{"id":"https://openalex.org/W6931532519","doi":"https://doi.org/10.5281/zenodo.7900170","title":"TIAToolbox as an end-to-end library for advanced tissue image analytics","display_name":"TIAToolbox as an end-to-end library for advanced tissue image analytics","publication_year":2023,"publication_date":"2023-05-05","ids":{"openalex":"https://openalex.org/W6931532519","doi":"https://doi.org/10.5281/zenodo.7900170"},"language":"en","primary_location":{"id":"pmh:oai:zenodo.org:7900170","is_oa":true,"landing_page_url":"https://zenodo.org/record/7900170","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},"type":"other","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://zenodo.org/record/7900170","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Pocock, Johnathan","orcid":"https://orcid.org/0000-0002-2866-981X"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Pocock, Johnathan","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Graham, Simon","orcid":"https://orcid.org/0000-0002-2214-8212"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Graham, Simon","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Vu, Quoc Dang","orcid":"https://orcid.org/0000-0003-2075-9201"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Vu, Quoc Dang","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Jahanifar, Mostafa","orcid":"https://orcid.org/0000-0001-5842-0460"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jahanifar, Mostafa","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Deshpande, Srijay","orcid":"https://orcid.org/0000-0003-3923-2944"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Deshpande, Srijay","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Hadjigeorghiou, Giorgos","orcid":"https://orcid.org/0000-0003-2734-8915"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hadjigeorghiou, Giorgos","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Shephard, Adam","orcid":"https://orcid.org/0000-0003-0969-2990"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shephard, Adam","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Bashir, Raja Muhammad Saad","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bashir, Raja Muhammad Saad","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Bilal, Mohsin","orcid":"https://orcid.org/0000-0001-8632-2729"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bilal, Mohsin","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Lu, Wenqi","orcid":"https://orcid.org/0000-0002-7838-0918"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lu, Wenqi","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Epstein, David","orcid":"https://orcid.org/0000-0001-8634-7168"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Epstein, David","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Minhas, Fayyaz","orcid":"https://orcid.org/0000-0001-9129-1189"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Minhas, Fayyaz","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":null,"display_name":"Rajpoot, Nasir M.","orcid":"https://orcid.org/0000-0002-4706-1308"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rajpoot, Nasir M.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":null,"display_name":"Raza, Shan E Ahmed","orcid":"https://orcid.org/0000-0002-1097-1738"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Raza, Shan E Ahmed","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":14,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":true,"primary_topic":{"id":"https://openalex.org/T11584","display_name":"Biochemical Analysis and Sensing Techniques","score":0.4343000054359436,"subfield":{"id":"https://openalex.org/subfields/2916","display_name":"Nutrition and Dietetics"},"field":{"id":"https://openalex.org/fields/29","display_name":"Nursing"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11584","display_name":"Biochemical Analysis and Sensing Techniques","score":0.4343000054359436,"subfield":{"id":"https://openalex.org/subfields/2916","display_name":"Nutrition and Dietetics"},"field":{"id":"https://openalex.org/fields/29","display_name":"Nursing"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11167","display_name":"Hair Growth and Disorders","score":0.08349999785423279,"subfield":{"id":"https://openalex.org/subfields/2748","display_name":"Urology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11204","display_name":"Ion Channels and Receptors","score":0.06949999928474426,"subfield":{"id":"https://openalex.org/subfields/2809","display_name":"Sensory Systems"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7505000233650208},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.5486000180244446},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.48590001463890076},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.4796000123023987},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.45339998602867126},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4025999903678894},{"id":"https://openalex.org/keywords/merge","display_name":"Merge (version control)","score":0.37400001287460327},{"id":"https://openalex.org/keywords/crawling","display_name":"Crawling","score":0.36640000343322754}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8378000259399414},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7505000233650208},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.5486000180244446},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.48590001463890076},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.4796000123023987},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.45719999074935913},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.45339998602867126},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4025999903678894},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3912000060081482},{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.37400001287460327},{"id":"https://openalex.org/C100368936","wikidata":"https://www.wikidata.org/wiki/Q1411725","display_name":"Crawling","level":2,"score":0.36640000343322754},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.36399999260902405},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3555999994277954},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.3490999937057495},{"id":"https://openalex.org/C79158427","wikidata":"https://www.wikidata.org/wiki/Q485396","display_name":"Analytics","level":2,"score":0.32269999384880066},{"id":"https://openalex.org/C42812","wikidata":"https://www.wikidata.org/wiki/Q1082910","display_name":"Partition (number theory)","level":2,"score":0.31839999556541443},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.3167000114917755},{"id":"https://openalex.org/C168065819","wikidata":"https://www.wikidata.org/wiki/Q845566","display_name":"Debugging","level":2,"score":0.3133000135421753},{"id":"https://openalex.org/C55439883","wikidata":"https://www.wikidata.org/wiki/Q360812","display_name":"Correctness","level":2,"score":0.2948000133037567},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.2786000072956085},{"id":"https://openalex.org/C160174412","wikidata":"https://www.wikidata.org/wiki/Q873806","display_name":"Thumbnail","level":3,"score":0.2782999873161316},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.2718000113964081},{"id":"https://openalex.org/C141441539","wikidata":"https://www.wikidata.org/wiki/Q1970908","display_name":"Boom","level":2,"score":0.2615000009536743},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.25949999690055847}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:zenodo.org:7900170","is_oa":true,"landing_page_url":"https://zenodo.org/record/7900170","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},{"id":"doi:10.5281/zenodo.7900170","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.7900170","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:zenodo.org:7900170","is_oa":true,"landing_page_url":"https://zenodo.org/record/7900170","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},"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":{"1.4.0":[0],"(2023-04-24)":[1],"Major":[2],"Updates":[3,152,158,174,236],"and":[4,22,54,167,187,242,251,279,310,314],"Feature":[5],"Improvements":[6],"Adds":[7,44,65,312],"Python":[8,13,26,295],"3.11":[9,14],"support":[10,28],"[experimental]":[11],"#500":[12],"is":[15],"not":[16],"fully":[17],"supported":[18],"by":[19,84,201,263],"<code>pytorch</code>":[20],"https://github.com/pytorch/pytorch/issues/86566":[21],"<code>openslide</code>":[23],"https://github.com/openslide/openslide-python/pull/188":[24],"Removes":[25,303],"3.7":[27,296],"This":[29,51],"allows":[30],"upgrading":[31],"all":[32],"the":[33,209],"dependencies":[34,290],"which":[35,291],"were":[36],"dependent":[37,293],"on":[38,164,294],"an":[39,70],"older":[40],"version":[41,240],"of":[42,57,62,92,98,205,277],"Python.":[43],"Neighbourhood":[45],"Querying":[46],"Support":[47],"To":[48],"AnnotationStore":[49],"#540":[50],"enables":[52],"easy":[53],"efficient":[55],"querying":[56],"annotations":[58],"within":[59],"a":[60,255],"neighbourhood":[61],"other":[63,182],"annotations.":[64],"<code>MultiTaskSegmentor</code>":[66],"engine":[67],"#424":[68],"Fixes":[69,94,186,190,198,203,213,215,221,247,260,265,270],"issue":[71],"with":[72,181,230,249],"stain":[73],"augmentation":[74,77],"to":[75,78,89,154,172,177,226,239,282,300],"apply":[76],"only":[79,254],"tissue":[80],"regions.":[81],"#546":[82],"contributed":[83],"@navidstuv":[85],"Filters":[86],"logger":[87],"output":[88],"stdout":[90],"instead":[91,276],"stderr.":[93],"#255":[95],"Allows":[96],"import":[97,115,125,141],"some":[99],"modules":[100],"at":[101,208],"higher":[102],"level":[103,211],"for":[104,160,162,268,307],"improved":[105],"usability":[106],"<code>WSIReader</code>":[107],"can":[108,118,134],"now":[109,119,135],"be":[110,120,136,155],"imported":[111,121,137],"as":[112,122,138,316],"<code>from":[113,123],"tiatoolbox.wsicore":[114,124],"WSIReader</code>":[116],"<code>WSIMeta</code>":[117],"WSIMeta</code>":[126],"<code>HoVerNet</code>,":[127],"<code>HoVerNetPlus</code>,":[128],"<code>IDaRS</code>,":[129],"<code>MapDe</code>,":[130],"<code>MicroNet</code>,":[131],"<code>NuClick</code>,":[132],"<code>SCCNN</code>":[133],"`from":[139],"tiatoolbox.models":[140],"HoVerNet,":[142],"HoVerNetPlus,":[143],"IDaRS,":[144],"MapDe,":[145],"MicroNet,":[146],"NuClick,":[147],"SCCNN":[148,175],"Improves":[149],"<code>PatchExtractor</code>":[150],"performance.":[151],"<code>WSIPatchDataset</code>":[153],"consistent.":[156],"#571":[157],"documentation":[159],"<code>License</code>":[161],"clarity":[163],"source":[165],"code":[166,220],"model":[168],"weights":[169],"license.":[170],"Changes":[171,189],"API":[173],"architecture":[176],"make":[178,227],"it":[179,228],"consistent":[180],"models.":[183],"#544":[184],"Bug":[185],"Other":[188],"Parsing":[191],"Missing":[192],"Omero":[193],"Version":[194],"NGFF":[195],"Metadata":[196],"#568":[197],"#535":[199],"raised":[200,262],"@benkamphaus":[202],"reading":[204],"DICOM":[206],"WSIs":[207],"correct":[210],"#564":[212],"#529":[214],"<code>scipy</code>,":[216],"<code>matplotlib</code>,":[217],"<code>scikit-image</code>":[218],"deprecated":[219],"breaking":[222,245],"changes":[223,288],"in":[224],"<code>DICOMWSIReader</code>":[225],"compatible":[229],"latest":[231],"<code>wsidicom</code>":[232],"version.":[233],"#539,":[234],"#580":[235],"<code>shapely</code>":[237],"dependency":[238],"&gt;=2.0.0":[241],"fixes":[243],"any":[244],"changes.":[246],"bug":[248],"<code>DictionaryStore.bquery</code>":[250],"<code>geometry=None</code>,":[252],"i.e.":[253],"where":[256],"predicate":[257],"given.":[258],"Partly":[259],"#532":[261],"@blaginin":[264],"local":[266],"tests":[267],"Windows/Linux":[269],"<code>flake8</code>,":[271],"<code>deepsource</code>":[272],"errors.":[273],"Uses":[274,305],"<code>logger</code>":[275],"<code>warnings</code>":[278],"<code>print</code>":[280],"statements":[281],"properly":[283],"log":[284],"runs.":[285],"Development":[286],"related":[287],"Upgrades":[289],"are":[292],"Moves":[297],"<code>requirements*.txt</code>":[298],"files":[299],"<code>requirements</code>":[301],"folder":[302],"<code>tox</code>":[304],"<code>pyproject.toml</code>":[306],"<code>bdist_wheel</code>,":[308],"<code>pytest</code>":[309],"<code>isort</code>":[311],"<code>joblib</code>":[313],"<code>numba</code>":[315],"dependencies.":[317]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
