{"status":"OK","data":{"id":296598,"identifier":"QI135J","persistentUrl":"https://doi.org/10.34894/QI135J","protocol":"doi","authority":"10.34894","separator":"/","publisher":"DataverseNL","publicationDate":"2022-05-04","storageIdentifier":"surf://10.34894/QI135J","effectiveDatasetFileCountLimit":10000,"datasetFileUploadsAvailable":9996,"datasetType":"dataset","locks":[],"latestVersion":{"id":23573,"datasetId":296598,"datasetPersistentId":"doi:10.34894/QI135J","datasetType":"dataset","storageIdentifier":"surf://10.34894/QI135J","versionNumber":2,"internalVersionNumber":14,"versionMinorNumber":0,"versionState":"RELEASED","latestVersionPublishingState":"DRAFT","deaccessionLink":"","lastUpdateTime":"2022-10-19T13:13:03Z","releaseTime":"2022-10-19T13:13:03Z","createTime":"2022-08-09T21:43:29Z","publicationDate":"2022-05-04","citationDate":"2022-05-04","effectiveDatasetFileCountLimit":10000,"datasetFileUploadsAvailable":9996,"termsOfUse":"The standard Data Sharing Agreement (DSA) of the UMC Utrecht must be signed without adjustments. 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","fileAccessRequest":false,"metadataBlocks":{"citation":{"displayName":"Citation Metadata","name":"citation","fields":[{"typeName":"title","multiple":false,"typeClass":"primitive","value":"ExpressScan: histological whole-slide image data from the Athero-Express (AE) and Aneurysm-Express (AAA) Biobank Studies"},{"typeName":"author","multiple":true,"typeClass":"compound","value":[{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Sander W. van der Laan"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0001-6888-1404"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Gerard Pasterkamp"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Gert Jan de Borst"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Dominique P.V. de Kleijn"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0003-2714-2140"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Joost A. van Herwaarden"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0003-1165-5179"}}]},{"typeName":"datasetContact","multiple":true,"typeClass":"compound","value":[{"datasetContactName":{"typeName":"datasetContactName","multiple":false,"typeClass":"primitive","value":"dLAB Data Management"},"datasetContactAffiliation":{"typeName":"datasetContactAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"}},{"datasetContactName":{"typeName":"datasetContactName","multiple":false,"typeClass":"primitive","value":"Sander W. van der Laan"},"datasetContactAffiliation":{"typeName":"datasetContactAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"}}]},{"typeName":"dsDescription","multiple":true,"typeClass":"compound","value":[{"dsDescriptionValue":{"typeName":"dsDescriptionValue","multiple":false,"typeClass":"primitive","value":"<b>Background</b></br>\nThe <b>ExpressScan</b> is an ongoing, unfunded project to scan pathological slides of atherosclerotic plaques and aneurysm tissues at high-resolution using pathology scanners into whole-slide images (WSI). Here we describe these histological WSI data available for the <a href=\"https://doi.org/10.34894/4IKE3T\" target=\"_blank\">Athero-Express (AE)</a> and <a href=\"https://doi.org/10.34894/AUUSS2\" target=\"_blank\">Aneurysm-Express (AAA) Biobank</a> Studies.  </br></br>\n\nThe AE started in 2002 and now includes over 3,500 patients who underwent surgery to remove atherosclerotic plaques (endarterectomy) from one (or more) of their major arteries (majority carotids and femorals). The AAA started in 2003 and now includes over 1,000 patients who underwent open surgery on arterial aneurysms, the majority on aortic aneurysms. The staining protocols are described by <a href=\"https://pubmed.ncbi.nlm.nih.gov/15678794/\" target=\"_blank\">Verhoeven <em>et al.