{"id":"https://openalex.org/W1950278426","doi":"https://doi.org/10.1093/bib/bbv093","title":"Image-based modelling of organogenesis","display_name":"Image-based modelling of organogenesis","publication_year":2015,"publication_date":"2015-10-27","ids":{"openalex":"https://openalex.org/W1950278426","doi":"https://doi.org/10.1093/bib/bbv093","mag":"1950278426","pmid":"https://pubmed.ncbi.nlm.nih.gov/26510443"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbv093","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv093","pdf_url":"https://academic.oup.com/bib/article-pdf/17/4/616/6687448/bbv093.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/17/4/616/6687448/bbv093.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000913635","display_name":"Dagmar Iber","orcid":"https://orcid.org/0000-0001-8051-1035"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I4210102611","display_name":"ICFAI Business School","ror":"https://ror.org/015v04m58","country_code":"IN","type":"education","lineage":["https://openalex.org/I4210102611"]}],"countries":["CH","IN"],"is_corresponding":false,"raw_author_name":"Dagmar Iber","raw_affiliation_strings":["Dagmar Iber studied mathematics and biochemistry in Regensburg, Cambridge and Oxford. She holds Master degrees and PhDs in both disciplines. After 3 years as a junior research fellow in St John\u2019s College, Oxford, Dagmar became a lecturer in Applied Mathematics at Imperial College London. Dagmar has joined ETH Zurich in 2008 after returning from an investment bank, where she worked as an oil option trader for 1 year. Dagmar Iber\u2019s current research mainly focuses on the spatio-temporal control of developmental processes","[ETH, Zurich]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dagmar Iber studied mathematics and biochemistry in Regensburg, Cambridge and Oxford. She holds Master degrees and PhDs in both disciplines. After 3 years as a junior research fellow in St John\u2019s College, Oxford, Dagmar became a lecturer in Applied Mathematics at Imperial College London. Dagmar has joined ETH Zurich in 2008 after returning from an investment bank, where she worked as an oil option trader for 1 year. Dagmar Iber\u2019s current research mainly focuses on the spatio-temporal control of developmental processes","institution_ids":["https://openalex.org/I4210102611"]},{"raw_affiliation_string":"[ETH, Zurich]","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066042437","display_name":"Zahra Karimaddini","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zahra Karimaddini","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5003386887","display_name":"Erkan \u00dcnal","orcid":"https://orcid.org/0000-0001-8024-7879"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Erkan \u00dcnal","raw_affiliation_strings":["Erkan \u00dcnal studied biology and biochemistry at the University of Zurich and ETH Zurich and recently completed his PhD studies on limb development at the University of Basel and ETH Zurich"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Erkan \u00dcnal studied biology and biochemistry at the University of Zurich and ETH Zurich and recently completed his PhD studies on limb development at the University of Basel and ETH Zurich","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":null,"fwci":2.6644,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.90259865,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"17","issue":"4","first_page":"616","last_page":"627"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10379","display_name":"Cellular Mechanics and Interactions","score":0.9944000244140625,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9908999800682068,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7298715114593506},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6613361835479736},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5303593277931213},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.49243149161338806},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.4625624418258667},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4505517780780792},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4392399191856384},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3903394341468811},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3548213541507721},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34783995151519775},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.2922018766403198},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.09064614772796631}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7298715114593506},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6613361835479736},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5303593277931213},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.49243149161338806},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.4625624418258667},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4505517780780792},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4392399191856384},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3903394341468811},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3548213541507721},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34783995151519775},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.2922018766403198},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.09064614772796631},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D038081","descriptor_name":"Organogenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038081","descriptor_name":"Organogenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D038081","descriptor_name":"Organogenesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbv093","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv093","pdf_url":"https://academic.oup.com/bib/article-pdf/17/4/616/6687448/bbv093.