{"id":"https://openalex.org/W7161269676","doi":"https://doi.org/10.48550/arxiv.2605.15093","title":"CoralLite: \u03bcCT Reconstruction of Coral Colonies from Individual Corallites","display_name":"CoralLite: \u03bcCT Reconstruction of Coral Colonies from Individual Corallites","publication_year":2026,"publication_date":"2026-05-14","ids":{"openalex":"https://openalex.org/W7161269676","doi":"https://doi.org/10.48550/arxiv.2605.15093"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2605.15093","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.15093","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2605.15093","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5136193317","display_name":"Jess Jones","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jones, Jess","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064924295","display_name":"Leonardo Bertini","orcid":"https://orcid.org/0000-0003-3920-4476"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bertini, Leonardo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128098833","display_name":"Kenneth Johnson","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Johnson, Kenneth","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5136273617","display_name":"Erica Hendy","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hendy, Erica","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5052504255","display_name":"Tilo Burghardt","orcid":"https://orcid.org/0000-0002-8506-012X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Burghardt, Tilo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"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/T10341","display_name":"Coral and Marine Ecosystems Studies","score":0.4887000024318695,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10341","display_name":"Coral and Marine Ecosystems Studies","score":0.4887000024318695,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11278","display_name":"Calcium Carbonate Crystallization and Inhibition","score":0.05640000104904175,"subfield":{"id":"https://openalex.org/subfields/2502","display_name":"Biomaterials"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11643","display_name":"Building materials and conservation","score":0.05559999868273735,"subfield":{"id":"https://openalex.org/subfields/1904","display_name":"Earth-Surface Processes"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/coral","display_name":"Coral","score":0.3880999982357025},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.374099999666214},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.37229999899864197},{"id":"https://openalex.org/keywords/surface","display_name":"Surface (topology)","score":0.367000013589859},{"id":"https://openalex.org/keywords/skeleton","display_name":"Skeleton (computer programming)","score":0.3571000099182129},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.3037000000476837},{"id":"https://openalex.org/keywords/projection","display_name":"Projection (relational algebra)","score":0.29919999837875366}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4659000039100647},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45730000734329224},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.4309000074863434},{"id":"https://openalex.org/C143020374","wikidata":"https://www.wikidata.org/wiki/Q2411228","display_name":"Coral","level":2,"score":0.3880999982357025},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.374099999666214},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.37229999899864197},{"id":"https://openalex.org/C2776799497","wikidata":"https://www.wikidata.org/wiki/Q484298","display_name":"Surface (topology)","level":2,"score":0.367000013589859},{"id":"https://openalex.org/C18969341","wikidata":"https://www.wikidata.org/wiki/Q1169129","display_name":"Skeleton (computer programming)","level":2,"score":0.3571000099182129},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.3492000102996826},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34790000319480896},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.3037000000476837},{"id":"https://openalex.org/C57493831","wikidata":"https://www.wikidata.org/wiki/Q3134666","display_name":"Projection (relational algebra)","level":2,"score":0.29919999837875366},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.29750001430511475},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.290800005197525},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.2883000075817108},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.2809999883174896},{"id":"https://openalex.org/C544519230","wikidata":"https://www.wikidata.org/wiki/Q32566","display_name":"Computed tomography","level":2,"score":0.2711000144481659},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.25780001282691956},{"id":"https://openalex.org/C22029948","wikidata":"https://www.wikidata.org/wiki/Q45089","display_name":"Dice","level":2,"score":0.2506999969482422}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2605.15093","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.15093","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2605.15093","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.15093","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[{"score":0.6776151657104492,"id":"https://metadata.un.org/sdg/14","display_name":"Life below water"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"The":[0,152],"life":[1],"history":[2],"of":[3,13,28,50,65,95,119,148,177,192,243,261],"an":[4,90,100],"individual":[5,237],"coral":[6,18,244],"is":[7,43,154],"archived":[8],"within":[9],"the":[10,14,61,69,79,178,181,195,225],"accreting":[11],"skeleton":[12],"colony.":[15],"While":[16],"reef-forming":[17],"colonies":[19],"(e.g.":[20],"massive":[21],"$\\textit{Porites}$":[22,149],"sp.)":[23],"may":[24],"live":[25],"for":[26,71,117,122,224,253],"hundreds":[27],"years":[29],"and":[30,38,63,68,99,133,160,198,201,219,249,271,275],"deposit":[31],"calcareous":[32,97],"structures":[33],"many":[34],"metres":[35],"in":[36,135,217],"height":[37],"width,":[39],"their":[40],"living":[41],"tissue":[42],"a":[44,56,137,207,251],"thin":[45],"outer":[46],"surface":[47],"layer":[48],"comprised":[49],"asexually-dividing":[51],"polyps":[52],"that":[53,228],"only":[54],"survive":[55],"few":[57],"years.":[58],"To":[59],"understand":[60],"rate":[62],"timing":[64],"polyp":[66],"division":[67],"consequences":[70],"colony":[72,127,197],"skeletal":[73,80],"growth,":[74],"scientists":[75],"need":[76],"to":[77,126,142],"track":[78],"corallite":[81,103,124,171,238],"deposited":[82],"around":[83],"each":[84,123],"polyp.":[85],"Here":[86],"we":[87,131,256],"propose":[88,132],"CoralLite,":[89],"annotated":[91,158,165],"$\u03bc$CT":[92,145,241,263],"scan":[93],"dataset":[94,260],"entire":[96],"skeletons":[98,245],"associated,":[101],"first":[102,226],"deep":[104],"learning":[105,231],"reconstruction":[106],"baseline.":[107],"CoralLite":[108],"combines":[109],"fully":[110,164],"quantified":[111],"volumetric":[112],"segmentations":[113],"with":[114,168,278],"cross-slice":[115],"linking":[116],"visualisations":[118],"3D":[120,236],"models":[121],"up":[125],"scale.":[128],"For":[129,247],"segmentation,":[130],"evaluate":[134],"detail":[136],"hybrid":[138],"V-Trans-UNet":[139],"architecture":[140],"applicable":[141],"segmenting":[143],"tiled":[144],"virtual":[146],"slabs":[147],"sp.":[150],"colonies.":[151],"model":[153,183],"pre-trained":[155],"on":[156,194,206],"weakly":[157],"data":[159],"topology-aware":[161],"fine-tuned":[162],"using":[163],"slice":[166,269],"sections":[167],"8k+":[169],"manual":[170],"region":[172],"annotations.":[173],"On":[174],"unseen":[175],"slices":[176],"same":[179,196],"colony,":[180],"resulting":[182],"reaches":[184],"0.94":[185],"topological":[186],"accuracy":[187],"at":[188],"mean":[189,203],"Dice":[190,204],"scores":[191,205],"0.77":[193],"projection":[199],"axis,":[200],"0.63":[202],"different,":[208],"biologically":[209],"unrelated":[210],"specimen.":[211],"Whilst":[212],"our":[213,221,258],"experiments":[214],"are":[215],"limited":[216],"scale":[218],"context,":[220],"results":[222],"show":[223],"time":[227],"visual":[229],"machine":[230],"can":[232],"effectively":[233],"support":[234],"full":[235,259,268],"modelling":[239],"from":[240],"scans":[242],"alone.":[246],"reproducibility":[248],"as":[250],"baseline":[252],"future":[254],"research":[255],"publish":[257],"697":[262],"slices,":[264],"37":[265],"partial":[266],"or":[267],"annotations,":[270],"all":[272],"network":[273],"weights":[274],"source":[276],"code":[277],"this":[279],"paper.":[280]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2026-05-16T00:00:00"}