</em> (AE)</a> and <a href=\"https://pubmed.ncbi.nlm.nih.gov/20720431/\" target=\"_blank\">Hurks <em>et al.</em> (AAA)</a>.</br></br>\n\nWhole-slide images are available for the several commonly used stains, but note that these are <em>not</em> available in <em>all</em> samples in <em>both</em> studies. A table showing the <em>approximate</em> numbers of available WSI is <a href=\"https://docs.google.com/spreadsheets/d/1dY0m6ErAlq7SfLi9rvWlD4BDIgaaj4Uzvp5C6k7WcCA/edit?usp=sharing\" target=\"_blank\">given here</a>.</br></br>\n\n<b>slideToolKit</b></br>\nThese data are also used for <a href=\"https://pubmed.ncbi.nlm.nih.gov/25372389/\" target=\"_blank\"><b>slideToolKit</b></a> and other <b>ExpressScan</b> projects (see below). Depending on the content of the project, a list of slides used is available to enable reproducible science. </br></br>\n\n<em>Associated <b>ExpressScan</b> projects</em></br>\n- Glycophorin C: <a href=\"https://doi.org/10.1101/2021.07.15.21260570\" target=\"_blank\">Mekke JM <em>et al.</em></a> and <a href=\"https://github.com/CirculatoryHealth/ExpressScan_Glycophorin\" target=\"_blank\">the associated GitHub repository.</a></br>\n- <a href=\"https://github.com/swvanderlaan/slideEMask\" target=\"_blank\">slideEMask</a>: entropy based tissue masker</a></br>\n- slideNormalize: normalize WSI<a href=\"https://github.com/swvanderlaan/slideNormalize\" target=\"_blank\">https://github.com/swvanderlaan/slideNormalize</a></br>\n- <a href=\"https://github.com/CirculatoryHealth/ExpressScan-Unlock\" target=\"_blank\">ExpressScan-Unlock</a>: local, on-campus webportal to inspect WSI (private, ongoing and unpublished)</br>\n- <a href=\"https://github.com/CirculatoryHealth/ExpressScan_QC\" target=\"_blank\">ExpressScan_QC</a>: quality control procedures to process results from <b>slideToolKit</b> (private, ongoing and unpublished)</br>\n- <a href=\"https://github.com/CirculatoryHealth/EntropyMasker\" target=\"_blank\">EntropyMasker</a>: improved method to automatically mask WSI using entropy (private, ongoing and unpublished)</br>\n- CONVOCALS: a deep-learning classification project on plaques (private, ongoing and unpublished)</br>\n- DEEP-ENIGMA: a deep-learning image-segmentation project on plaques (private, ongoing and unpublished)</br></br>\n\nA link to the public GitHub repository for <strong>slideToolKit</strong> can be found here: <a href=\"https://github.com/swvanderlaan/slideToolKit\" target=\"_blank\">https://github.com/swvanderlaan/slideToolKit</a>.</br></br>\n\n<b>Important notice on availability of data</b></br>\nThe amount of data is huge: over 25,000 WSI on average 1Gb size per WSI. There are also restrictions on use by commercial parties, and on sharing openly based on (inter)national laws and regulations and the written informed consent. Therefore these data (and additional clinical data) are only available upon discussion and signing a Data Sharing Agreement (see Terms of Access) and within a specially designed UMC Utrecht provided environment.</br></br>"},"dsDescriptionDate":{"typeName":"dsDescriptionDate","multiple":false,"typeClass":"primitive","value":"2022-05-04"}}]},{"typeName":"subject","multiple":true,"typeClass":"controlledVocabulary","value":["Medicine, Health and Life Sciences"]},{"typeName":"keyword","multiple":true,"typeClass":"compound","value":[{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"Histology"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"Atherosclerosis"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"Plaque"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"Carotid"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"Whole-slide images"}}]},{"typeName":"depositor","multiple":false,"typeClass":"primitive","value":"van der Laan, Sander W."