NIH Image to ImageJ: 25 years of image analysis
TLDR
The origins, challenges and solutions of NIH Image and ImageJ software are discussed, and how their history can serve to advise and inform other software projects.Abstract:
For the past 25 years NIH Image and ImageJ software have been pioneers as open tools for the analysis of scientific images. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.read more
Citations
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Antiviral Potential of ERK/MAPK and PI3K/AKT/mTOR Signaling Modulation for Middle East Respiratory Syndrome Coronavirus Infection as Identified by Temporal Kinome Analysis
Jason Kindrachuk,Britini L. Ork,Brit J. Hart,Steven Mazur,Michael R. Holbrook,Matthew B. Frieman,Dawn Traynor,Reed F. Johnson,Julie Dyall,Jens H. Kuhn,Gene G. Olinger,Lisa E. Hensley,Peter B. Jahrling +12 more
TL;DR: In this paper, the authors performed temporal kinome analysis on human hepatocytes infected with the Erasmus isolate of MERS-CoV with peptide kinome arrays and found that ERK/MAPK and PI3K/AKT/mTOR signaling responses were specifically modulated in response to infection in vitro throughout the course of infection.
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Prophage WO genes recapitulate and enhance Wolbachia -induced cytoplasmic incompatibility
Daniel P. LePage,Jason A. Metcalf,Sarah R. Bordenstein,Jungmin On,Jessamyn I. Perlmutter,J. Dylan Shropshire,Emily M. Layton,Lisa J. Funkhouser-Jones,John F. Beckmann,Seth R. Bordenstein +9 more
TL;DR: Comparison and transgenic approaches are used to demonstrate that two differentially transcribed, co-diverging genes in the eukaryotic association module of prophage WO from Wolbachia strain wMel recapitulate and enhance cytoplasmic incompatibility.
Journal ArticleDOI
T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation.
Moshe Biton,Moshe Biton,Adam L. Haber,Noga Rogel,Grace Burgin,Semir Beyaz,Semir Beyaz,Semir Beyaz,Alexandra Schnell,Orr Ashenberg,Chien-wen Su,Christopher Smillie,Karthik Shekhar,Zuojia Chen,Chuan Wu,Jose Ordovas-Montanes,David Alvarez,Rebecca H. Herbst,Rebecca H. Herbst,Mei Zhang,Itay Tirosh,Itay Tirosh,Danielle Dionne,Lan T. Nguyen,Michael E. Xifaras,Alex K. Shalek,Ulrich H. von Andrian,Daniel B. Graham,Orit Rozenblatt-Rosen,Hai Ning Shi,Vijay K. Kuchroo,Vijay K. Kuchroo,Ömer H. Yilmaz,Ömer H. Yilmaz,Ömer H. Yilmaz,Aviv Regev,Aviv Regev,Ramnik J. Xavier +37 more
TL;DR: It is shown that MHCII+ Lgr5+ ISCs are non-conventional antigen-presenting cells in co-cultures with CD4+ T helper (Th) cells, which orchestrate tissue-wide responses to external signals.
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A combination of ontogeny and CNS environment establishes microglial identity.
F. Chris Bennett,Mariko L. Bennett,Fazeela Yaqoob,Sara B. Mulinyawe,Gerald A. Grant,Melanie Hayden Gephart,Edward D. Plowey,Ben A. Barres +7 more
TL;DR: A brain macrophage transplantation system is created to disentangle how environment and ontogeny specify microglial identity, and it is found that donor cells extensively engraft in the CNS of microglia-deficient mice, and even after exposure to a cell culture environment,microglia fully regain their identity when returned to the CNS.
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Nanoparticles promote in vivo breast cancer cell intravasation and extravasation by inducing endothelial leakiness.
Fei Peng,Magdiel Inggrid Setyawati,Jie Kai Tee,Xianguang Ding,Jinping Wang,Min En Nga,Han Kiat Ho,David Tai Leong +7 more
TL;DR: It is shown that intravenously injected titanium dioxide, silica and gold nanoparticles significantly accelerate both intravasation and extravasation of breast cancer cells in animal models, increasing the extent of existing metastasis and promoting the appearance of new metastatic sites.
References
More filters
Journal ArticleDOI
Fiji: an open-source platform for biological-image analysis
Johannes Schindelin,Ignacio Arganda-Carreras,Erwin Frise,Verena Kaynig,Mark Longair,Tobias Pietzsch,Stephan Preibisch,Curtis Rueden,Stephan Saalfeld,Benjamin Schmid,Jean-Yves Tinevez,Daniel J. White,Volker Hartenstein,Kevin W. Eliceiri,Pavel Tomancak,Albert Cardona +15 more
TL;DR: Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis that facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system.
Journal ArticleDOI
CellProfiler: image analysis software for identifying and quantifying cell phenotypes
Anne E. Carpenter,Thouis R. Jones,Michael R. Lamprecht,Colin Clarke,In Han Kang,Ola Friman,David A. Guertin,Joo Han Chang,Robert A. Lindquist,Jason Moffat,Polina Golland,David M. Sabatini +11 more
TL;DR: The first free, open-source system designed for flexible, high-throughput cell image analysis, CellProfiler is described, which can address a variety of biological questions quantitatively.
Journal ArticleDOI
ImageJ for microscopy
TL;DR: The near-comprehensive range of import filters that allow easy access to image and meta-data, a broad suite processing and analysis routine, and enthusiastic support from a friendly mailing list are invaluable for all microscopy labs and facilities-not just those on a budget.
Journal ArticleDOI
Computer control of microscopes using µManager.
Arthur D. Edelstein,Nenad Amodaj,Karl Hoover,Ronald D. Vale,Ronald D. Vale,Nico Stuurman,Nico Stuurman +6 more
TL;DR: This unit provides step‐by‐step protocols describing how to get started working with µManager, as well as some starting points for advanced use of the software.
Journal ArticleDOI
Icy: an open bioimage informatics platform for extended reproducible research
Fabrice de Chaumont,Stephane Dallongeville,Nicolas Chenouard,Nicolas Hervé,Sorin Pop,Thomas Provoost,Vannary Meas-Yedid,Praveen Pankajakshan,Timothee Lecomte,Yoann Le Montagner,Thibault Lagache,Alexandre Dufour,Jean-Christophe Olivo-Marin +12 more
TL;DR: Icy is a collaborative bioimage informatics platform that combines a community website for contributing and sharing tools and material, and software with a high-end visual programming framework for seamless development of sophisticated imaging workflows.