{"id":"https://openalex.org/W2097376308","doi":"https://doi.org/10.1093/bioinformatics/bth045","title":"SPI: a tool for incorporating gene expression data into a four-dimensional database of Caenorhabditis elegans embryogenesis","display_name":"SPI: a tool for incorporating gene expression data into a four-dimensional database of Caenorhabditis elegans embryogenesis","publication_year":2004,"publication_date":"2004-02-05","ids":{"openalex":"https://openalex.org/W2097376308","doi":"https://doi.org/10.1093/bioinformatics/bth045","mag":"2097376308","pmid":"https://pubmed.ncbi.nlm.nih.gov/14764544"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth045","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth045","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073565413","display_name":"Yohei Minakuchi","orcid":null},"institutions":[{"id":"https://openalex.org/I113198587","display_name":"National Institute of Genetics","ror":"https://ror.org/02xg1m795","country_code":"JP","type":"facility","lineage":["https://openalex.org/I113198587","https://openalex.org/I1319490839","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yohei Minakuchi","raw_affiliation_strings":["Genome Biology Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Biology Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan","institution_ids":["https://openalex.org/I113198587"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039831856","display_name":"Masahiro Ito","orcid":"https://orcid.org/0000-0001-8364-8440"},"institutions":[{"id":"https://openalex.org/I113198587","display_name":"National Institute of Genetics","ror":"https://ror.org/02xg1m795","country_code":"JP","type":"facility","lineage":["https://openalex.org/I113198587","https://openalex.org/I1319490839","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masahiro Ito","raw_affiliation_strings":["Genome Biology Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Biology Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan","institution_ids":["https://openalex.org/I113198587"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020422862","display_name":"Yuji Kohara","orcid":"https://orcid.org/0000-0002-5980-5255"},"institutions":[{"id":"https://openalex.org/I113198587","display_name":"National Institute of Genetics","ror":"https://ror.org/02xg1m795","country_code":"JP","type":"facility","lineage":["https://openalex.org/I113198587","https://openalex.org/I1319490839","https://openalex.org/I4210158934"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuji Kohara","raw_affiliation_strings":["Genome Biology Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Biology Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan","institution_ids":["https://openalex.org/I113198587"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5073565413"],"corresponding_institution_ids":["https://openalex.org/I113198587"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3985,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.48576676,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"20","issue":"7","first_page":"1097","last_page":"1109"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10676","display_name":"Genetics, Aging, and Longevity in Model Organisms","score":0.9340000152587891,"subfield":{"id":"https://openalex.org/subfields/1302","display_name":"Aging"},"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/T10676","display_name":"Genetics, Aging, and Longevity in Model Organisms","score":0.9340000152587891,"subfield":{"id":"https://openalex.org/subfields/1302","display_name":"Aging"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.012299999594688416,"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/T10364","display_name":"Reproductive Biology and Fertility","score":0.0038999998942017555,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/caenorhabditis-elegans","display_name":"Caenorhabditis elegans","score":0.8965858221054077},{"id":"https://openalex.org/keywords/embryogenesis","display_name":"Embryogenesis","score":0.5531547665596008},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5425063371658325},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5146175622940063},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4684921205043793},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4258323311805725},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.42009443044662476},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.330902636051178},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3075781464576721},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08250129222869873}],"concepts":[{"id":"https://openalex.org/C2778944004","wikidata":"https://www.wikidata.org/wiki/Q91703","display_name":"Caenorhabditis elegans","level":3,"score":0.8965858221054077},{"id":"https://openalex.org/C87073359","wikidata":"https://www.wikidata.org/wiki/Q33196","display_name":"Embryogenesis","level":3,"score":0.5531547665596008},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5425063371658325},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5146175622940063},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4684921205043793},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4258323311805725},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.42009443044662476},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.330902636051178},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3075781464576721},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08250129222869873}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005314","descriptor_name":"Embryonic and Fetal Development","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005314","descriptor_name":"Embryonic and Fetal Development","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005314","descriptor_name":"Embryonic and Fetal Development","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D007090","descriptor_name":"Image Interpretation, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007090","descriptor_name":"Image Interpretation, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007090","descriptor_name":"Image Interpretation, Computer-Assisted","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":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013347","descriptor_name":"Subcellular Fractions","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013347","descriptor_name":"Subcellular Fractions","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013347","descriptor_name":"Subcellular