1.55

β-Arrestin drives MAP kinase signalling from clathrin-coated structures after GPCR dissociation. Nat Cell Biol (2016) 1.54

Loss of fibronectin from the aged stem cell niche affects the regenerative capacity of skeletal muscle in mice. Nat Med (2016) 1.54

Neuronal morphology goes digital: a research hub for cellular and system neuroscience. Neuron (2013) 1.53

Direct observations of amyloid β self-assembly in live cells provide insights into differences in the kinetics of Aβ(1-40) and Aβ(1-42) aggregation. Chem Biol (2014) 1.53

Domestication selected for deceleration of the circadian clock in cultivated tomato. Nat Genet (2015) 1.53

Prostasin interacts with the epithelial Na+ channel and facilitates cleavage of the γ-subunit by a second protease. Am J Physiol Renal Physiol (2014) 1.52

Diffusion-Weighted Imaging in 3.0 Tesla Breast MRI: Diagnostic Performance and Tumor Characterization Using Small Subregions vs. Whole Tumor Regions of Interest. PLoS One (2015) 1.51

Autophagosome-lysosome fusion triggers a lysosomal response mediated by TLR9 and controlled by OCRL. Nat Cell Biol (2016) 1.51

Silencing the Menkes copper-transporting ATPase (Atp7a) gene in rat intestinal epithelial (IEC-6) cells increases iron flux via transcriptional induction of ferroportin 1 (Fpn1). J Nutr (2013) 1.51

An endogenous nanomineral chaperones luminal antigen and peptidoglycan to intestinal immune cells. Nat Nanotechnol (2015) 1.50

The Structural Basis of Actin Organization by Vinculin and Metavinculin. J Mol Biol (2015) 1.50

Saccadic Corollary Discharge Underlies Stable Visual Perception. J Neurosci (2016) 1.49

Applying systems-level spectral imaging and analysis to reveal the organelle interactome. Nature (2017) 1.49

Pathogen Virulence Impedes Mutualist-Mediated Enhancement of Host Juvenile Growth via Inhibition of Protein Digestion. Cell Host Microbe (2015) 1.48

A chemoproteomic platform to quantitatively map targets of lipid-derived electrophiles. Nat Methods (2013) 1.48

Tumor-induced pressure in the bone microenvironment causes osteocytes to promote the growth of prostate cancer bone metastases. Cancer Res (2015) 1.47

OTUB1 de-ubiquitinating enzyme promotes prostate cancer cell invasion in vitro and tumorigenesis in vivo. Mol Cancer (2015) 1.47

Metformin Induces Cell Cycle Arrest, Reduced Proliferation, Wound Healing Impairment In Vivo and Is Associated to Clinical Outcomes in Diabetic Foot Ulcer Patients. PLoS One (2016) 1.46

Prophage WO genes recapitulate and enhance Wolbachia-induced cytoplasmic incompatibility. Nature (2017) 1.46

Putting life on ice: bacteria that bind to frozen water. J R Soc Interface (2016) 1.45

The mTORC1/4E-BP pathway coordinates hemoglobin production with L-leucine availability. Sci Signal (2015) 1.44

Caenorhabditis elegans PAQR-2 and IGLR-2 Protect against Glucose Toxicity by Modulating Membrane Lipid Composition. PLoS Genet (2016) 1.44

IHC Profiler: an open source plugin for the quantitative evaluation and automated scoring of immunohistochemistry images of human tissue samples. PLoS One (2014) 1.44

Progressive degeneration of dopaminergic neurons through TRP channel-induced cell death. J Neurosci (2014) 1.43

A Wolbachia deubiquitylating enzyme induces cytoplasmic incompatibility. Nat Microbiol (2017) 1.43

Water Spinach, Ipomoea aquatic (Convolvulaceae), Ameliorates Lead Toxicity by Inhibiting Oxidative Stress and Apoptosis. PLoS One (2015) 1.43

Bacillus subtilis KCTC 11782BP-produced alginate oligosaccharide effectively suppresses asthma via T-helper cell type 2-related cytokines. PLoS One (2015) 1.43

Molecular genetic and physical analysis of gas vesicles in buoyant enterobacteria. Environ Microbiol (2016) 1.43

A Single-Strand Annealing Protein Clamps DNA to Detect and Secure Homology. PLoS Biol (2015) 1.43

The aspartate-less receiver (ALR) domains: distribution, structure and function. PLoS Pathog (2015) 1.43

Orientation of myosin binding protein C in the cardiac muscle sarcomere determined by domain-specific immuno-EM. J Mol Biol (2014) 1.43

Zebrabow: multispectral cell labeling for cell tracing and lineage analysis in zebrafish. Development (2013) 1.43

Effects of traumatic brain injury on intestinal contractility. Neurogastroenterol Motil (2013) 1.43

Fibrosis and Fibrotic Gene Expression in Pediatric and Adult Patients with Idiopathic Dilated Cardiomyopathy. J Card Fail (2016) 1.42

