{"id":"https://openalex.org/W6931502437","doi":"https://doi.org/10.5281/zenodo.6800275","title":"TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics","display_name":"TIAToolbox: An End-to-End Toolbox for Advanced Tissue Image Analytics","publication_year":2022,"publication_date":"2022-07-05","ids":{"openalex":"https://openalex.org/W6931502437","doi":"https://doi.org/10.5281/zenodo.6800275"},"language":"en","primary_location":{"id":"pmh:oai:zenodo.org:6800275","is_oa":true,"landing_page_url":"https://zenodo.org/record/6800275","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/6800275","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":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7103999853134155},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.6721000075340271},{"id":"https://openalex.org/keywords/upgrade","display_name":"Upgrade","score":0.49309998750686646},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.4699999988079071},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4611999988555908},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.39320001006126404},{"id":"https://openalex.org/keywords/analytics","display_name":"Analytics","score":0.3734000027179718},{"id":"https://openalex.org/keywords/data-integrity","display_name":"Data integrity","score":0.3711000084877014},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.3594000041484833},{"id":"https://openalex.org/keywords/decoding-methods","display_name":"Decoding methods","score":0.3483999967575073},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.3449999988079071}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8111000061035156},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7103999853134155},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.6721000075340271},{"id":"https://openalex.org/C2780615140","wikidata":"https://www.wikidata.org/wiki/Q920419","display_name":"Upgrade","level":2,"score":0.49309998750686646},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.4699999988079071},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4611999988555908},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.45879998803138733},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40400001406669617},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.39320001006126404},{"id":"https://openalex.org/C79158427","wikidata":"https://www.wikidata.org/wiki/Q485396","display_name":"Analytics","level":2,"score":0.3734000027179718},{"id":"https://openalex.org/C33762810","wikidata":"https://www.wikidata.org/wiki/Q461671","display_name":"Data integrity","level":2,"score":0.3711000084877014},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.3594000041484833},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.3483999967575073},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.3449999988079071},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33250001072883606},{"id":"https://openalex.org/C88468194","wikidata":"https://www.wikidata.org/wiki/Q1172416","display_name":"Data-flow analysis","level":3,"score":0.33009999990463257},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.33000001311302185},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3255000114440918},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.32350000739097595},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.3140999972820282},{"id":"https://openalex.org/C168065819","wikidata":"https://www.wikidata.org/wiki/Q845566","display_name":"Debugging","level":2,"score":0.30300000309944153},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3028999865055084},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.29649999737739563},{"id":"https://openalex.org/C1009929","wikidata":"https://www.wikidata.org/wiki/Q179550","display_name":"Software bug","level":3,"score":0.2930000126361847},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.27880001068115234},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.2782000005245209},{"id":"https://openalex.org/C113775141","wikidata":"https://www.wikidata.org/wiki/Q428691","display_name":"Computer engineering","level":1,"score":0.2775999903678894},{"id":"https://openalex.org/C152124472","wikidata":"https://www.wikidata.org/wiki/Q1204361","display_name":"Redundancy (engineering)","level":2,"score":0.2727000117301941},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.2711000144481659},{"id":"https://openalex.org/C169590947","wikidata":"https://www.wikidata.org/wiki/Q47506","display_name":"Compiler","level":2,"score":0.26969999074935913},{"id":"https://openalex.org/C199519371","wikidata":"https://www.wikidata.org/wiki/Q942695","display_name":"Source lines of code","level":3,"score":0.262800008058548},{"id":"https://openalex.org/C103088060","wikidata":"https://www.wikidata.org/wiki/Q1062839","display_name":"Error detection and correction","level":2,"score":0.2605000138282776},{"id":"https://openalex.org/C68859911","wikidata":"https://www.wikidata.org/wiki/Q1503724","display_name":"Pattern matching","level":2,"score":0.25859999656677246},{"id":"https://openalex.org/C160191386","wikidata":"https://www.wikidata.org/wiki/Q868299","display_name":"Control flow","level":2,"score":0.2515000104904175},{"id":"https://openalex.org/C79403827","wikidata":"https://www.wikidata.org/wiki/Q3988","display_name":"Real-time computing","level":1,"score":0.25040000677108765},{"id":"https://openalex.org/C139968098","wikidata":"https://www.wikidata.org/wiki/Q3055454","display_name":"Development environment","level":2,"score":0.24969999492168427},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.24950000643730164},{"id":"https://openalex.org/C174348530","wikidata":"https://www.wikidata.org/wiki/Q188635","display_name":"Bridging (networking)","level":2,"score":0.24899999797344208},{"id":"https://openalex.org/C489000","wikidata":"https://www.wikidata.org/wiki/Q747385","display_name":"Data flow diagram","level":2,"score":0.24609999358654022},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.24570000171661377}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:zenodo.org:6800275","is_oa":true,"landing_page_url":"https://zenodo.org/record/6800275","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.6800275","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.6800275","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:6800275","is_oa":true,"landing_page_url":"https://zenodo.org/record/6800275","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Major":[0],"Updates":[1],"and":[2,52,94,103],"Feature":[3],"Improvements":[4],"Adds":[5,10,17,23,133],"support":[6,18],"for":[7,13,19,25,108,136],"Python":[8],"3.10":[9],"short":[11],"description":[12],"IDARS":[14],"algorithm":[15],"#383":[16],"NGFF":[20],"v0.4":[21],"OME-ZARR.":[22],"CLI":[24],"launching":[26],"tile":[27],"server.":[28],"Changes":[29,54],"to":[30,35,70,106,128],"API":[31],"Renames":[32],"<code>stainnorm_target()</code>":[33],"function":[34],"<code>stain_norm_target()</code>.":[36],"Removes":[37],"<code>get_wsireader</code>":[38],"Replaces":[39],"the":[40,46,67,73,82,86,139],"custom":[41],"PlattScaler":[42],"in":[43,57,63,66,81,101,151],"<code>tools/scale.py</code>":[44],"with":[45,72,85,99,116,125],"regular":[47],"Scikit-Learn":[48],"LogisticRegression.":[49],"Bug":[50],"Fixes":[51,55,91,96,114,123],"Other":[53],"bugs":[56],"UNET":[58],"architecture.":[59],"Number":[60],"of":[61],"channels":[62],"Batchnorm":[64],"argument":[65],"decoding":[68],"path":[69,121],"match":[71],"input":[74,120],"channels.":[75],"Padding":[76],"<code>0</code>":[77],"creates":[78],"feature":[79],"maps":[80],"decoder":[83],"part":[84],"same":[87],"size":[88],"as":[89],"encoder.":[90],"linter":[92],"issues":[93],"typos":[95],"incorrect":[97],"output":[98],"overlap":[100],"<code>predictor.merge_predictions()</code>":[102],"<code>return_raw=True</code>":[104],"Thanks":[105],"@paulhacosta":[107],"raising":[109],"#356,":[110],"Fixed":[111],"by":[112],"#358.":[113],"errors":[115,124],"JP2":[117],"read.":[118],"Checks":[119],"exists.":[122],"torch":[126],"upgrade":[127],"1.12.":[129],"Development":[130],"related":[131],"changes":[132],"pre-commit":[134],"hooks":[135],"consistency":[137],"across":[138],"repo.":[140],"Sets":[141],"up":[142],"GitHub":[143],"Actions":[144],"Workflow.":[145],"Travis":[146],"CI":[147],"will":[148],"be":[149],"removed":[150],"future":[152],"release.":[153]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
