{"id":"https://openalex.org/W4406686338","doi":"https://doi.org/10.1186/s12859-025-06039-x","title":"ClearFinder: a Python GUI for annotating cells in cleared mouse brain","display_name":"ClearFinder: a Python GUI for annotating cells in cleared mouse brain","publication_year":2025,"publication_date":"2025-01-21","ids":{"openalex":"https://openalex.org/W4406686338","doi":"https://doi.org/10.1186/s12859-025-06039-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/39838291"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06039-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06039-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06039-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06039-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068769363","display_name":"Stefan Pastore","orcid":null},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Stefan Pastore","raw_affiliation_strings":["Institute for Human Genetics, University Medical Center Johannes Gutenberg University, 55131, Mainz, Germany","Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, 55128, Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Human Genetics, University Medical Center Johannes Gutenberg University, 55131, Mainz, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]},{"raw_affiliation_string":"Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, 55128, Mainz, Germany","institution_ids":["https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030060817","display_name":"Philipp Hillenbrand","orcid":null},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Philipp Hillenbrand","raw_affiliation_strings":["Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, 55128, Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, 55128, Mainz, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5099518856","display_name":"Nils Molnar","orcid":null},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Nils Molnar","raw_affiliation_strings":["Institute for Human Genetics, University Medical Center Johannes Gutenberg University, 55131, Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Human Genetics, University Medical Center Johannes Gutenberg University, 55131, Mainz, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002785095","display_name":"Irina Kovlyagina","orcid":"https://orcid.org/0000-0003-0210-0550"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Irina Kovlyagina","raw_affiliation_strings":["Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, 55128, Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, 55128, Mainz, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002178404","display_name":"Monika Chanu Chongtham","orcid":null},"institutions":[{"id":"https://openalex.org/I4210093049","display_name":"Leibniz Institute for Resilience Research","ror":"https://ror.org/00q5t0010","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210093049"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Monika Chanu Chongtham","raw_affiliation_strings":["Leibniz Institute for Resilience Research, 55122, Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Leibniz Institute for Resilience Research, 55122, Mainz, Germany","institution_ids":["https://openalex.org/I4210093049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036910193","display_name":"Stanislav Sys","orcid":"https://orcid.org/0000-0001-5402-1542"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Stanislav Sys","raw_affiliation_strings":["Institute for Human Genetics, University Medical Center Johannes Gutenberg University, 55131, Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Human Genetics, University Medical Center Johannes Gutenberg University, 55131, Mainz, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023263973","display_name":"Beat Lutz","orcid":"https://orcid.org/0000-0002-1062-6889"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210093049","display_name":"Leibniz Institute for Resilience Research","ror":"https://ror.org/00q5t0010","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210093049"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Beat Lutz","raw_affiliation_strings":["Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, 55128, Mainz, Germany","Leibniz Institute for Resilience Research, 55122, Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, 55128, Mainz, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]},{"raw_affiliation_string":"Leibniz Institute for Resilience Research, 55122, Mainz, Germany","institution_ids":["https://openalex.org/I4210093049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023922858","display_name":"Margaryta Tevosian","orcid":"https://orcid.org/0000-0002-2225-682X"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210093049","display_name":"Leibniz Institute for Resilience Research","ror":"https://ror.org/00q5t0010","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210093049"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Margarita Tevosian","raw_affiliation_strings":["Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, 55128, Mainz, Germany. mtevosian@uni-mainz.de","Leibniz Institute for Resilience Research, 55122, Mainz, Germany. mtevosian@uni-mainz.de","Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, 55128, Mainz, Germany","Leibniz Institute for Resilience Research, 55122, Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, 55128, Mainz, Germany. mtevosian@uni-mainz.de","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]},{"raw_affiliation_string":"Leibniz Institute for Resilience Research, 55122, Mainz, Germany. mtevosian@uni-mainz.de","institution_ids":["https://openalex.org/I4210093049"]},{"raw_affiliation_string":"Institute of Physiological Chemistry, University Medical Center Johannes Gutenberg University, 55128, Mainz, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]},{"raw_affiliation_string":"Leibniz Institute for Resilience Research, 55122, Mainz, Germany","institution_ids":["https://openalex.org/I4210093049"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006364288","display_name":"Susanne Gerber","orcid":"https://orcid.org/0000-0001-9513-0729"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Susanne Gerber","raw_affiliation_strings":["Institute for Human Genetics, University Medical Center Johannes Gutenberg University, 55131, Mainz, Germany. sugerber@uni-mainz.de","Institute for Human Genetics, University Medical Center Johannes Gutenberg University, 55131, Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Human Genetics, University Medical Center Johannes Gutenberg University, 55131, Mainz, Germany. sugerber@uni-mainz.de","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]},{"raw_affiliation_string":"Institute for Human Genetics, University Medical Center Johannes Gutenberg University, 55131, Mainz, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5006364288","https://openalex.org/A5023922858"],"corresponding_institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210093049","https://openalex.org/I4210094062"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00656106,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"1","first_page":"24","last_page":"24"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9538000226020813,"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":0.9538000226020813,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.01140000019222498,"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"}},{"id":"https://openalex.org/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.007199999876320362,"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/computer-science","display_name":"Computer