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26510443","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26510443","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:open-archive.highwire.org:bib:17/4/616","is_oa":false,"landing_page_url":"http://bib.oxfordjournals.org/cgi/content/short/17/4/616","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bib/bbv093","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv093","pdf_url":"https://academic.oup.com/bib/article-pdf/17/4/616/6687448/bbv093.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321652","display_name":"Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich","ror":"https://ror.org/05a28rw58"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W1950278426.pdf"},"referenced_works_count":88,"referenced_works":["https://openalex.org/W562590299","https://openalex.org/W595147118","https://openalex.org/W1482413706","https://openalex.org/W1487395029","https://openalex.org/W1487901126","https://openalex.org/W1509329028","https://openalex.org/W1604333309","https://openalex.org/W1608232345","https://openalex.org/W1611954649","https://openalex.org/W1667272544","https://openalex.org/W1794489744","https://openalex.org/W1921195350","https://openalex.org/W1965558704","https://openalex.org/W1969365435","https://openalex.org/W1969431187","https://openalex.org/W1970480709","https://openalex.org/W1970884399","https://openalex.org/W1973106215","https://openalex.org/W1980661496","https://openalex.org/W1985320488","https://openalex.org/W1988418842","https://openalex.org/W1992172233","https://openalex.org/W1992963104","https://openalex.org/W1998219322","https://openalex.org/W1999175626","https://openalex.org/W1999452558","https://openalex.org/W2003499095","https://openalex.org/W2005403893","https://openalex.org/W2010567868","https://openalex.org/W2012483260","https://openalex.org/W2016350172","https://openalex.org/W2018857251","https://openalex.org/W2026211608","https://openalex.org/W2031312855","https://openalex.org/W2034763647","https://openalex.org/W2038882764","https://openalex.org/W2038981297","https://openalex.org/W2039657602","https://openalex.org/W2041416094","https://openalex.org/W2041435551","https://openalex.org/W2044773914","https://openalex.org/W2045480992","https://openalex.org/W2052435388","https://openalex.org/W2061220010","https://openalex.org/W2068909410","https://openalex.org/W2073881036","https://openalex.org/W2074099368","https://openalex.org/W2086988962","https://openalex.org/W2087002642","https://openalex.org/W2091643574","https://openalex.org/W2092140523","https://openalex.org/W2101539302","https://openalex.org/W2102329898","https://openalex.org/W2113760653","https://openalex.org/W2119549820","https://openalex.org/W2120508792","https://openalex.org/W2122407134","https://openalex.org/W2122969640","https://openalex.org/W2127117631","https://openalex.org/W2128409098","https://openalex.org/W2129003022","https://openalex.org/W2133059755","https://openalex.org/W2136323920","https://openalex.org/W2136926016","https://openalex.org/W2142801207","https://openalex.org/W2143368326","https://openalex.org/W2151103961","https://openalex.org/W2153717411","https://openalex.org/W2156375169","https://openalex.org/W2156995638","https://openalex.org/W2162689493","https://openalex.org/W2165351239","https://openalex.org/W2165716533","https://openalex.org/W2166566250","https://openalex.org/W2168394646","https://openalex.org/W2416901147","https://openalex.org/W2463934001","https://openalex.org/W2478738321","https://openalex.org/W2501907080","https://openalex.org/W2505756961","https://openalex.org/W2740373864","https://openalex.org/W2963623381","https://openalex.org/W3083743358","https://openalex.org/W3100191241","https://openalex.org/W3124229194","https://openalex.org/W4211057669","https://openalex.org/W4251147723","https://openalex.org/W4251354162"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W2992516105","https://openalex.org/W4224009465","https://openalex.org/W4285299921","https://openalex.org/W4286629047","https://openalex.org/W4306321456","https://openalex.org/W4285260836","https://openalex.org/W3046775127","https://openalex.org/W4383176055"],"abstract_inverted_index":{"One":[0],"of":[1,10,40,97,112,116,122,124,135,142,148],"the":[2,8,29,59,110,114,120,129,139,146],"major":[3],"challenges":[4],"in":[5,78],"biology":[6],"concerns":[7],"integration":[9],"data":[11],"across":[12],"length":[13],"and":[14,25,65,84,92,119,145,154],"time":[15],"scales":[16],"into":[17],"a":[18,38],"consistent":[19],"framework:":[20],"how":[21,33,50,66],"do":[22],"macroscopic":[23,60],"properties":[24],"functionalities":[26],"arise":[27],"from":[28,72],"molecular":[30,52,63],"regulatory":[31],"networks-and":[32],"can":[34,70],"they":[35],"change":[36],"as":[37],"result":[39],"mutations?":[41],"Morphogenesis":[42],"provides":[43],"an":[44],"excellent":[45],"model":[46],"system":[47],"to":[48,90],"study":[49],"simple":[51],"networks":[53],"robustly":[54],"control":[55],"complex":[56],"processes":[57],"on":[58,128],"scale":[61],"despite":[62],"noise,":[64],"important":[67],"functional":[68],"variants":[69],"emerge":[71],"small":[73],"genetic":[74],"changes.":[75],"Recent":[76],"advancements":[77],"three-dimensional":[79],"imaging":[80],"technologies,":[81],"computer":[82,85],"algorithms":[83],"power":[86],"now":[87],"allow":[88],"us":[89],"develop":[91],"analyse":[93],"increasingly":[94],"realistic":[95],"models":[96,150],"biological":[98],"control.":[99],"Here,":[100],"we":[101],"present":[102],"our":[103],"pipeline":[104],"for":[105],"image-based":[106],"modelling":[107],"that":[108],"includes":[109],"segmentation":[111],"images,":[113],"determination":[115],"displacement":[117],"fields":[118],"solution":[121],"systems":[123],"partial":[125],"differential":[126],"equations":[127],"growing,":[130],"embryonic":[131],"domains.":[132],"The":[133],"development":[134],"suitable":[136],"mathematical":[137],"models,":[138],"data-based":[140],"inference":[141],"parameter":[143],"sets":[144],"evaluation":[147],"competing":[149],"are":[151,157],"still":[152],"challenging,":[153],"current":[155],"approaches":[156],"discussed.":[158]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}