{"id":"https://openalex.org/W4392516129","doi":"https://doi.org/10.1093/bioinformatics/btae133","title":"pyM2aia: Python interface for mass spectrometry imaging with focus on deep learning","display_name":"pyM2aia: Python interface for mass spectrometry imaging with focus on deep learning","publication_year":2024,"publication_date":"2024-03-01","ids":{"openalex":"https://openalex.org/W4392516129","doi":"https://doi.org/10.1093/bioinformatics/btae133","pmid":"https://pubmed.ncbi.nlm.nih.gov/38445753"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae133","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae133","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae133/56874497/btae133.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae133/56874497/btae133.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031276133","display_name":"Jonas Cordes","orcid":"https://orcid.org/0000-0003-3148-4282"},"institutions":[{"id":"https://openalex.org/I112756935","display_name":"Technische Hochschule Mannheim","ror":"https://ror.org/04p61dj41","country_code":"DE","type":"education","lineage":["https://openalex.org/I112756935"]},{"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"]},{"id":"https://openalex.org/I4210156450","display_name":"University Medical Centre Mannheim","ror":"https://ror.org/05sxbyd35","country_code":"DE","type":"funder","lineage":["https://openalex.org/I4210156450"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Jonas Cordes","raw_affiliation_strings":["Faculty of Computer Science, Mannheim University of Applied Sciences , Mannheim 68163, Germany","Medical Faculty Mannheim, Heidelberg University , Mannheim 68167, Germany"],"raw_orcid":"https://orcid.org/0000-0003-3148-4282","affiliations":[{"raw_affiliation_string":"Faculty of Computer Science, Mannheim University of Applied Sciences , Mannheim 68163, Germany","institution_ids":["https://openalex.org/I112756935"]},{"raw_affiliation_string":"Medical Faculty Mannheim, Heidelberg University , Mannheim 68167, Germany","institution_ids":["https://openalex.org/I4210156450","https://openalex.org/I223822909","https://openalex.org/I2802164966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037312886","display_name":"Thomas Enzlein","orcid":"https://orcid.org/0000-0003-1789-4090"},"institutions":[{"id":"https://openalex.org/I112756935","display_name":"Technische Hochschule Mannheim","ror":"https://ror.org/04p61dj41","country_code":"DE","type":"education","lineage":["https://openalex.org/I112756935"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Thomas Enzlein","raw_affiliation_strings":["Center for Mass Spectrometry and Optical Spectroscopy, Mannheim University of Applied Sciences , Mannheim 68163, Germany"],"raw_orcid":"https://orcid.org/0000-0003-1789-4090","affiliations":[{"raw_affiliation_string":"Center for Mass Spectrometry and Optical Spectroscopy, Mannheim University of Applied Sciences , Mannheim 68163, Germany","institution_ids":["https://openalex.org/I112756935"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062905648","display_name":"Carsten Hopf","orcid":"https://orcid.org/0000-0003-0802-6451"},"institutions":[{"id":"https://openalex.org/I112756935","display_name":"Technische Hochschule Mannheim","ror":"https://ror.org/04p61dj41","country_code":"DE","type":"education","lineage":["https://openalex.org/I112756935"]},{"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"]},{"id":"https://openalex.org/I4210156450","display_name":"University Medical Centre Mannheim","ror":"https://ror.org/05sxbyd35","country_code":"DE","type":"funder","lineage":["https://openalex.org/I4210156450"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Carsten Hopf","raw_affiliation_strings":["Center for Mass Spectrometry and Optical Spectroscopy, Mannheim University of Applied Sciences , Mannheim 68163, Germany","Medical Faculty Mannheim, Heidelberg University , Mannheim 68167, Germany","Medical Faculty, Heidelberg University , Heidelberg 69120, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Mass Spectrometry and Optical Spectroscopy, Mannheim University of Applied Sciences , Mannheim 68163, Germany","institution_ids":["https://openalex.org/I112756935"]},{"raw_affiliation_string":"Medical Faculty Mannheim, Heidelberg University , Mannheim 68167, Germany","institution_ids":["https://openalex.org/I4210156450","https://openalex.org/I223822909","https://openalex.org/I2802164966"]},{"raw_affiliation_string":"Medical Faculty, Heidelberg University , Heidelberg 69120, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029228546","display_name":"Ivo Wolf","orcid":"https://orcid.org/0000-0002-6519-6484"},"institutions":[{"id":"https://openalex.org/I112756935","display_name":"Technische Hochschule Mannheim","ror":"https://ror.org/04p61dj41","country_code":"DE","type":"education","lineage":["https://openalex.org/I112756935"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ivo Wolf","raw_affiliation_strings":["Faculty of Computer Science, Mannheim University of Applied Sciences , Mannheim 68163, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer Science, Mannheim University of Applied Sciences , Mannheim 