Icy: an open bioimage informatics platform for extended reproducible research View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2012-07

AUTHORS

Fabrice de Chaumont, 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/. More... »

PAGES

690

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nmeth.2075

DOI

http://dx.doi.org/10.1038/nmeth.2075

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1045173751

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22743774


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0803", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Computer Software", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/08", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Information and Computing Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Algorithms", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Biomedical Research", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Computational Biology", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Information Dissemination", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Internet", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Software", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Validation Studies as Topic", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "name": [
            "Institut Pasteur, Unit\u00e9 d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unit\u00e9 de Recherche Associ\u00e9e 2582, Paris, France."
          ], 
          "type": "Organization"
        }, 
        "familyName": "de Chaumont", 
        "givenName": "Fabrice", 
        "id": "sg:person.01267504411.19", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01267504411.19"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institut Pasteur, Unit\u00e9 d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unit\u00e9 de Recherche Associ\u00e9e 2582, Paris, France."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Dallongeville", 
        "givenName": "St\u00e9phane", 
        "id": "sg:person.0632416267.95", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0632416267.95"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institut Pasteur, Unit\u00e9 d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unit\u00e9 de Recherche Associ\u00e9e 2582, Paris, France."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Chenouard", 
        "givenName": "Nicolas", 
        "id": "sg:person.0700531467.43", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0700531467.43"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institut Pasteur, Unit\u00e9 d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unit\u00e9 de Recherche Associ\u00e9e 2582, Paris, France."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Herv\u00e9", 
        "givenName": "Nicolas", 
        "id": "sg:person.014327244317.82", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014327244317.82"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institut Pasteur, Unit\u00e9 d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unit\u00e9 de Recherche Associ\u00e9e 2582, Paris, France."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Pop", 
        "givenName": "Sorin", 
        "id": "sg:person.0602005606.77", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0602005606.77"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institut Pasteur, Unit\u00e9 d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unit\u00e9 de Recherche Associ\u00e9e 2582, Paris, France."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Provoost", 
        "givenName": "Thomas", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institut Pasteur, Unit\u00e9 d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unit\u00e9 de Recherche Associ\u00e9e 2582, Paris, France."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Meas-Yedid", 
        "givenName": "Vannary", 
        "id": "sg:person.01131206467.53", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01131206467.53"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institut Pasteur, Unit\u00e9 d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unit\u00e9 de Recherche Associ\u00e9e 2582, Paris, France."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Pankajakshan", 
        "givenName": "Praveen", 
        "id": "sg:person.01345065623.18", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01345065623.18"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institut Pasteur, Unit\u00e9 d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unit\u00e9 de Recherche Associ\u00e9e 2582, Paris, France."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lecomte", 
        "givenName": "Timoth\u00e9e", 
        "id": "sg:person.012356670511.87", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012356670511.87"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institut Pasteur, Unit\u00e9 d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unit\u00e9 de Recherche Associ\u00e9e 2582, Paris, France."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Le Montagner", 
        "givenName": "Yoann", 
        "id": "sg:person.016147732047.16", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016147732047.16"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institut Pasteur, Unit\u00e9 d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unit\u00e9 de Recherche Associ\u00e9e 2582, Paris, France."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lagache", 
        "givenName": "Thibault", 
        "id": "sg:person.01233673655.32", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01233673655.32"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institut Pasteur, Unit\u00e9 d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unit\u00e9 de Recherche Associ\u00e9e 2582, Paris, France."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Dufour", 
        "givenName": "Alexandre", 
        "id": "sg:person.01315312405.20", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01315312405.20"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institut Pasteur, Unit\u00e9 d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unit\u00e9 de Recherche Associ\u00e9e 2582, Paris, France."
          ], 
          "type": "Organization"
        }, 
        "familyName": "Olivo-Marin", 
        "givenName": "Jean-Christophe", 
        "id": "sg:person.0704372567.22", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0704372567.22"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1002/cyto.a.20022", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002906095"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature04752", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004343426", 