Fractions","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014018","descriptor_name":"Tissue Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014018","descriptor_name":"Tissue Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014018","descriptor_name":"Tissue Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017173","descriptor_name":"Caenorhabditis elegans","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018613","descriptor_name":"Microscopy, Confocal","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018613","descriptor_name":"Microscopy, Confocal","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018613","descriptor_name":"Microscopy, Confocal","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D029742","descriptor_name":"Caenorhabditis elegans Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029742","descriptor_name":"Caenorhabditis elegans Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029742","descriptor_name":"Caenorhabditis elegans Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029742","descriptor_name":"Caenorhabditis elegans Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029742","descriptor_name":"Caenorhabditis elegans Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029742","descriptor_name":"Caenorhabditis elegans Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bth045","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth045","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:14764544","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14764544","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.575.5221","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.575.5221","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/20/7/1097.full.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320338075","display_name":"Core Research for Evolutional Science and Technology","ror":"https://ror.org/00097mb19"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1623080549","https://openalex.org/W1912833571","https://openalex.org/W1926437597","https://openalex.org/W1944127002","https://openalex.org/W1989952069","https://openalex.org/W1991839252","https://openalex.org/W1999074985","https://openalex.org/W2004436791","https://openalex.org/W2039490988","https://openalex.org/W2042844848","https://openalex.org/W2064339093","https://openalex.org/W2065260586","https://openalex.org/W2066233909","https://openalex.org/W2075280003","https://openalex.org/W2077896867","https://openalex.org/W2083017809","https://openalex.org/W2087656882","https://openalex.org/W2096810446","https://openalex.org/W2099290282","https://openalex.org/W2104095591","https://openalex.org/W2107817133","https://openalex.org/W2113065005","https://openalex.org/W2118270653","https://openalex.org/W2162870748","https://openalex.org/W2170419840"],"related_works":["https://openalex.org/W4313474347","https://openalex.org/W2993659554","https://openalex.org/W4384347930","https://openalex.org/W2183871674","https://openalex.org/W390558816","https://openalex.org/W4385516583","https://openalex.org/W978202925","https://openalex.org/W2356164561","https://openalex.org/W3131791460","https://openalex.org/W3170225129"],"abstract_inverted_index":{"MOTIVATION:":[0],"A":[1],"comprehensive":[2],"gene":[3,36,84,169,221,298,306,312],"expression":[4,37,66,307],"database":[5,34,308],"is":[6,19,94,159,317],"essential":[7],"for":[8,38,150,154,167,203,255,271],"computer":[9,57],"modeling":[10],"and":[11,25,97,164,188,291,295,321],"simulation":[12],"of":[13,35,42,50,68,71,80,83,88,128,136,141,145,176,179,190,196,199,208,216,219,233,247,297],"biological":[14],"phenomena,":[15],"including":[16],"development.":[17],"Development":[18],"a":[20,32,48,69,110,122,160],"four-dimensional":[21],"(4D;":[22],"3D":[23,81],"structure":[24],"time":[26],"course)":[27],"phenomenon.":[28],"We":[29,99,260,301],"are":[30],"constructing":[31],"4D":[33,52,305],"the":[39,43,51,65,74,78,132,155,168,180,191,200,212,217,227,248,264,269,274,288,293],"early":[40],"embryogenesis":[41],"nematode":[44],"Caenorhabditis":[45],"elegans.":[46],"As":[47],"framework":[49],"database,":[53],"we":[54,62,108],"have":[55],"constructed":[56],"graphics":[58],"(CG),":[59],"into":[60],"which":[61,158],"will":[63],"incorporate":[64],"data":[67,120],"number":[70],"genes":[72],"at":[73,90,273,319],"subcellular":[75],"level.":[76],"However,":[77],"assignment":[79,215,296],"distribution":[82],"products":[85],"(protein,":[86],"mRNA),":[87],"embryos":[89,267,272],"various":[91],"developmental":[92,186,249],"stages,":[93],"both":[95],"difficult":[96],"tedious.":[98],"need":[100],"to":[101,171,240,242,257,280],"automate":[102],"this":[103,106,129],"process.":[104],"For":[105],"purpose,":[107],"developed":[109],"new":[111],"system,":[112],"named":[113],"SPI":[114],"after":[115],"superimposing":[116],"fluorescent":[117,142],"confocal":[118,143],"microscopic":[119],"onto":[121,211],"CG":[123,197,290],"framework.":[124],"RESULTS:":[125],"The":[126,223,230,245],"scheme":[127],"system":[130,286,316],"comprises":[131],"following:":[133],"(1)":[134],"acquirement":[135],"serial":[137,209],"sections":[138,210],"(40":[139],"slices)":[140],"images":[144,198],"three":[146],"colors":[147],"(4',6'-diamino-2-phenylindole":[148],"(DAPI)":[149],"nuclei,":[151],"indodicarbocyanine":[152],"(Cy-3)":[153],"internal":[156,192],"marker,":[157],"germline-specific":[161],"protein":[162],"POS-1":[163],"indocarbocyanine":[165],"(Cy-5)":[166],"product":[170,299],"be":[172],"examined);":[173],"(2)":[174],"identification":[175],"several":[177],"features":[178],"stained":[181],"embryos,":[182],"such":[183],"as":[184],"contour,":[185],"stage":[187,202,250,266],"position":[189,218],"marker;":[193],"(3)":[194],"selection":[195],"corresponding":[201],"template":[204],"matching;":[205],"(4)":[206],"superimposition":[207],"CG;":[213],"(5)":[214],"superimposed":[220],"products.":[222,313],"Snakes":[224],"algorithm":[225],"identified":[226],"embryo":[228,234],"contour.":[229],"detection":[231],"accuracy":[232,246,270],"contours":[235],"was":[236,253,277],"92.1%":[237],"when":[238],"applied":[239],"2-":[241,256],"28-cell-stage":[243],"embryos.":[244,259],"prediction":[251],"method":[252],"81.2%":[254],"8-cell-stage":[258],"manually":[261],"judged":[262],"only":[263],"later":[265,275],"because":[268],"stages":[276],"unsatisfactory":[278],"due":[279],"experimental":[281],"noise":[282],"effects.":[283],"Finally,":[284],"our":[285],"chose":[287],"optimal":[289],"performed":[292],"superposition":[294],"distribution.":[300],"established":[302],"an":[303],"initial":[304],"with":[309],"56":[310],"maternal":[311],"AVAILABILITY:":[314],"This":[315],"available":[318],"http://anti.lab.nig.ac.jp/spi/":[320],"http://anti.lab.nig.ac.jp/4ddb/":[322]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}