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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

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:

The WSIs in this dataset can be viewed using the open-source software ASAP or Open Slide.

Due to the large size of the complete dataset, the data has been split up in to multiple archives.

The data from the training set:

  • Training masks (N=62) 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.
  • A subset of the color deconvolution masks (N=25) on which manual annotations have been made. Within these regions, stain and other artifacts have been removed.
  • Mask files (N=62) containing the P63&CK8/18 channel 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.
  • peso_training_wsi_{1-6}.zip: Zip files containing the whole slide images of the training set (N=62). Each archive contains 10 slides, excluding the last which contains 12. These images are exported at a pixel resolution of 0.48mu/pixels. 

The data from the test set:

  • 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.
  • Export of the test set regions in PNG format (2500x2500 pixels per region).
  • 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.
  • peso_testset_mapping.csv: 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.
  • peso_testset_wsi_{1-4}.zip: 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. 

This study was financed by a grant from the Dutch Cancer Society (KWF), grant number KUN 2015-7970.

If you make use of this dataset please cite both the dataset itself and the corresponding paper:

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