          "https://doi.org/10.1038/nature04752"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature04752", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004343426", 
          "https://doi.org/10.1038/nature04752"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature04752", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004343426", 
          "https://doi.org/10.1038/nature04752"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09634", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007203753", 
          "https://doi.org/10.1038/nature09634"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09634", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007203753", 
          "https://doi.org/10.1038/nature09634"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1523/jneurosci.2633-06.2006", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015647415"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1896", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016358112", 
          "https://doi.org/10.1038/nmeth.1896"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/iai.74.2.1407-1411.2006", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017639470"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.2047", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019871185", 
          "https://doi.org/10.1038/nmeth.2047"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1091/mbc.e08-04-0360", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023655929"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btq212", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024398834"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.2019", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026706357", 
          "https://doi.org/10.1038/nmeth.2019"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/mcse.2009.14", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027019277"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0031-3203(01)00127-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027076769"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/biot.200900030", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028213939"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/biot.200900030", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028213939"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1462-5822.2012.01752.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030873979"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth928", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032514394", 
          "https://doi.org/10.1038/nmeth928"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth928", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032514394", 
          "https://doi.org/10.1038/nmeth928"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1600-0854.2010.01075.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033263423"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1600-0854.2010.01075.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033263423"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.ppat.1000862", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039001681"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2006-7-10-r100", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040889351", 
          "https://doi.org/10.1186/gb-2006-7-10-r100"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature10836", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044347308", 
          "https://doi.org/10.1038/nature10836"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ncb1841", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049752138", 
          "https://doi.org/10.1038/ncb1841"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1924", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050297596", 
          "https://doi.org/10.1038/nmeth.1924"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/msp.2006.1628878", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1061422583"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/msp.2009.932122", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1061423266"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/tip.2005.852790", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1061641214"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/tip.2006.872323", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1061641413"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/tip.2010.2099125", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1061642722"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1109/tpami.2005.214", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1061742868"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1082602", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062447946"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2012-07", 
    "datePublishedReg": "2012-07-01", 
    "description": "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/.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/nmeth.2075", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1033763", 
        "issn": [
          "1548-7091", 
          "1548-7105"
        ], 
        "name": "Nature Methods", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "7", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "9"
      }
    ], 
    "name": "Icy: an open bioimage informatics platform for extended reproducible research", 
    "pagination": "690", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "d72d9bc5dc91f51aa98a4fe6ef53d14ee15102ef854ea07c0d67399a2cb94afb"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "22743774"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101215604"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/nmeth.2075"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1045173751"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/nmeth.2075", 
      "https://app.dimensions.ai/details/publication/pub.1045173751"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T13:57", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8660_00000436.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://www.nature.com/articles/nmeth.2075"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/nmeth.2075'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/nmeth.2075'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nmeth.2075'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nmeth.2075'


