Literature DB >> 22743774

Icy: an open bioimage informatics platform for extended reproducible research.

Fabrice de Chaumont1, Stéphane Dallongeville, Nicolas Chenouard, Nicolas Hervé, Sorin Pop, Thomas Provoost, Vannary Meas-Yedid, Praveen Pankajakshan, Timothée Lecomte, Yoann Le Montagner, Thibault Lagache, Alexandre Dufour, Jean-Christophe Olivo-Marin.   

Abstract

Current research in biology uses evermore complex computational and imaging tools. Here we describe Icy, 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. Icy extends the reproducible research principles, by encouraging and facilitating the reusability, modularity, standardization and management of algorithms and protocols. Icy is free, open-source and available at http://icy.bioimageanalysis.org/.

Mesh：

Year:  2012        PMID： 22743774     DOI： 10.1038/nmeth.2075

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  24 in total

1.  Computerized video analysis of social interactions in mice.

Authors:  Fabrice de Chaumont; Renata Dos-Santos Coura; Pierre Serreau; Arnaud Cressant; Jonathan Chabout; Sylvie Granon; Jean-Christophe Olivo-Marin
Journal:  Nat Methods       Date:  2012-03-04       Impact factor: 28.547

2.  Gene expression divergence recapitulates the developmental hourglass model.

Authors:  Alex T Kalinka; Karolina M Varga; Dave T Gerrard; Stephan Preibisch; David L Corcoran; Julia Jarrells; Uwe Ohler; Casey M Bergman; Pavel Tomancak
Journal:  Nature       Date:  2010-12-09       Impact factor: 49.962

3.  Multiple particle tracking in 3-D+t microscopy: method and application to the tracking of endocytosed quantum dots.

Authors:  Auguste Genovesio; Tim Liedl; Valentina Emiliani; Wolfgang J Parak; Maité Coppey-Moisan; Jean-Christophe Olivo-Marin
Journal:  IEEE Trans Image Process       Date:  2006-05       Impact factor: 10.856

4.  Pak1 phosphorylation enhances cortactin-N-WASP interaction in clathrin-caveolin-independent endocytosis.

Authors:  Alexandre Grassart; Vannary Meas-Yedid; Alexandre Dufour; Jean-Christophe Olivo-Marin; Alice Dautry-Varsat; Nathalie Sauvonnet
Journal:  Traffic       Date:  2010-04-28       Impact factor: 6.215

5.  SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope.

Authors:  Ghislain G Cabal; Auguste Genovesio; Susana Rodriguez-Navarro; Christophe Zimmer; Olivier Gadal; Annick Lesne; Henri Buc; Frank Feuerbach-Fournier; Jean-Christophe Olivo-Marin; Eduard C Hurt; Ulf Nehrbass
Journal:  Nature       Date:  2006-06-08       Impact factor: 49.962

6.  Newly visualized fibrillar collagen scaffolds dictate Entamoeba histolytica invasion route in the human colon.

Authors:  Roman Thibeaux; Alexandre Dufour; Pascal Roux; Michèle Bernier; Anne-Catherine Baglin; Pascal Frileux; Jean Chrisophe Olivo-Marin; Nancy Guillén; Elisabeth Labruyère
Journal:  Cell Microbiol       Date:  2012-02-15       Impact factor: 3.715

7.  Escape of HIV-1-infected dendritic cells from TRAIL-mediated NK cell cytotoxicity during NK-DC cross-talk--a pivotal role of HMGB1.

Authors:  Marie-Thérèse Melki; Héla Saïdi; Alexandre Dufour; Jean-Christophe Olivo-Marin; Marie-Lise Gougeon
Journal:  PLoS Pathog       Date:  2010-04-15       Impact factor: 6.823

8.  Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model.