68163, Germany","institution_ids":["https://openalex.org/I112756935"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5031276133"],"corresponding_institution_ids":["https://openalex.org/I112756935","https://openalex.org/I223822909","https://openalex.org/I2802164966","https://openalex.org/I4210156450"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.6815,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.81599764,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"40","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.8865000009536743,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.8865000009536743,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.043699998408555984,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.018699999898672104,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.9191584587097168},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8310561180114746},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.6720997095108032},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.509650468826294},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.4608542323112488},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.42510920763015747},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36524417996406555},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.23247703909873962}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9191584587097168},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8310561180114746},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.6720997095108032},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.509650468826294},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.4608542323112488},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.42510920763015747},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36524417996406555},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.23247703909873962}],"mesh":[{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071253","descriptor_name":"Metadata","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","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":"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":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae133","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae133","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae133/56874497/btae133.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38445753","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38445753","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:pubmedcentral.nih.gov:10948279","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10948279","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10948279/pdf/btae133.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae133","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae133","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae133/56874497/btae133.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.7300000190734863,"display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G4141865022","display_name":null,"funder_award_id":"13FH8I08IA","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4392516129.pdf","grobid_xml":"https://content.openalex.org/works/W4392516129.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W3017343831","https://openalex.org/W3126670745","https://openalex.org/W3173619885","https://openalex.org/W3185152944","https://openalex.org/W3199720170","https://openalex.org/W3215837549"],"related_works":["https://openalex.org/W2392768766","https://openalex.org/W2058118494","https://openalex.org/W2382021449","https://openalex.org/W2095118173","https://openalex.org/W2341492732","https://openalex.org/W2104269053","https://openalex.org/W2106424170","https://openalex.org/W3187193180","https://openalex.org/W2207495067","https://openalex.org/W1906486629"],"abstract_inverted_index":{"SUMMARY:":[0],"Python":[1,13,32,150],"is":[2],"the":[3,74,92,112],"most":[4],"commonly":[5],"used":[6],"language":[7],"for":[8,15,24,34,48,63,104,133],"deep":[9],"learning":[10],"(DL).":[11],"Existing":[12],"packages":[14],"mass":[16],"spectrometry":[17],"imaging":[18],"(MSI)":[19],"data":[20,36,68,80,88,107],"are":[21,155],"not":[22],"optimized":[23],"DL":[25,49,98,128],"tasks.":[26],"We,":[27],"therefore,":[28],"introduce":[29],"pyM2aia,":[30],"a":[31,39],"package":[33,113],"MSI":[35,67,106],"analysis":[37],"with":[38],"focus":[40],"on":[41],"memory-efficient":[42],"handling,":[43],"processing":[44,83],"and":[45,65,77,82,90,96,131,138,143,153],"convenient":[46],"data-access":[47],"applications.":[50],"pyM2aia":[51,72],"provides":[52],"interfaces":[53],"to":[54],"its":[55],"parent":[56],"application":[57],"M2aia,":[58,86],"which":[59],"offers":[60],"interactive":[61],"capabilities":[62],"exploring":[64],"annotating":[66],"in":[69,114,126],"imzML":[70,118],"format.":[71],"utilizes":[73],"image":[75],"input":[76],"output":[78],"routines,":[79],"formats,":[81],"functions":[84],"of":[85,94],"ensures":[87],"interchangeability,":[89],"enables":[91],"writing":[93],"readable":[95],"easy-to-maintain":[97],"pipelines":[99],"by":[100],"providing":[101],"batch":[102],"generators":[103],"typical":[105],"access":[108],"strategies.":[109],"We":[110],"showcase":[111],"several":[115],"examples,":[116],"including":[117],"metadata":[119],"parsing,":[120],"signal":[121],"processing,":[122],"ion-image":[123],"generation,":[124],"and,":[125],"particular,":[127],"model":[129],"training":[130],"inference":[132],"spectrum-wise":[134],"approaches,":[135,137],"ion-image-based":[136],"approaches":[139],"that":[140],"use":[141],"spectral":[142],"spatial":[144],"information":[145],"simultaneously.":[146],"AVAILABILITY":[147],"AND":[148],"IMPLEMENTATION:":[149],"package,":[151],"code":[152],"examples":[154],"available":[156],"at":[157],"(https://m2aia.github.io/m2aia).":[158]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":2}],"updated_date":"2026-06-19T17:40:00.097472","created_date":"2025-10-10T00:00:00"}