 

This table displays all metadata directly associated to this object as RDF triples.

297 TRIPLES      21 PREDICATES      64 URIs      28 LITERALS      16 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/nmeth.2075 schema:about N06dd203021fb4a2e9de3dc8b51548369
2 N80d41201e165439cab8fc86fb75363e2
3 Nae8e1b814d2a49ceaf86930daa0edab8
4 Nb93660c798954ef9b60fcaf3803143fb
5 Nceb365c353d44be0917c8e46a6c6cc7d
6 Ncedd4c038d814bb7956b5eff006f08c5
7 Nf248548137e84ad19ffaab965b0bbfff
8 anzsrc-for:08
9 anzsrc-for:0803
10 schema:author Na15ccf74ae0b493a8dabc039c57a8f6c
11 schema:citation sg:pub.10.1038/nature04752
12 sg:pub.10.1038/nature09634
13 sg:pub.10.1038/nature10836
14 sg:pub.10.1038/ncb1841
15 sg:pub.10.1038/nmeth.1896
16 sg:pub.10.1038/nmeth.1924
17 sg:pub.10.1038/nmeth.2019
18 sg:pub.10.1038/nmeth.2047
19 sg:pub.10.1038/nmeth928
20 sg:pub.10.1186/gb-2006-7-10-r100
21 https://doi.org/10.1002/biot.200900030
22 https://doi.org/10.1002/cyto.a.20022
23 https://doi.org/10.1016/s0031-3203(01)00127-3
24 https://doi.org/10.1091/mbc.e08-04-0360
25 https://doi.org/10.1093/bioinformatics/btq212
26 https://doi.org/10.1109/mcse.2009.14
27 https://doi.org/10.1109/msp.2006.1628878
28 https://doi.org/10.1109/msp.2009.932122
29 https://doi.org/10.1109/tip.2005.852790
30 https://doi.org/10.1109/tip.2006.872323
31 https://doi.org/10.1109/tip.2010.2099125
32 https://doi.org/10.1109/tpami.2005.214
33 https://doi.org/10.1111/j.1462-5822.2012.01752.x
34 https://doi.org/10.1111/j.1600-0854.2010.01075.x
35 https://doi.org/10.1126/science.1082602
36 https://doi.org/10.1128/iai.74.2.1407-1411.2006
37 https://doi.org/10.1371/journal.ppat.1000862
38 https://doi.org/10.1523/jneurosci.2633-06.2006
39 schema:datePublished 2012-07
40 schema:datePublishedReg 2012-07-01
41 schema:description 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/.
42 schema:genre research_article
43 schema:inLanguage en
44 schema:isAccessibleForFree false
45 schema:isPartOf N2868bf2580da4dfa8ea9af8c576e475b
46 N96d136cebb834d7597cd55e2bd2d2643
47 sg:journal.1033763
48 schema:name Icy: an open bioimage informatics platform for extended reproducible research
49 schema:pagination 690
50 schema:productId N3a17595be1fc4874ad80737fd95eb130
51 N71fdc1ea44514540b33398a0915be91d
52 Ndbd0548478a64d0c8305c0efdb77c2bb
53 Ne5f2382dd3384c10bc2101e5ac153734
54 Nf06505421d3345eebe5cf0e8ca56cf88
55 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045173751
56 https://doi.org/10.1038/nmeth.2075
57 schema:sdDatePublished 2019-04-10T13:57
58 schema:sdLicense https://scigraph.springernature.com/explorer/license/
59 schema:sdPublisher N14fbde8391a74c21a624917dab0f341f
60 schema:url https://www.nature.com/articles/nmeth.2075
61 sgo:license sg:explorer/license/
62 sgo:sdDataset articles
63 rdf:type schema:ScholarlyArticle
64 N06dd203021fb4a2e9de3dc8b51548369 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
65 schema:name Computational Biology
66 rdf:type schema:DefinedTerm
67 N0ddf6d9d59494643a4c436000ee5ffb5 schema:name Institut Pasteur, Unité d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, Paris, France.
68 rdf:type schema:Organization
69 N1320d89cc14c4e6da5e6e8987fa0cf80 schema:name Institut Pasteur, Unité d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, Paris, France.
70 rdf:type schema:Organization
71 N140c986472bb4998b9465e2e0bf8d4f5 rdf:first sg:person.01131206467.53
72 rdf:rest N3618cc318c3b433898705573ca8a9964
73 N14fbde8391a74c21a624917dab0f341f schema:name Springer Nature - SN SciGraph project
74 rdf:type schema:Organization
75 N2288c3ca8a5d4cc28c5a614ee093a48a schema:affiliation N6dac4985e48242099afb8ce1f1767fef
76 schema:familyName Provoost
77 schema:givenName Thomas
78 rdf:type schema:Person
79 N25ef6c5e703948e5a0e6626bef8063c7 schema:name Institut Pasteur, Unité d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, Paris, France.
80 rdf:type schema:Organization
81 N2868bf2580da4dfa8ea9af8c576e475b schema:volumeNumber 9
82 rdf:type schema:PublicationVolume
83 N2cf605b0959a4f2d9d6810a0d29e4e22 schema:name Institut Pasteur, Unité d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, Paris, France.