Authors:  Hanchuan Peng; Zongcai Ruan; Deniz Atasoy; Scott Sternson
Journal:  Bioinformatics       Date:  2010-06-15       Impact factor: 6.937

9.  OMERO: flexible, model-driven data management for experimental biology.

Authors:  Chris Allan; Jean-Marie Burel; Josh Moore; Colin Blackburn; Melissa Linkert; Scott Loynton; Donald Macdonald; William J Moore; Carlos Neves; Andrew Patterson; Michael Porter; Aleksandra Tarkowska; Brian Loranger; Jerome Avondo; Ingvar Lagerstedt; Luca Lianas; Simone Leo; Katherine Hands; Ron T Hay; Ardan Patwardhan; Christoph Best; Gerard J Kleywegt; Gianluigi Zanetti; Jason R Swedlow
Journal:  Nat Methods       Date:  2012-02-28       Impact factor: 28.547

10.  CellProfiler: image analysis software for identifying and quantifying cell phenotypes.

Authors:  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
Journal:  Genome Biol       Date:  2006-10-31       Impact factor: 13.583
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  457 in total

1.  BioImageXD: an open, general-purpose and high-throughput image-processing platform.

Authors:  Pasi Kankaanpää; Lassi Paavolainen; Silja Tiitta; Mikko Karjalainen; Joacim Päivärinne; Jonna Nieminen; Varpu Marjomäki; Jyrki Heino; Daniel J White
Journal:  Nat Methods       Date:  2012-06-28       Impact factor: 28.547

2.  Current challenges in open-source bioimage informatics.

Authors:  Albert Cardona; Pavel Tomancak
Journal:  Nat Methods       Date:  2012-06-28       Impact factor: 28.547

3.  Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping.

Authors:  Ken Y Chan; Nicholas C Flytzanis; Bin Yang; Jennifer B Treweek; Benjamin E Deverman; Alon Greenbaum; Antti Lignell; Cheng Xiao; Long Cai; Mark S Ladinsky; Pamela J Bjorkman; Charless C Fowlkes; Viviana Gradinaru
Journal:  Nat Protoc       Date:  2015-10-22       Impact factor: 13.491

4.  Slide Set: Reproducible image analysis and batch processing with ImageJ.

Authors:  Benjamin A Nanes
Journal:  Biotechniques       Date:  2015-11-01       Impact factor: 1.993

5.  Absence of γ-Chain in Keratinocytes Alters Chemokine Secretion, Resulting in Reduced Immune Cell Recruitment.

Authors:  Karolin Nowak; Daniela Linzner; Adrian J Thrasher; Paul F Lambert; Wei-Li Di; Siobhan O Burns
Journal:  J Invest Dermatol       Date:  2017-06-17       Impact factor: 8.551

6.  β-Glucan-induced reprogramming of human macrophages inhibits NLRP3 inflammasome activation in cryopyrinopathies.

Authors:  Giorgio Camilli; Mathieu Bohm; Alícia Corbellini Piffer; Rachel Lavenir; David L Williams; Benedicte Neven; Gilles Grateau; Sophie Georgin-Lavialle; Jessica Quintin
Journal:  J Clin Invest       Date:  2020-09-01       Impact factor: 14.808

7.  Extensible visualization and analysis for multidimensional images using Vaa3D.

Authors:  Hanchuan Peng; Alessandro Bria; Zhi Zhou; Giulio Iannello; Fuhui Long
Journal:  Nat Protoc       Date:  2014-01-02       Impact factor: 13.491

8.  Endrov: an integrated platform for image analysis.

Authors:  Johan Henriksson; Jürgen Hench; Yong Guang Tong; Arvid Johansson; David Johansson; Thomas R Bürglin
Journal:  Nat Methods       Date:  2013-06       Impact factor: 28.547

9.  αTAT1 catalyses microtubule acetylation at clathrin-coated pits.

Authors:  Guillaume Montagnac; Vannary Meas-Yedid; Marie Irondelle; Antonio Castro-Castro; Michel Franco; Toshinobu Shida; Maxence V Nachury; Alexandre Benmerah; Jean-Christophe Olivo-Marin; Philippe Chavrier
Journal:  Nature       Date:  2013-10-06       Impact factor: 49.962

10.  Altered social behavior in mice carrying a cortical Foxp2 deletion.

Authors:  Vera P Medvedeva; Michael A Rieger; Beate Vieth; Cédric Mombereau; Christoph Ziegenhain; Tanay Ghosh; Arnaud Cressant; Wolfgang Enard; Sylvie Granon; Joseph D Dougherty; Matthias Groszer
Journal:  Hum Mol Genet       Date:  2019-03-01       Impact factor: 6.150
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