{"id":"https://openalex.org/W7147281328","doi":"https://doi.org/10.48550/arxiv.2603.26811","title":"Implicit neural representations for larval zebrafish brain microscopy: a reproducible benchmark on the MapZebrain atlas","display_name":"Implicit neural representations for larval zebrafish brain microscopy: a reproducible benchmark on the MapZebrain atlas","publication_year":2026,"publication_date":"2026-03-26","ids":{"openalex":"https://openalex.org/W7147281328","doi":"https://doi.org/10.48550/arxiv.2603.26811"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2603.26811","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.26811","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":null,"license_id":null,"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.2603.26811","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5132552584","display_name":"Agnieszka Pregowska","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Pregowska, Agnieszka","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5132552584"],"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.5569000244140625,"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":0.5569000244140625,"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/T11685","display_name":"Zebrafish Biomedical Research Applications","score":0.14470000565052032,"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.06430000066757202,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/haar","display_name":"Haar","score":0.5526999831199646},{"id":"https://openalex.org/keywords/brain-atlas","display_name":"Brain atlas","score":0.5045999884605408},{"id":"https://openalex.org/keywords/fourier-transform","display_name":"Fourier transform","score":0.47049999237060547},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.44179999828338623},{"id":"https://openalex.org/keywords/atlas","display_name":"Atlas (anatomy)","score":0.40549999475479126},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.3953000009059906},{"id":"https://openalex.org/keywords/magnetoencephalography","display_name":"Magnetoencephalography","score":0.36469998955726624},{"id":"https://openalex.org/keywords/pixel","display_name":"Pixel","score":0.36399999260902405},{"id":"https://openalex.org/keywords/fourier-analysis","display_name":"Fourier analysis","score":0.35749998688697815}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6715999841690063},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5623000264167786},{"id":"https://openalex.org/C187029792","wikidata":"https://www.wikidata.org/wiki/Q2179112","display_name":"Haar","level":3,"score":0.5526999831199646},{"id":"https://openalex.org/C2780972224","wikidata":"https://www.wikidata.org/wiki/Q17047956","display_name":"Brain atlas","level":2,"score":0.5045999884605408},{"id":"https://openalex.org/C102519508","wikidata":"https://www.wikidata.org/wiki/Q6520159","display_name":"Fourier transform","level":2,"score":0.47049999237060547},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.44179999828338623},{"id":"https://openalex.org/C2776673561","wikidata":"https://www.wikidata.org/wiki/Q655357","display_name":"Atlas (anatomy)","level":2,"score":0.40549999475479126},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.39910000562667847},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.3953000009059906},{"id":"https://openalex.org/C556910895","wikidata":"https://www.wikidata.org/wiki/Q384188","display_name":"Magnetoencephalography","level":3,"score":0.36469998955726624},{"id":"https://openalex.org/C160633673","wikidata":"https://www.wikidata.org/wiki/Q355198","display_name":"Pixel","level":2,"score":0.36399999260902405},{"id":"https://openalex.org/C203024314","wikidata":"https://www.wikidata.org/wiki/Q1365258","display_name":"Fourier analysis","level":3,"score":0.35749998688697815},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.33469998836517334},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.3239000141620636},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.32330000400543213},{"id":"https://openalex.org/C2777831001","wikidata":"https://www.wikidata.org/wiki/Q1981429","display_name":"Neuropil","level":3,"score":0.3163999915122986},{"id":"https://openalex.org/C2776459999","wikidata":"https://www.wikidata.org/wiki/Q2119376","display_name":"Fidelity","level":2,"score":0.3068999946117401},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.304500013589859},{"id":"https://openalex.org/C168460219","wikidata":"https://www.wikidata.org/wiki/Q1502167","display_name":"Iterated