{"id":"https://openalex.org/W6969192067","doi":"https://doi.org/10.5281/zenodo.6800344","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/W6969192067","doi":"https://doi.org/10.5281/zenodo.6800344"},"language":"en","primary_location":{"id":"pmh:oai:zenodo.org:6800344","is_oa":true,"landing_page_url":"https://zenodo.org/record/6800344","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/6800344","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/T10041","display_name":"COVID-19 Clinical Research Studies","score":0.04769999906420708,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10041","display_name":"COVID-19 Clinical Research Studies","score":0.04769999906420708,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"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/T11368","display_name":"Long-Term Effects of COVID-19","score":0.033900000154972076,"subfield":{"id":"https://openalex.org/subfields/2728","display_name":"Neurology"},"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/T11987","display_name":"COVID-19 Impact on Reproduction","score":0.033399999141693115,"subfield":{"id":"https://openalex.org/subfields/2729","display_name":"Obstetrics and Gynecology"},"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/nucleofection","display_name":"Nucleofection","score":0.43299999833106995},{"id":"https://openalex.org/keywords/gestational-period","display_name":"Gestational period","score":0.33309999108314514},{"id":"https://openalex.org/keywords/hyporeflexia","display_name":"Hyporeflexia","score":0.3246000111103058},{"id":"https://openalex.org/keywords/tsg101","display_name":"TSG101","score":0.31119999289512634},{"id":"https://openalex.org/keywords/proteogenomics","display_name":"Proteogenomics","score":0.3046000003814697},{"id":"https://openalex.org/keywords/diafiltration","display_name":"Diafiltration","score":0.3046000003814697},{"id":"https://openalex.org/keywords/fusible-alloy","display_name":"Fusible alloy","score":0.29319998621940613},{"id":"https://openalex.org/keywords/articular-cartilage-damage","display_name":"Articular cartilage damage","score":0.2896000146865845}],"concepts":[{"id":"https://openalex.org/C144251240","wikidata":"https://www.wikidata.org/wiki/Q7068229","display_name":"Nucleofection","level":4,"score":0.43299999833106995},{"id":"https://openalex.org/C2992336715","wikidata":"https://www.wikidata.org/wiki/Q63431143","display_name":"Gestational period","level":4,"score":0.33309999108314514},{"id":"https://openalex.org/C2777158700","wikidata":"https://www.wikidata.org/wiki/Q1419356","display_name":"Hyporeflexia","level":3,"score":0.3246000111103058},{"id":"https://openalex.org/C2778283623","wikidata":"https://www.wikidata.org/wiki/Q18032200","display_name":"TSG101","level":5,"score":0.31119999289512634},{"id":"https://openalex.org/C145741570","wikidata":"https://www.wikidata.org/wiki/Q7251534","display_name":"Proteogenomics","level":5,"score":0.3046000003814697},{"id":"https://openalex.org/C18743360","wikidata":"https://www.wikidata.org/wiki/Q1208096","display_name":"Diafiltration","level":4,"score":0.3046000003814697},{"id":"https://openalex.org/C133074676","wikidata":"https://www.wikidata.org/wiki/Q428729","display_name":"Fusible alloy","level":2,"score":0.29319998621940613},{"id":"https://openalex.org/C2781032047","wikidata":"https://www.wikidata.org/wiki/Q938793","display_name":"Articular cartilage damage","level":5,"score":0.2896000146865845},{"id":"https://openalex.org/C2777054765","wikidata":"https://www.wikidata.org/wiki/Q6402731","display_name":"Dysgeusia","level":3,"score":0.27799999713897705},{"id":"https://openalex.org/C2776356786","wikidata":"https://www.wikidata.org/wiki/Q1048573","display_name":"Tubulopathy","level":3,"score":0.2775999903678894},{"id":"https://openalex.org/C2777742743","wikidata":"https://www.wikidata.org/wiki/Q19904005","display_name":"Durvalumab","level":5,"score":0.2694000005722046},{"id":"https://openalex.org/C2778902089","wikidata":"https://www.wikidata.org/wiki/Q5608642","display_name":"Subpoena","level":2,"score":0.2669999897480011},{"id":"https://openalex.org/C135979968","wikidata":"https://www.wikidata.org/wiki/Q609809","display_name":"Protein