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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    <dct:title>PESO: Prostate Epithelium Segmentation on H&amp;E-stained prostatectomy whole slide images</dct:title>
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    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2018</dct:issued>
    <dcat:keyword>pathology</dcat:keyword>
    <dcat:keyword>prostate</dcat:keyword>
    <dcat:keyword>cancer</dcat:keyword>
    <dcat:keyword>epithelium</dcat:keyword>
    <dcat:keyword>whole slide image</dcat:keyword>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2018-11-20</dct:issued>
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    <dct:description>&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;</dct:description>
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