},{"typeName":"dateOfDeposit","multiple":false,"typeClass":"primitive","value":"2022-05-04"}]},"dansDataVaultMetadata":{"displayName":"Data Vault Metadata","name":"dansDataVaultMetadata","fields":[{"typeName":"dansDataversePid","multiple":false,"typeClass":"primitive","value":"doi:10.34894/QI135J"},{"typeName":"dansDataversePidVersion","multiple":false,"typeClass":"primitive","value":"2.0"},{"typeName":"dansBagId","multiple":false,"typeClass":"primitive","value":"urn:uuid:972f311f-f405-4b58-bf48-55ff94a32e11"},{"typeName":"dansNbn","multiple":false,"typeClass":"primitive","value":"urn:nbn:nl:ui:13-5a303350-5cd8-4936-abb0-2d96ef031a1e"}]}},"files":[{"description":"METC Approval of the Athero-Express Biobank Study","label":"20020410_Approval_Protocol_TME_Athero-Express_Biobank_Study.pdf","restricted":true,"version":2,"datasetVersionId":23573,"dataFile":{"id":296599,"persistentId":"","filename":"20020410_Approval_Protocol_TME_Athero-Express_Biobank_Study.pdf","contentType":"application/pdf","friendlyType":"Adobe PDF","filesize":61663,"description":"METC Approval of the Athero-Express Biobank Study","storageIdentifier":"surf://store:1808ea1cc7e-8096a9040a1e","rootDataFileId":-1,"checksum":{"type":"SHA-1","value":"7af1184782ed6d4c33f554077390c88f0ab184b4"},"tabularData":false,"creationDate":"2022-05-04","publicationDate":"2022-05-04","lastUpdateTime":"2022-10-19T13:13:03Z","fileAccessRequest":false}},{"description":"DMP of the Athero-Express Biobank Study","label":"20211007_DMP_Athero-Express_Biobank_Study.pdf","restricted":true,"version":2,"datasetVersionId":23573,"dataFile":{"id":296600,"persistentId":"","filename":"20211007_DMP_Athero-Express_Biobank_Study.pdf","contentType":"application/pdf","friendlyType":"Adobe PDF","filesize":64158,"description":"DMP of the Athero-Express Biobank Study","storageIdentifier":"surf://store:1808ea1d005-7fb53c42e7b2","rootDataFileId":-1,"checksum":{"type":"SHA-1","value":"a733a0cddb4a49961748170591890e5aa47494d1"},"tabularData":false,"creationDate":"2022-05-04","publicationDate":"2022-05-04","lastUpdateTime":"2022-10-19T13:13:03Z","fileAccessRequest":false}},{"description":"Example Informed Consent of the Athero-Express Biobank Study","label":"Athero-Express_Biobank_Study_IC_versie_4.doc","restricted":true,"version":2,"datasetVersionId":23573,"dataFile":{"id":296601,"persistentId":"","filename":"Athero-Express_Biobank_Study_IC_versie_4.doc","contentType":"application/msword","friendlyType":"MS Word","filesize":34816,"description":"Example Informed Consent of the Athero-Express Biobank Study","storageIdentifier":"surf://store:1808ea1ce17-b05110f0c3fc","rootDataFileId":-1,"checksum":{"type":"SHA-1","value":"40b3106353e85b47a9d1185093e95d91bceea03b"},"tabularData":false,"creationDate":"2022-05-04","publicationDate":"2022-05-04","lastUpdateTime":"2022-10-19T13:13:03Z","fileAccessRequest":false}},{"label":"README.txt","restricted":false,"version":1,"datasetVersionId":23573,"dataFile":{"id":314856,"persistentId":"","filename":"README.txt","contentType":"text/plain","friendlyType":"Plain Text","filesize":2904,"storageIdentifier":"surf://store:183ef8536ef-382bfb498070","rootDataFileId":-1,"checksum":{"type":"SHA-1","value":"220b9a87233844e2a33871a7061df25a0045f08f"},"tabularData":false,"creationDate":"2022-10-19","publicationDate":"2022-10-19","lastUpdateTime":"2022-10-19T13:13:03Z","fileAccessRequest":false}}]}}}