{"status":"OK","data":{"id":308950,"identifier":"GN4YOS","persistentUrl":"https://doi.org/10.34894/GN4YOS","protocol":"doi","authority":"10.34894","separator":"/","publisher":"DataverseNL","publicationDate":"2022-08-24","storageIdentifier":"surf://10.34894/GN4YOS","effectiveDatasetFileCountLimit":10000,"datasetFileUploadsAvailable":9994,"datasetType":"dataset","locks":[],"latestVersion":{"id":24382,"datasetId":308950,"datasetPersistentId":"doi:10.34894/GN4YOS","datasetType":"dataset","storageIdentifier":"surf://10.34894/GN4YOS","versionNumber":2,"internalVersionNumber":10,"versionMinorNumber":0,"versionState":"RELEASED","latestVersionPublishingState":"RELEASED","deaccessionLink":"","lastUpdateTime":"2022-10-19T13:12:06Z","releaseTime":"2022-10-19T13:12:06Z","createTime":"2022-10-18T12:03:42Z","publicationDate":"2022-08-24","citationDate":"2022-08-24","effectiveDatasetFileCountLimit":10000,"datasetFileUploadsAvailable":9994,"termsOfUse":"The standard Data Sharing Agreement (DSA) of the UMC Utrecht must be signed without adjustments. This DSA is in compliance with Dutch law. No costs are involved.","confidentialityDeclaration":"no","specialPermissions":"To obtain access to the data, a <a href=\"https://www.umcutrecht.nl/en/data-request-form-umc-utrecht\">request form</a> has to be completed. In addition to a completed request form, a  Data Sharing Agreement (DSA) in line with GDPR regulations and/or a Research Collaboration Agreement (RCA) should be signed before data is shared. Only data requests in line with the Terms of Use will be taken into consideration. ","restrictions":"See Data Sharing Agreement.","citationRequirements":"See Data Sharing Agreement.","conditions":"To access and use the dataset please read the Terms of Use and the Terms of Access.","disclaimer":"See Data Sharing Agreement.","termsOfAccess":"By downloading or otherwise accessing the materials, the downloader represents his/her acceptance of the Terms of Use. ","fileAccessRequest":true,"metadataBlocks":{"citation":{"displayName":"Citation Metadata","name":"citation","fields":[{"typeName":"title","multiple":false,"typeClass":"primitive","value":"Replication Data for: EntropyMasker"},{"typeName":"author","multiple":true,"typeClass":"compound","value":[{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Yipei Song"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"University of Virginia"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Craig Glastonbury"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"Human Technopole"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0001-5542-2225"}},{"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":"Clint L. Miller"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"University of Virginia"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0003-4276-3607"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Francesco Cisternino"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"Human Technopole"}}]},{"typeName":"datasetContact","multiple":true,"typeClass":"compound","value":[{"datasetContactName":{"typeName":"datasetContactName","multiple":false,"typeClass":"primitive","value":"dLAB Datamanagement"},"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":"<strong>Background</strong></br>\n<strong>EntropyMasker</strong> is a fully automated approach for separating foreground (tissue) and background in bright-field microscopic whole-slide images of (immuno)histologically stained samples. This method is unaffected by changes in scanning or image processing conditions, by using a measure of local entropy and generating corresponding binary tissue masks.</br>\n</br>\n<b>ExpressScan</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 used for the <strong>EntropyMasker</strong> project from the Athero-Express (AE) Biobank Studies. </br></br>\n\n<strong>Athero-Express Biobank Study</strong></br>\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); this is further described <a href=\"https://doi.org/10.34894/4IKE3T\" target=\"_blank\">here</a>. The study design and staining protocols are described by <a href=\"https://pubmed.ncbi.nlm.nih.gov/15678794/\" target=\"_blank\">Verhoeven <em>et al.