84 rdf:type schema:Organization
85 N3618cc318c3b433898705573ca8a9964 rdf:first sg:person.01345065623.18
86 rdf:rest Nd03196fd687e4c40b8caeba1f22c5c56
87 N3a17595be1fc4874ad80737fd95eb130 schema:name dimensions_id
88 schema:value pub.1045173751
89 rdf:type schema:PropertyValue
90 N4d0fb1981b8147f7baa7591387e1e4a0 rdf:first sg:person.0602005606.77
91 rdf:rest Need32318d02e4c1ebb1f9d81443a7e1c
92 N5ab7dd6f893241beb030c76f81a4aa98 schema:name Institut Pasteur, Unité d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, Paris, France.
93 rdf:type schema:Organization
94 N6dac4985e48242099afb8ce1f1767fef schema:name Institut Pasteur, Unité d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, Paris, France.
95 rdf:type schema:Organization
96 N70e3d5da0dcc4354b96c3c608db8a386 schema:name Institut Pasteur, Unité d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, Paris, France.
97 rdf:type schema:Organization
98 N71fdc1ea44514540b33398a0915be91d schema:name nlm_unique_id
99 schema:value 101215604
100 rdf:type schema:PropertyValue
101 N7b882047312a4f14af5fe5022fef690e schema:name Institut Pasteur, Unité d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, Paris, France.
102 rdf:type schema:Organization
103 N80d41201e165439cab8fc86fb75363e2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
104 schema:name Algorithms
105 rdf:type schema:DefinedTerm
106 N86ed2bf558ef4618be5a8e4c7a305c50 rdf:first sg:person.01315312405.20
107 rdf:rest Na03536f3908644f39dd4605ad24ee054
108 N92a5e5f7928d42798823b57546f6755b schema:name Institut Pasteur, Unité d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, Paris, France.
109 rdf:type schema:Organization
110 N96d136cebb834d7597cd55e2bd2d2643 schema:issueNumber 7
111 rdf:type schema:PublicationIssue
112 Na03536f3908644f39dd4605ad24ee054 rdf:first sg:person.0704372567.22
113 rdf:rest rdf:nil
114 Na15ccf74ae0b493a8dabc039c57a8f6c rdf:first sg:person.01267504411.19
115 rdf:rest Nca9872152ac14a78a624e70928caf708
116 Nae8e1b814d2a49ceaf86930daa0edab8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
117 schema:name Validation Studies as Topic
118 rdf:type schema:DefinedTerm
119 Nb6ab9ed3feb44fff9786bb3e41ad9d2e rdf:first sg:person.016147732047.16
120 rdf:rest Ne3fd8254d1c245fd922e5d11474207bb
121 Nb93660c798954ef9b60fcaf3803143fb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
122 schema:name Information Dissemination
123 rdf:type schema:DefinedTerm
124 Nca9872152ac14a78a624e70928caf708 rdf:first sg:person.0632416267.95
125 rdf:rest Ned5df8b0e6174a9e84219ce8e319ff05
126 Nce3ff19d98534af8b8158636245b4112 schema:name Institut Pasteur, Unité d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, Paris, France.
127 rdf:type schema:Organization
128 Nceb365c353d44be0917c8e46a6c6cc7d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
129 schema:name Biomedical Research
130 rdf:type schema:DefinedTerm
131 Ncedd4c038d814bb7956b5eff006f08c5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
132 schema:name Software
133 rdf:type schema:DefinedTerm
134 Nd03196fd687e4c40b8caeba1f22c5c56 rdf:first sg:person.012356670511.87
135 rdf:rest Nb6ab9ed3feb44fff9786bb3e41ad9d2e
136 Ndbd0548478a64d0c8305c0efdb77c2bb schema:name readcube_id
137 schema:value d72d9bc5dc91f51aa98a4fe6ef53d14ee15102ef854ea07c0d67399a2cb94afb
138 rdf:type schema:PropertyValue
139 Ndfb192bf0fda4b43a2108ab7ad6a1bbb rdf:first sg:person.014327244317.82
140 rdf:rest N4d0fb1981b8147f7baa7591387e1e4a0
141 Ne061e7719b0c41638a6652419b1e7548 schema:name Institut Pasteur, Unité d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, Paris, France.
142 rdf:type schema:Organization
143 Ne336cbdc858b4952beb0475f112e0dfa schema:name Institut Pasteur, Unité d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, Paris, France.
144 rdf:type schema:Organization
145 Ne3fd8254d1c245fd922e5d11474207bb rdf:first sg:person.01233673655.32
146 rdf:rest N86ed2bf558ef4618be5a8e4c7a305c50
147 Ne5f2382dd3384c10bc2101e5ac153734 schema:name pubmed_id
148 schema:value 22743774
149 rdf:type schema:PropertyValue
150 Ned5df8b0e6174a9e84219ce8e319ff05 rdf:first sg:person.0700531467.43
