Dataset Open Access

PESO: Prostate Epithelium Segmentation on H&E-stained prostatectomy whole slide images

Bulten, Wouter; Bándi, Péter; Hoven, Jeffrey; Loo, Rob van de; Lotz, Johannes; Weiss, Nick; Laak, Jeroen van der; Ginneken, Bram van; Hulsbergen-van de Kaa, Christina; Litjens, Geert


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  <identifier identifierType="DOI">10.5281/zenodo.1485967</identifier>
  <creators>
    <creator>
      <creatorName>Bulten, Wouter</creatorName>
      <givenName>Wouter</givenName>
      <familyName>Bulten</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-6129-5039</nameIdentifier>
      <affiliation>Radboud University Medical Center</affiliation>
    </creator>
    <creator>
      <creatorName>Bándi, Péter</creatorName>
      <givenName>Péter</givenName>
      <familyName>Bándi</familyName>
      <affiliation>Radboud University Medical Center</affiliation>
    </creator>
    <creator>
      <creatorName>Hoven, Jeffrey</creatorName>
      <givenName>Jeffrey</givenName>
      <familyName>Hoven</familyName>
      <affiliation>Radboud University Medical Center</affiliation>
    </creator>
    <creator>
      <creatorName>Loo, Rob van de</creatorName>
      <givenName>Rob van de</givenName>
      <familyName>Loo</familyName>
      <affiliation>Radboud University Medical Center</affiliation>
    </creator>
    <creator>
      <creatorName>Lotz, Johannes</creatorName>
      <givenName>Johannes</givenName>
      <familyName>Lotz</familyName>
      <affiliation>Fraunhofer MEVIS</affiliation>
    </creator>
    <creator>
      <creatorName>Weiss, Nick</creatorName>
      <givenName>Nick</givenName>
      <familyName>Weiss</familyName>
      <affiliation>Fraunhofer MEVIS</affiliation>
    </creator>
    <creator>
      <creatorName>Laak, Jeroen van der</creatorName>
      <givenName>Jeroen van der</givenName>
      <familyName>Laak</familyName>
      <affiliation>Radboud University Medical Center</affiliation>
    </creator>
    <creator>
      <creatorName>Ginneken, Bram van</creatorName>
      <givenName>Bram van</givenName>
      <familyName>Ginneken</familyName>
      <affiliation>Radboud University Medical Center</affiliation>
    </creator>
    <creator>
      <creatorName>Hulsbergen-van de Kaa, Christina</creatorName>
      <givenName>Christina</givenName>
      <familyName>Hulsbergen-van de Kaa</familyName>
      <affiliation>Radboud University Medical Center</affiliation>
    </creator>
    <creator>
      <creatorName>Litjens, Geert</creatorName>
      <givenName>Geert</givenName>
      <familyName>Litjens</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-1554-1291</nameIdentifier>
      <affiliation>Radboud University Medical Center</affiliation>
    </creator>
  </creators>
  <titles>
    <title>PESO: Prostate Epithelium Segmentation on H&amp;E-stained prostatectomy whole slide images</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2018</publicationYear>
  <subjects>
    <subject>pathology</subject>
    <subject>prostate</subject>
    <subject>cancer</subject>
    <subject>epithelium</subject>
    <subject>whole slide image</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2018-11-20</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/1485967</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsDocumentedBy">10.1038/s41598-018-37257-4</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.1485966</relatedIdentifier>
  </relatedIdentifiers>
  <version>1</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode">Creative Commons Attribution Non Commercial Share Alike 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;Large set of whole-slide-images (WSI) of prostatectomy specimens with various grades of prostate cancer (PCa). More information can be found in the corresponding paper:&amp;nbsp;&lt;a href="https://doi.org/10.1038/s41598-018-37257-4"&gt;https://doi.org/10.1038/s41598-018-37257-4&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;The WSIs in this dataset can be viewed using the open-source software &lt;a href="https://github.com/computationalpathologygroup/ASAP"&gt;ASAP&lt;/a&gt;&amp;nbsp;or &lt;a href="https://openslide.org/"&gt;Open Slide&lt;/a&gt;.&lt;/p&gt;

&lt;p&gt;Due to the large size of the complete dataset, the data has been split up in to multiple archives.&lt;/p&gt;

&lt;p&gt;The data from the training set:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;&lt;strong&gt;peso_training_masks.zip:&amp;nbsp;&lt;/strong&gt;Training masks (N=62)&amp;nbsp;that have been used to train the main network of our paper. These masks are generated by a trained U-Net on the corresponding IHC slides.&lt;/li&gt;
	&lt;li&gt;&lt;strong&gt;peso_training_masks_corrected.zip:&amp;nbsp;&lt;/strong&gt;A subset of the color deconvolution masks (N=25)&amp;nbsp;on which manual annotations have been made. Within these regions, stain and other artifacts have been removed.&lt;/li&gt;
	&lt;li&gt;&lt;strong&gt;peso_training_colordeconvolution.zip:&amp;nbsp;&lt;/strong&gt;Mask files (N=62)&amp;nbsp;containing the P63&amp;amp;CK8/18 channel&amp;nbsp;of the color deconvolution operation. These masks mark all regions that are stained by either P63 or CK8/18 in the IHC version of the slides.&lt;/li&gt;
	&lt;li&gt;&lt;strong&gt;peso_training_wsi_{1-6}.zip:&amp;nbsp;&lt;/strong&gt;Zip files containing the whole slide images of the training set (N=62). Each archive contains 10 slides, excluding the last which contains 12.&amp;nbsp;These images are exported at a pixel resolution of 0.48mu/pixels.&amp;nbsp;&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;The data from the test set:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;&lt;strong&gt;peso_testset_regions.zip:&amp;nbsp;&lt;/strong&gt;Collection of annotation XML files with outlines of the test regions. These can be used to view the test regions in more detail using ASAP.&lt;/li&gt;
	&lt;li&gt;&lt;strong&gt;peso_testset_png.zip:&amp;nbsp;&lt;/strong&gt;Export of the test set regions in PNG format (2500x2500 pixels per region).&lt;/li&gt;
	&lt;li&gt;&lt;strong&gt;peso_testset_png_padded.zip:&amp;nbsp;&lt;/strong&gt;Export of the test regions in PNG format padded with a 500 pixel wide border (3500x3500 pixels per region). Useful for segmenting pixels at the border of the regions.&lt;/li&gt;
	&lt;li&gt;&lt;strong&gt;peso_testset_mapping.csv:&amp;nbsp;&lt;/strong&gt;A csv file mapping files from the test set (numbered 1-160) to regions in the xml files. The csv file also contains the label (benign or cancer) for each region.&lt;/li&gt;
	&lt;li&gt;&lt;strong&gt;peso_testset_wsi_{1-4}.zip:&amp;nbsp;&lt;/strong&gt;Zip files containing the whole slide images of the test set (N=40). Each archive contains 10 slides of the test set. These images are exported at a pixel resolution of 0.48mu/pixels.&amp;nbsp;&lt;/li&gt;
&lt;/ul&gt;

&lt;p&gt;This study was financed by a grant from the Dutch Cancer Society (KWF), grant number KUN 2015-7970.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;If you make use of this dataset please cite both the dataset itself and the corresponding paper:&amp;nbsp;&lt;/strong&gt;&lt;a href="https://doi.org/10.1038/s41598-018-37257-4"&gt;https://doi.org/10.1038/s41598-018-37257-4&lt;/a&gt;&lt;/p&gt;</description>
    <description descriptionType="Other">{"references": ["https://doi.org/10.1038/s41598-018-37257-4"]}</description>
  </descriptions>
</resource>
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