{"id":"https://openalex.org/W4393607155","doi":"https://doi.org/10.5281/zenodo.7836864","title":"A large brain organoid dataset reveals extensive improvement potential of state-of-the-art analysis pipelines","display_name":"A large brain organoid dataset reveals extensive improvement potential of state-of-the-art analysis pipelines","publication_year":2023,"publication_date":"2023-04-17","ids":{"openalex":"https://openalex.org/W4393607155","doi":"https://doi.org/10.5281/zenodo.7836864"},"language":"en","primary_location":{"id":"pmh:oai:zenodo.org:7836864","is_oa":true,"landing_page_url":"https://zenodo.org/record/7836864","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"dataset"},"type":"dataset","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://zenodo.org/record/7836864","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010209112","display_name":"Julian Schr\u00f6ter","orcid":"https://orcid.org/0000-0003-4231-887X"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Schr\u00f6ter, Julian","raw_affiliation_strings":["University Hospital Heidelberg"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University Hospital Heidelberg","institution_ids":["https://openalex.org/I2802164966","https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053639650","display_name":"Luca Deininger","orcid":"https://orcid.org/0009-0005-5125-6422"},"institutions":[{"id":"https://openalex.org/I102335020","display_name":"Karlsruhe Institute of Technology","ror":"https://ror.org/04t3en479","country_code":"DE","type":"education","lineage":["https://openalex.org/I102335020","https://openalex.org/I1305996414"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Deininger, Luca","raw_affiliation_strings":["Karlsruhe Institute of Technology"],"raw_orcid":"https://orcid.org/0009-0005-5125-6422","affiliations":[{"raw_affiliation_string":"Karlsruhe Institute of Technology","institution_ids":["https://openalex.org/I102335020"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071465536","display_name":"Petra Richter","orcid":"https://orcid.org/0000-0003-4848-6567"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Richter, Petra","raw_affiliation_strings":["University Hospital Heidelberg"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University Hospital Heidelberg","institution_ids":["https://openalex.org/I2802164966","https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083154542","display_name":"Steffen Syrbe","orcid":"https://orcid.org/0000-0003-2543-4844"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Syrbe, Steffen","raw_affiliation_strings":["University Hospital Heidelberg"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University Hospital Heidelberg","institution_ids":["https://openalex.org/I2802164966","https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001459055","display_name":"Ralf Mikut","orcid":"https://orcid.org/0000-0001-9100-5496"},"institutions":[{"id":"https://openalex.org/I102335020","display_name":"Karlsruhe Institute of Technology","ror":"https://ror.org/04t3en479","country_code":"DE","type":"education","lineage":["https://openalex.org/I102335020","https://openalex.org/I1305996414"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Mikut, Ralf","raw_affiliation_strings":["Karlsruhe Institute of Technology"],"raw_orcid":"https://orcid.org/0000-0001-9100-5496","affiliations":[{"raw_affiliation_string":"Karlsruhe Institute of Technology","institution_ids":["https://openalex.org/I102335020"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081240384","display_name":"Sabine Jung\u2010Klawitter","orcid":"https://orcid.org/0000-0001-8851-672X"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jung-Klawitter, Sabine","raw_affiliation_strings":["University Hospital Heidelberg"],"raw_orcid":"https://orcid.org/0000-0001-8851-672X","affiliations":[{"raw_affiliation_string":"University Hospital Heidelberg","institution_ids":["https://openalex.org/I2802164966","https://openalex.org/I223822909"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13702","display_name":"Machine Learning in Healthcare","score":0.5418999791145325,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T13702","display_name":"Machine Learning in Healthcare","score":0.5418999791145325,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10241","display_name":"Functional Brain Connectivity Studies","score":0.5349000096321106,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/organoid","display_name":"Organoid","score":0.8825421929359436},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.5429908633232117},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4746675491333008},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.4542246162891388},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.2900075316429138},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18595096468925476},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.17227962613105774}],"concepts":[{"id":"https://openalex.org/C31695470","wikidata":"https://www.wikidata.org/wiki/Q11293125","display_name":"Organoid","level":2,"score":0.8825421929359436},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.5429908633232117},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4746675491333008},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.4542246162891388},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.2900075316429138},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18595096468925476},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.17227962613105774},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:zenodo.org:7836864","is_oa":true,"landing_page_url":"https://zenodo.org/record/7836864","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"dataset"},{"id":"doi:10.5281/zenodo.7836864","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.7836864","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Dataset"}],"best_oa_location":{"id":"pmh:oai:zenodo.org:7836864","is_oa":true,"landing_page_url":"https://zenodo.org/record/7836864","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"dataset"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4386439204","https://openalex.org/W3033121461","https://openalex.org/W3094248195","https://openalex.org/W3047600752","https://openalex.org/W3047590429","https://openalex.org/W4307092668","https://openalex.org/W3048825385","https://openalex.org/W2811397904","https://openalex.org/W4388777186"],"abstract_inverted_index":{"This":[0,20,32],"dataset":[1,11,21,40],"is":[2,48,102,141],"presented":[3],"in":[4,124,137],"the":[5,56,62,66,72,79,89,93,111,115,132,138,144,150,154],"paper":[6],"<em>A":[7],"large":[8],"brain":[9],"organoid":[10,67,73,82],"reveals":[12],"extensive":[13],"improvement":[14],"potential":[15],"of":[16,25,88,122],"state-of-the-art":[17],"analysis":[18],"pipelines.</em>":[19],"encompasses":[22],"two":[23],"sources":[24],"data:":[26],"A":[27,120],"comma-separated":[28],"values":[29],"(\u2018CSV\u2019)":[30],"file.":[31],"file":[33,148,152],"serves":[34],"as":[35,114],"a":[36,103],"key":[37],"to":[38],"our":[39],"with":[41,55,110],"one":[42],"image":[43,47,52,94,116,140,147],"per":[44],"row.":[45],"Each":[46],"represented":[49],"by":[50,143],"its":[51],"identifier":[53],"(\u2018img_id\u2019)":[54],"format":[57],"[img_nr]_d[imaging_day]_[clone].":[58],"For":[59,85,160],"each":[60,86],"image,":[61],"CSV":[63],"also":[64],"specifies":[65],"size":[68,74,113],"for":[69],"convenience.":[70],"Alternatively,":[71],"can":[75],"be":[76],"calculated":[77],"using":[78,165],"ground":[80],"truth":[81],"segmentation":[83,161],"(org_seg<sub>GT</sub>).":[84],"row":[87],"CSV,":[90],"we":[91],"provide":[92],"(.jpg":[95],"file)":[96],"and":[97,149,158,162],"org_seg<sub>GT</sub>":[98,101,125,151],"(.npy":[99],"file).":[100],"manually":[104],"created":[105],"binary":[106],"2D":[107],"NumPy":[108],"array":[109],"same":[112,133],"(1024":[117],"x":[118],"768).":[119],"value":[121],"1":[123],"at":[126],"position":[127,134],"(x,":[128,135],"y)":[129,136],"means":[130],"that":[131],"corresponding":[139],"covered":[142],"organoid.":[145],"The":[146],"have":[153],"following":[155],"format:":[156],"[img_id].jpg":[157],"[img_id]_org-mask.npy.":[159],"growth":[163],"monitoring":[164],"this":[166],"dataset,":[167],"please":[168],"see":[169],"https://github.com/deiluca/robust_monitoring_organoid_growth.":[170]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2025-10-10T00:00:00"}