function system","level":3,"score":0.29319998621940613},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.287200003862381},{"id":"https://openalex.org/C205372480","wikidata":"https://www.wikidata.org/wiki/Q210521","display_name":"Image resolution","level":2,"score":0.27410000562667847},{"id":"https://openalex.org/C65909025","wikidata":"https://www.wikidata.org/wiki/Q1945033","display_name":"Monocular","level":2,"score":0.26750001311302185},{"id":"https://openalex.org/C115051666","wikidata":"https://www.wikidata.org/wiki/Q6522493","display_name":"Ranging","level":2,"score":0.26190000772476196},{"id":"https://openalex.org/C75172450","wikidata":"https://www.wikidata.org/wiki/Q623950","display_name":"Fast Fourier transform","level":2,"score":0.25929999351501465},{"id":"https://openalex.org/C142575187","wikidata":"https://www.wikidata.org/wiki/Q3358290","display_name":"Pyramid (geometry)","level":2,"score":0.2565999925136566},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.25110000371932983}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2603.26811","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.26811","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2603.26811","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.26811","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Implicit":[0],"neural":[1],"representations":[2],"(INRs)":[3],"offer":[4],"continuous":[5],"coordinate-based":[6],"encodings":[7,171],"for":[8,26,47,207],"atlas":[9,77,194],"registration,":[10,195],"cross-modality":[11],"resampling,":[12],"sparse-view":[13],"completion,":[14],"and":[15,35,67,79,97,112,150,157,169,184,198],"compact":[16],"sharing":[17],"of":[18,92],"neuroanatomical":[19,175],"data.":[20],"Yet":[21],"reproducible":[22,44],"evaluation":[23],"is":[24,39,100,129],"lacking":[25],"high-resolution":[27],"larval":[28,50],"zebrafish":[29,51],"microscopy,":[30],"where":[31],"preserving":[32],"neuropil":[33],"boundaries":[34,160],"fine":[36],"neuronal":[37],"processes":[38],"critical.":[40],"We":[41],"present":[42],"a":[43,55,68,103,204],"INR":[45],"benchmark":[46],"the":[48,109,115,127,146],"MapZebrain":[49,181],"brain":[52],"atlas.":[53],"Using":[54],"unified,":[56],"seed-controlled":[57],"protocol,":[58],"we":[59],"compare":[60],"SIREN,":[61],"Fourier":[62,113,158,185],"features,":[63],"Haar":[64,111,156,183],"positional":[65],"encoding,":[66],"multi-resolution":[69],"grid":[70,128],"on":[71,120,141],"950":[72],"grayscale":[73],"microscopy":[74],"images,":[75],"including":[76],"slices":[78],"single-neuron":[80],"projections.":[81],"Images":[82],"are":[83,186],"normalized":[84],"with":[85,102],"per-image":[86],"(1,99)":[87],"percentiles":[88],"estimated":[89],"from":[90],"10%":[91],"pixels":[93],"in":[94,135,145],"non-held-out":[95],"columns,":[96],"spatial":[98],"generalization":[99],"tested":[101],"deterministic":[104],"40%":[105],"column-wise":[106],"hold-out":[107],"along":[108],"X-axis.":[110],"achieve":[114],"strongest":[116],"macro-averaged":[117],"reconstruction":[118],"fidelity":[119],"held-out":[121],"columns":[122],"(about":[123],"26":[124],"dB),":[125],"while":[126,201],"moderately":[130],"behind.":[131],"SIREN":[132,202],"performs":[133],"worse":[134],"macro":[136],"averages":[137,144],"but":[138],"remains":[139,203],"competitive":[140],"area-weighted":[142],"micro":[143],"all-in-one":[147],"regime.":[148],"SSIM":[149],"edge-focused":[151],"error":[152],"further":[153],"show":[154],"that":[155,166],"preserve":[159],"more":[161],"accurately.":[162],"These":[163],"results":[164],"indicate":[165],"explicit":[167],"spectral":[168],"multiscale":[170],"better":[172],"capture":[173],"high-frequency":[174],"detail":[176],"than":[177],"smoother-bias":[178],"alternatives.":[179],"For":[180],"workflows,":[182],"best":[187],"suited":[188],"to":[189],"boundary-sensitive":[190],"tasks":[191],"such":[192],"as":[193],"label":[196],"transfer,":[197],"morphology-preserving":[199],"sharing,":[200],"lightweight":[205],"baseline":[206],"background":[208],"modelling":[209],"or":[210],"denoising.":[211]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2026-04-02T00:00:00"}