isoform","level":5,"score":0.2669000029563904},{"id":"https://openalex.org/C2777968768","wikidata":"https://www.wikidata.org/wiki/Q1280161","display_name":"Emperipolesis","level":4,"score":0.2662999927997589},{"id":"https://openalex.org/C180938184","wikidata":"https://www.wikidata.org/wiki/Q2142270","display_name":"Liquation","level":3,"score":0.26350000500679016},{"id":"https://openalex.org/C2777738910","wikidata":"https://www.wikidata.org/wiki/Q3790542","display_name":"Sulfinpyrazone","level":3,"score":0.2547999918460846},{"id":"https://openalex.org/C104545631","wikidata":"https://www.wikidata.org/wiki/Q464858","display_name":"Demotion","level":3,"score":0.25369998812675476},{"id":"https://openalex.org/C2779627259","wikidata":"https://www.wikidata.org/wiki/Q779763","display_name":"Pretext","level":3,"score":0.2529999911785126},{"id":"https://openalex.org/C2777935831","wikidata":"https://www.wikidata.org/wiki/Q3144949","display_name":"Hemopericardium","level":3,"score":0.2522999942302704}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:zenodo.org:6800344","is_oa":true,"landing_page_url":"https://zenodo.org/record/6800344","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.6800344","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.6800344","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:6800344","is_oa":true,"landing_page_url":"https://zenodo.org/record/6800344","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":{"1.2.0":[0],"(2022-07-05)":[1],"Major":[2],"Updates":[3],"and":[4,54,96,105],"Feature":[5],"Improvements":[6],"Adds":[7,12,19,25,135],"support":[8,20],"for":[9,15,21,27,110,138],"Python":[10],"3.10":[11],"short":[13],"description":[14],"IDARS":[16],"algorithm":[17],"#383":[18],"NGFF":[22],"v0.4":[23],"OME-ZARR.":[24],"CLI":[26],"launching":[28],"tile":[29],"server.":[30],"Changes":[31,56],"to":[32,37,72,108,130],"API":[33],"Renames":[34],"<code>stainnorm_target()</code>":[35],"function":[36],"<code>stain_norm_target()</code>.":[38],"Removes":[39],"<code>get_wsireader</code>":[40],"Replaces":[41],"the":[42,48,69,75,84,88,141],"custom":[43],"PlattScaler":[44],"in":[45,59,65,68,83,103,153],"<code>tools/scale.py</code>":[46],"with":[47,74,87,101,118,127],"regular":[49],"Scikit-Learn":[50],"LogisticRegression.":[51],"Bug":[52],"Fixes":[53,57,93,98,116,125],"Other":[55],"bugs":[58],"UNET":[60],"architecture.":[61],"Number":[62],"of":[63],"channels":[64],"Batchnorm":[66],"argument":[67],"decoding":[70],"path":[71,123],"match":[73],"input":[76,122],"channels.":[77],"Padding":[78],"<code>0</code>":[79],"creates":[80],"feature":[81],"maps":[82],"decoder":[85],"part":[86],"same":[89],"size":[90],"as":[91],"encoder.":[92],"linter":[94],"issues":[95],"typos":[97],"incorrect":[99],"output":[100],"overlap":[102],"<code>predictor.merge_predictions()</code>":[104],"<code>return_raw=True</code>":[106],"Thanks":[107],"@paulhacosta":[109],"raising":[111],"#356,":[112],"Fixed":[113],"by":[114],"#358.":[115],"errors":[117,126],"JP2":[119],"read.":[120],"Checks":[121],"exists.":[124],"torch":[128],"upgrade":[129],"1.12.":[131],"Development":[132],"related":[133],"changes":[134],"pre-commit":[136],"hooks":[137],"consistency":[139],"across":[140],"repo.":[142],"Sets":[143],"up":[144],"GitHub":[145],"Actions":[146],"Workflow.":[147],"Travis":[148],"CI":[149],"will":[150],"be":[151],"removed":[152],"future":[154],"release.":[155]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