151 rdf:rest Ndfb192bf0fda4b43a2108ab7ad6a1bbb
152 Need32318d02e4c1ebb1f9d81443a7e1c rdf:first N2288c3ca8a5d4cc28c5a614ee093a48a
153 rdf:rest N140c986472bb4998b9465e2e0bf8d4f5
154 Nf06505421d3345eebe5cf0e8ca56cf88 schema:name doi
155 schema:value 10.1038/nmeth.2075
156 rdf:type schema:PropertyValue
157 Nf2151fee560f421fb4859dede71a39ab schema:name Institut Pasteur, Unité d'Analyse d'Images Quantitative, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2582, Paris, France.
158 rdf:type schema:Organization
159 Nf248548137e84ad19ffaab965b0bbfff schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
160 schema:name Internet
161 rdf:type schema:DefinedTerm
162 anzsrc-for:08 schema:inDefinedTermSet anzsrc-for:
163 schema:name Information and Computing Sciences
164 rdf:type schema:DefinedTerm
165 anzsrc-for:0803 schema:inDefinedTermSet anzsrc-for:
166 schema:name Computer Software
167 rdf:type schema:DefinedTerm
168 sg:journal.1033763 schema:issn 1548-7091
169 1548-7105
170 schema:name Nature Methods
171 rdf:type schema:Periodical
172 sg:person.01131206467.53 schema:affiliation N25ef6c5e703948e5a0e6626bef8063c7
173 schema:familyName Meas-Yedid
174 schema:givenName Vannary
175 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01131206467.53
176 rdf:type schema:Person
177 sg:person.01233673655.32 schema:affiliation Ne336cbdc858b4952beb0475f112e0dfa
178 schema:familyName Lagache
179 schema:givenName Thibault
180 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01233673655.32
181 rdf:type schema:Person
182 sg:person.012356670511.87 schema:affiliation Ne061e7719b0c41638a6652419b1e7548
183 schema:familyName Lecomte
184 schema:givenName Timothée
185 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012356670511.87
186 rdf:type schema:Person
187 sg:person.01267504411.19 schema:affiliation N5ab7dd6f893241beb030c76f81a4aa98
188 schema:familyName de Chaumont
189 schema:givenName Fabrice
190 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01267504411.19
191 rdf:type schema:Person
192 sg:person.01315312405.20 schema:affiliation N0ddf6d9d59494643a4c436000ee5ffb5
193 schema:familyName Dufour
194 schema:givenName Alexandre
195 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01315312405.20
196 rdf:type schema:Person
197 sg:person.01345065623.18 schema:affiliation N92a5e5f7928d42798823b57546f6755b
198 schema:familyName Pankajakshan
199 schema:givenName Praveen
200 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01345065623.18
201 rdf:type schema:Person
202 sg:person.014327244317.82 schema:affiliation Nce3ff19d98534af8b8158636245b4112
203 schema:familyName Hervé
204 schema:givenName Nicolas
205 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014327244317.82
206 rdf:type schema:Person
207 sg:person.016147732047.16 schema:affiliation Nf2151fee560f421fb4859dede71a39ab
208 schema:familyName Le Montagner
209 schema:givenName Yoann
210 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016147732047.16
211 rdf:type schema:Person
212 sg:person.0602005606.77 schema:affiliation N1320d89cc14c4e6da5e6e8987fa0cf80
213 schema:familyName Pop
214 schema:givenName Sorin
215 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0602005606.77
216 rdf:type schema:Person
217 sg:person.0632416267.95 schema:affiliation N70e3d5da0dcc4354b96c3c608db8a386
218 schema:familyName Dallongeville
219 schema:givenName Stéphane
220 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0632416267.95
221 rdf:type schema:Person
222 sg:person.0700531467.43 schema:affiliation N7b882047312a4f14af5fe5022fef690e
223 schema:familyName Chenouard
224 schema:givenName Nicolas
225 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0700531467.43
226 rdf:type schema:Person
227 sg:person.0704372567.22 schema:affiliation N2cf605b0959a4f2d9d6810a0d29e4e22
228 schema:familyName Olivo-Marin
229 schema:givenName Jean-Christophe
230 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0704372567.22
231 rdf:type schema:Person
232 sg:pub.10.1038/nature04752 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004343426
233 https://doi.org/10.1038/nature04752
234 rdf:type schema:CreativeWork