Design of a hyperstable 60-subunit protein icosahedron. Nature (2016) 1.42

The extracellular matrix Component Psl provides fast-acting antibiotic defense in Pseudomonas aeruginosa biofilms. PLoS Pathog (2013) 1.42

Apical targeting of the P2Y(4) receptor is directed by hydrophobic and basic residues in the cytoplasmic tail. Am J Physiol Cell Physiol (2012) 1.42

Glucagon-like peptide-1 analogue, liraglutide, in experimental cerebral malaria: implications for the role of oxidative stress in cerebral malaria. Malar J (2016) 1.42

Drosophila americana Diapausing Females Show Features Typical of Young Flies. PLoS One (2015) 1.42

MicroRNAs Are Involved in the Regulation of Ovary Development in the Pathogenic Blood Fluke Schistosoma japonicum. PLoS Pathog (2016) 1.42

Articles by these authors

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software. Bioinformatics (2011) 12.98

Metadata matters: access to image data in the real world. J Cell Biol (2010) 12.49

Collagen reorganization at the tumor-stromal interface facilitates local invasion. BMC Med (2006) 6.44

Collagen density promotes mammary tumor initiation and progression. BMC Med (2008) 5.13

In vivo multiphoton microscopy of NADH and FAD redox states, fluorescence lifetimes, and cellular morphology in precancerous epithelia. Proc Natl Acad Sci U S A (2007) 4.53

Aligned collagen is a prognostic signature for survival in human breast carcinoma. Am J Pathol (2011) 3.70

Contact guidance mediated three-dimensional cell migration is regulated by Rho/ROCK-dependent matrix reorganization. Biophys J (2008) 3.49

Bioimage informatics for experimental biology. Annu Rev Biophys (2009) 3.04

Open source bioimage informatics for cell biology. Trends Cell Biol (2009) 2.93

Multiphoton microscopy of endogenous fluorescence differentiates normal, precancerous, and cancerous squamous epithelial tissues. Cancer Res (2005) 2.28

Metabolic mapping of MCF10A human breast cells via multiphoton fluorescence lifetime imaging of the coenzyme NADH. Cancer Res (2005) 2.15

Postpartum mammary gland involution drives progression of ductal carcinoma in situ through collagen and COX-2. Nat Med (2011) 2.12

In vivo multiphoton fluorescence lifetime imaging of protein-bound and free nicotinamide adenine dinucleotide in normal and precancerous epithelia. J Biomed Opt (2007) 2.09

The collagen receptor discoidin domain receptor 2 stabilizes SNAIL1 to facilitate breast cancer metastasis. Nat Cell Biol (2013) 1.93

OpenSPIM: an open-access light-sheet microscopy platform. Nat Methods (2013) 1.88

Mammary epithelial-specific disruption of focal adhesion kinase retards tumor formation and metastasis in a transgenic mouse model of human breast cancer. Am J Pathol (2008) 1.82

Multiphoton microscopy and fluorescence lifetime imaging microscopy (FLIM) to monitor metastasis and the tumor microenvironment. Clin Exp Metastasis (2008) 1.51

Optical workstation with concurrent, independent multiphoton imaging and experimental laser microbeam capabilities. Rev Sci Instrum (2003) 1.48

Filamin A-beta1 integrin complex tunes epithelial cell response to matrix tension. Mol Biol Cell (2009) 1.47

Transition to invasion in breast cancer: a microfluidic in vitro model enables examination of spatial and temporal effects. Integr Biol (Camb) (2010) 1.41

A call for bioimaging software usability. Nat Methods (2012) 1.39

Control of 3-dimensional collagen matrix polymerization for reproducible human mammary fibroblast cell culture in microfluidic devices. Biomaterials (2009) 1.37

Cortical granule exocytosis in C. elegans is regulated by cell cycle components including separase. Development (2007) 1.33

VisBio: a computational tool for visualization of multidimensional biological image data. Traffic (2004) 1.22

Simultaneous two-photon spectral and lifetime fluorescence microscopy. Appl Opt (2004) 1.15

Stiff collagen matrices increase tumorigenic prolactin signaling in breast cancer cells. J Biol Chem (2013) 1.15

Visualization approaches for multidimensional biological image data. Biotechniques (2007) 1.15

Microtubules regulate GEF-H1 in response to extracellular matrix stiffness. Mol Biol Cell (2012) 1.14

Nonlinear optical imaging and spectral-lifetime computational analysis of endogenous and exogenous fluorophores in breast cancer. J Biomed Opt (2008) 1.14

Fluorescence lifetime imaging of endogenous fluorophores in histopathology sections reveals differences between normal and tumor epithelium in carcinoma in situ of the breast. Cell Biochem Biophys (2009) 1.13

Shining new light on 3D cell motility and the metastatic process. Trends Cell Biol (2009) 1.09

CGEF-1 and CHIN-1 regulate CDC-42 activity during asymmetric division in the Caenorhabditis elegans embryo. Mol Biol Cell (2009) 1.07

Goniometric measurements of thick tissue using Monte Carlo simulations to obtain the single scattering anisotropy coefficient. Biomed Opt Express (2012) 1.06