</em></a>.</br></br>\n\nA link to the public GitHub repository for <strong>EntropyMasker</strong> can be found here: <a href=\"https://github.com/CirculatoryHealth/EntropyMasker\" target=\"_blank\">https://github.com/CirculatoryHealth/EntropyMasker</a>.</br></br>\n\n<b>Important notice on availability of data</b></br>\nThe amount of data is huge 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":"2022-10-18"}}]},{"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":"whole-slide image"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"image-masking"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"atherosclerosis"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"plaque"}}]},{"typeName":"depositor","multiple":false,"typeClass":"primitive","value":"van der Laan, Sander W."},{"typeName":"dateOfDeposit","multiple":false,"typeClass":"primitive","value":"2022-08-11"}]},"dansDataVaultMetadata":{"displayName":"Data Vault Metadata","name":"dansDataVaultMetadata","fields":[{"typeName":"dansDataversePid","multiple":false,"typeClass":"primitive","value":"doi:10.34894/GN4YOS"},{"typeName":"dansDataversePidVersion","multiple":false,"typeClass":"primitive","value":"2.0"},{"typeName":"dansBagId","multiple":false,"typeClass":"primitive","value":"urn:uuid:006d7308-90ab-484b-a824-792d8e2ad615"},{"typeName":"dansNbn","multiple":false,"typeClass":"primitive","value":"urn:nbn:nl:ui:13-fb885376-bc8b-4c6b-9f4e-2c168f5fca6f"}]}},"files":[{"label":"20020410_Approval_Protocol_TME_Athero-Express_Biobank_Study.pdf","restricted":true,"version":1,"datasetVersionId":24382,"dataFile":{"id":308951,"persistentId":"","filename":"20020410_Approval_Protocol_TME_Athero-Express_Biobank_Study.pdf","contentType":"application/pdf","friendlyType":"Adobe PDF","filesize":61663,"storageIdentifier":"surf://store:1828d570651-613311c3800f","rootDataFileId":-1,"checksum":{"type":"SHA-1","value":"7af1184782ed6d4c33f554077390c88f0ab184b4"},"tabularData":false,"creationDate":"2022-08-11","publicationDate":"2022-08-24","lastUpdateTime":"2022-10-19T13:12:06Z","fileAccessRequest":true}},{"label":"20211007_DMP_Athero-Express_Biobank_Study.pdf","restricted":true,"version":1,"datasetVersionId":24382,"dataFile":{"id":308953,"persistentId":"","filename":"20211007_DMP_Athero-Express_Biobank_Study.pdf","contentType":"application/pdf","friendlyType":"Adobe PDF","filesize":64158,"storageIdentifier":"surf://store:1828d5706ed-ca29789d8836","rootDataFileId":-1,"checksum":{"type":"SHA-1","value":"a733a0cddb4a49961748170591890e5aa47494d1"},"tabularData":false,"creationDate":"2022-08-11","publicationDate":"2022-08-24","lastUpdateTime":"2022-10-19T13:12:06Z","fileAccessRequest":true}},{"label":"Athero-Express_Biobank_Study_IC_versie_4.doc","restricted":true,"version":1,"datasetVersionId":24382,"dataFile":{"id":308952,"persistentId":"","filename":"Athero-Express_Biobank_Study_IC_versie_4.doc","contentType":"application/msword","friendlyType":"MS Word","filesize":34816,"storageIdentifier":"surf://store:1828d570783-b0ffd1c07808","rootDataFileId":-1,"checksum":{"type":"SHA-1","value":"40b3106353e85b47a9d1185093e95d91bceea03b"},"tabularData":false,"creationDate":"2022-08-11","publicationDate":"2022-08-24","lastUpdateTime":"2022-10-19T13:12:06Z","fileAccessRequest":true}},{"description":"These are the image-files used for this project. They are restricted (this file too) given their sensitive nature.","label":"EntropyMasker_image_files_used.txt","restricted":true,"version":1,"datasetVersionId":24382,"dataFile":{"id":308997,"persistentId":"","filename":"EntropyMasker_image_files_used.txt","contentType":"text/plain","friendlyType":"Plain Text","filesize":3611,"description":"These are the image-files used for this project. 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