235 sg:pub.10.1038/nature09634 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007203753
236 https://doi.org/10.1038/nature09634
237 rdf:type schema:CreativeWork
238 sg:pub.10.1038/nature10836 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044347308
239 https://doi.org/10.1038/nature10836
240 rdf:type schema:CreativeWork
241 sg:pub.10.1038/ncb1841 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049752138
242 https://doi.org/10.1038/ncb1841
243 rdf:type schema:CreativeWork
244 sg:pub.10.1038/nmeth.1896 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016358112
245 https://doi.org/10.1038/nmeth.1896
246 rdf:type schema:CreativeWork
247 sg:pub.10.1038/nmeth.1924 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050297596
248 https://doi.org/10.1038/nmeth.1924
249 rdf:type schema:CreativeWork
250 sg:pub.10.1038/nmeth.2019 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026706357
251 https://doi.org/10.1038/nmeth.2019
252 rdf:type schema:CreativeWork
253 sg:pub.10.1038/nmeth.2047 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019871185
254 https://doi.org/10.1038/nmeth.2047
255 rdf:type schema:CreativeWork
256 sg:pub.10.1038/nmeth928 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032514394
257 https://doi.org/10.1038/nmeth928
258 rdf:type schema:CreativeWork
259 sg:pub.10.1186/gb-2006-7-10-r100 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040889351
260 https://doi.org/10.1186/gb-2006-7-10-r100
261 rdf:type schema:CreativeWork
262 https://doi.org/10.1002/biot.200900030 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028213939
263 rdf:type schema:CreativeWork
264 https://doi.org/10.1002/cyto.a.20022 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002906095
265 rdf:type schema:CreativeWork
266 https://doi.org/10.1016/s0031-3203(01)00127-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027076769
267 rdf:type schema:CreativeWork
268 https://doi.org/10.1091/mbc.e08-04-0360 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023655929
269 rdf:type schema:CreativeWork
270 https://doi.org/10.1093/bioinformatics/btq212 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024398834
271 rdf:type schema:CreativeWork
272 https://doi.org/10.1109/mcse.2009.14 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027019277
273 rdf:type schema:CreativeWork
274 https://doi.org/10.1109/msp.2006.1628878 schema:sameAs https://app.dimensions.ai/details/publication/pub.1061422583
275 rdf:type schema:CreativeWork
276 https://doi.org/10.1109/msp.2009.932122 schema:sameAs https://app.dimensions.ai/details/publication/pub.1061423266
277 rdf:type schema:CreativeWork
278 https://doi.org/10.1109/tip.2005.852790 schema:sameAs https://app.dimensions.ai/details/publication/pub.1061641214
279 rdf:type schema:CreativeWork
280 https://doi.org/10.1109/tip.2006.872323 schema:sameAs https://app.dimensions.ai/details/publication/pub.1061641413
281 rdf:type schema:CreativeWork
282 https://doi.org/10.1109/tip.2010.2099125 schema:sameAs https://app.dimensions.ai/details/publication/pub.1061642722
283 rdf:type schema:CreativeWork
284 https://doi.org/10.1109/tpami.2005.214 schema:sameAs https://app.dimensions.ai/details/publication/pub.1061742868
285 rdf:type schema:CreativeWork
286 https://doi.org/10.1111/j.1462-5822.2012.01752.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1030873979
287 rdf:type schema:CreativeWork
288 https://doi.org/10.1111/j.1600-0854.2010.01075.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1033263423
289 rdf:type schema:CreativeWork
290 https://doi.org/10.1126/science.1082602 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062447946
291 rdf:type schema:CreativeWork
292 https://doi.org/10.1128/iai.74.2.1407-1411.2006 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017639470
293 rdf:type schema:CreativeWork
294 https://doi.org/10.1371/journal.ppat.1000862 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039001681
295 rdf:type schema:CreativeWork
296 https://doi.org/10.1523/jneurosci.2633-06.2006 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015647415
297 rdf:type schema:CreativeWork
 




Preview window. Press ESC to close (or click here)


...