Nonlinear optical imaging of cellular processes in breast cancer. Microsc Microanal (2008) 1.04

Structural changes in mixed Col I/Col V collagen gels probed by SHG microscopy: implications for probing stromal alterations in human breast cancer. Biomed Opt Express (2011) 1.01

Unifying Biological Image Formats with HDF5. Commun ACM (2009) 1.00

Nonlinear optical microscopy and ultrasound imaging of human cervical structure. J Biomed Opt (2013) 0.99

Quantification of collagen organization and extracellular matrix factors within the healing ligament. Microsc Microanal (2011) 0.98

Applications of combined spectral lifetime microscopy for biology. Biotechniques (2006) 0.96

Spatial and temporal analysis of extracellular matrix proteins in the developing murine heart: a blueprint for regeneration. Tissue Eng Part A (2013) 0.93

BioClips of symmetric and asymmetric cell division. Biol Cell (2007) 0.91

Engineering three-dimensional collagen matrices to provide contact guidance during 3D cell migration. Curr Protoc Cell Biol (2010) 0.90

Laser scanning confocal microscopy: history, applications, and related optical sectioning techniques. Methods Mol Biol (2014) 0.89

A shift in energy metabolism anticipates the onset of sarcopenia in rhesus monkeys. Aging Cell (2013) 0.89

Multiphoton flow cytometry to assess intrinsic and extrinsic fluorescence in cellular aggregates: applications to stem cells. Microsc Microanal (2010) 0.88

Bimolecular fluorescence complementation analysis of eukaryotic fusion products. Biol Cell (2010) 0.88

A nondenatured, noncrosslinked collagen matrix to deliver stem cells to the heart. Regen Med (2011) 0.88

Cell death, non-invasively assessed by intrinsic fluorescence intensity of NADH, is a predictive indicator of functional differentiation of embryonic stem cells. Biol Cell (2012) 0.87

RhoA is down-regulated at cell-cell contacts via p190RhoGAP-B in response to tensional homeostasis. Mol Biol Cell (2013) 0.87

Simultaneous determination of the second-harmonic generation emission directionality and reduced scattering coefficient from three-dimensional imaging of thick tissues. J Biomed Opt (2013) 0.85

Integrated studies of biology: multiplexed imaging assays from molecules to man and back. Curr Opin Biotechnol (2009) 0.85

The effect of micro-ECoG substrate footprint on the meningeal tissue response. J Neural Eng (2014) 0.84

Resveratrol metabolites do not elicit early pro-apoptotic mechanisms in neuroblastoma cells. J Agric Food Chem (2011) 0.84

Lrrc10 is required for early heart development and function in zebrafish. Dev Biol (2007) 0.83

Association of cellular and molecular responses in the rat mammary gland to 17β-estradiol with susceptibility to mammary cancer. BMC Cancer (2013) 0.82

ECM-incorporated hydrogels cross-linked via native chemical ligation to engineer stem cell microenvironments. Biomacromolecules (2013) 0.82

Nonlinear optical microscopy and computational analysis of intrinsic signatures in breast cancer. Conf Proc IEEE Eng Med Biol Soc (2009) 0.82

Image-inspired 3D multiphoton excited fabrication of extracellular matrix structures by modulated raster scanning. Opt Express (2013) 0.82

A bioengineered heterotypic stroma-cancer microenvironment model to study pancreatic ductal adenocarcinoma. Lab Chip (2013) 0.82 an inquiry-rich educational web portal for research resources of Caenorhabditis elegans. CBE Life Sci Educ (2007) 0.82

Imaging cardiac extracellular matrices: a blueprint for regeneration. Trends Biotechnol (2011) 0.81

Experimental and simulation study of the wavelength dependent second harmonic generation of collagen in scattering tissues. Opt Lett (2014) 0.80

Closed-Loop Optogenetic Brain Interface. IEEE Trans Biomed Eng (2015) 0.78

Mesenchymal stem cell interactions with 3D ECM modules fabricated via multiphoton excited photochemistry. Biomacromolecules (2012) 0.77

A chronic window imaging device for the investigation of in vivo peripheral nerves. Conf Proc IEEE Eng Med Biol Soc (2014) 0.77

Student learning of early embryonic development via the utilization of research resources from the nematode Caenorhabditis elegans. CBE Life Sci Educ (2008) 0.76

Endogenous fluorescence signatures in living pluripotent stem cells change with loss of potency. PLoS One (2012) 0.76

Visualization of morphological and molecular features associated with chronic ischemia in bioengineered human skin. Microsc Microanal (2010) 0.75

Fast localized wavefront correction using area-mapped phase-shift interferometry. Opt Lett (2011) 0.75

Multi-view second-harmonic generation imaging of mouse tail tendon via reflective micro-prisms. Opt Lett (2015) 0.75


Automated and Robust Quantification of Colocalization in Dual-Color Fluorescence Microscopy: A Nonparametric Statistical Approach. IEEE Trans Image Process (2017) 0.75

Wavelet compression of three-dimensional time-lapse biological image data. Microsc Microanal (2005) 0.75