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: https://doi.org/10.1038/s41598-018-37257-4

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:

  • peso_training_masks.zip: 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.
  • peso_training_masks_corrected.zip: 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.
  • peso_training_colordeconvolution.zip: 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:

  • peso_testset_regions.zip: 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.
  • peso_testset_png.zip: Export of the test set regions in PNG format (2500x2500 pixels per region).
  • peso_testset_png_padded.zip: 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: https://doi.org/10.1038/s41598-018-37257-4

Files (138.1 GB)
Name Size
peso_testset_mapping.csv
md5:c267372ed522e1d15b8b550f3f3a8454
3.0 kB Download
peso_testset_png.zip
md5:c212aa96a7f79eb177ce1e4bfedb1ac1
205.2 MB Download
peso_testset_png_padded.zip
md5:0c054a0ad3ae341988fa8c79591e2fe0
400.1 MB Download
peso_testset_regions.zip
md5:9ec87b07fec0f1df7a17cf2de86aff99
17.1 kB Download
peso_testset_wsi_1.zip
md5:88342979339ed915272a50a4a3140a6d
13.1 GB Download
peso_testset_wsi_2.zip
md5:e74424f99b8f60baa455c9291ceaa994
13.0 GB Download
peso_testset_wsi_3.zip
md5:bd661a495ff00aae6009c4dd7e003f08
14.2 GB Download
peso_testset_wsi_4.zip
md5:088d6b472d3b6305af8a31ff77e3cb15
14.1 GB Download
peso_training_colordeconvolution.zip
md5:8a6ec1f175d4479bec3c32b5ee82955a
1.4 GB Download
peso_training_masks.zip
md5:e3db7901434a0b2d51dfa57f4e59ebbe
1.7 GB Download
peso_training_masks_corrected.zip
md5:8e2c86fcecfafe09c9d48a60b42441b5
587.3 MB Download
peso_training_wsi_1.zip
md5:8e4e53d7ba855fc2f318dce94b05fe31
14.4 GB Download
peso_training_wsi_2.zip
md5:bfcae8b444c12c0ecbb717dc37334020
13.9 GB Download
peso_training_wsi_3.zip
md5:f7d484acec429c3a9d9e685969edd82b
12.1 GB Download
peso_training_wsi_4.zip
md5:75a350b450193b48e9bed3a3484f639d
13.2 GB Download
peso_training_wsi_5.zip
md5:bc94373db95c5e2ceefe08c45a8e54db
11.0 GB Download
peso_training_wsi_6.zip
md5:4fa8cdd4b748d67b6c39a982be7b627a
15.0 GB Download
  • https://doi.org/10.1038/s41598-018-37257-4

996
1,220
views
downloads
All versions This version
Views 9961,017
Downloads 1,2201,220
Data volume 8.6 TB8.6 TB
Unique views 921941
Unique downloads 520520

Share

Cite as