science","score":0.7684777975082397},{"id":"https://openalex.org/keywords/clearance","display_name":"Clearance","score":0.7605002522468567},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.731163740158081},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.681909441947937},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.6196531057357788},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5076831579208374},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4545908570289612},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.4367353618144989},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.307245135307312},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13663944602012634},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1036100685596466}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7684777975082397},{"id":"https://openalex.org/C138944611","wikidata":"https://www.wikidata.org/wiki/Q1163287","display_name":"Clearance","level":2,"score":0.7605002522468567},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.731163740158081},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.681909441947937},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.6196531057357788},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5076831579208374},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4545908570289612},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.4367353618144989},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.307245135307312},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13663944602012634},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1036100685596466},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C126894567","wikidata":"https://www.wikidata.org/wiki/Q105650","display_name":"Urology","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"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":"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":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":true},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D009474","descriptor_name":"Neurons","qualifier_ui":"Q000166","qualifier_name":"cytology","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":"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":"D014584","descriptor_name":"User-Computer Interface","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":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06039-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06039-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06039-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39838291","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39838291","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11753021","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11753021","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11753021/pdf/12859_2025_Article_6039.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:de4d87bcabbe4524b5e024f3274f129c","is_oa":true,"landing_page_url":"https://doaj.org/article/de4d87bcabbe4524b5e024f3274f129c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-13 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06039-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06039-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06039-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.550000011920929,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G8206998002","display_name":null,"funder_award_id":"INST247_1013-1 FUGG","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4406686338.pdf","grobid_xml":"https://content.openalex.org/works/W4406686338.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1935339094","https://openalex.org/W2066502238","https://openalex.org/W2085974955","https://openalex.org/W2408110716","https://openalex.org/W2465504877","https://openalex.org/W2605897695","https://openalex.org/W2621218559","https://openalex.org/W2921462375","https://openalex.org/W2969940812","https://openalex.org/W2998583117","https://openalex.org/W3006529112","https://openalex.org/W3021105102","https://openalex.org/W3165457844","https://openalex.org/W4223483385","https://openalex.org/W4229331936","https://openalex.org/W4308077167","https://openalex.org/W4318677259","https://openalex.org/W4377940119","https://openalex.org/W4395010806","https://openalex.org/W6949894457"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2000169967","https://openalex.org/W4240625990"],"abstract_inverted_index":{"BACKGROUND:":[0],"Tissue":[1],"clearing":[2],"combined":[3],"with":[4,140],"light-sheet":[5],"microscopy":[6],"is":[7],"gaining":[8],"popularity":[9],"among":[10],"neuroscientists":[11],"interested":[12],"in":[13,19,41,62,148,184],"unbiased":[14],"assessment":[15],"of":[16,25,45,99,132,187],"their":[17],"samples":[18,139],"3D":[20],"volume.":[21],"However,":[22,49],"the":[23,137,146,164],"analysis":[24,78,98,176],"such":[26,108],"data":[27,77,121],"remains":[28],"a":[29,53,81,129],"challenge.":[30],"ClearMap":[31],"and":[32,75,96,111,114,123,169,174,181],"CellFinder":[33],"are":[34],"tools":[35,51],"for":[36,93,119,135,178],"analyzing":[37],"neuronal":[38],"activity":[39],"maps":[40],"an":[42,88],"intact":[43],"volume":[44],"cleared":[46,101,188],"mouse":[47,103],"brains.":[48,104,189],"these":[50],"lack":[52],"user":[54,91],"interface,":[55],"restricting":[56],"accessibility":[57],"primarily":[58],"to":[59,71,80,162],"scientists":[60],"proficient":[61],"advanced":[63],"Python":[64],"programming.":[65],"The":[66],"application":[67],"presented":[68],"here":[69],"aims":[70],"bridge":[72],"this":[73],"gap":[74],"make":[76],"accessible":[79,157],"wider":[82],"scientific":[83],"community.":[84],"RESULTS:":[85],"We":[86],"developed":[87],"easy-to-adopt":[89],"graphical":[90],"interface":[92],"cell":[94,142,149,179],"quantification":[95],"group":[97],"whole":[100,185],"adult":[102],"Fundamental":[105],"statistical":[106],"analysis,":[107],"as":[109],"PCA":[110],"box":[112],"plots,":[113],"additional":[115],"visualization":[116],"features":[117],"allow":[118],"quick":[120],"evaluation":[122],"quality":[124,171],"checks.":[125],"Furthermore,":[126],"we":[127],"present":[128],"use":[130],"case":[131],"ClearFinder":[133],"GUI":[134],"cross-analyzing":[136],"same":[138],"two":[141],"counting":[143],"tools,":[144],"highlighting":[145],"discrepancies":[147],"detection":[150,180],"efficiency":[151],"between":[152],"them.":[153],"CONCLUSIONS:":[154],"Our":[155],"easily":[156],"tool":[158],"allows":[159],"more":[160],"researchers":[161],"implement":[163],"methodology,":[165],"troubleshoot":[166],"arising":[167],"issues,":[168],"develop":[170],"checks,":[172],"benchmarking,":[173],"standardized":[175],"pipelines":[177],"region":[182],"annotation":[183],"volumes":[186]},"counts_by_year":[],"updated_date":"2026-06-17T06:14:20.161405","created_date":"2025-10-10T00:00:00"}