Normalization of HE-Stained Histological Images using Cycle Consistent Generative Adversarial Networks [Dataset]

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Normalization of HE-Stained Histological Images using Cycle Consistent Generative Adversarial Networks [Dataset]
Runz, Marlen; Weis, Cleo-Aron, 2021, "Normalization of HE-Stained Histological Images using Cycle Consistent Generative Adversarial Networks [Dataset]", https://doi.org/10.11588/data/8LKEZF, heiDATA, V1
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Description

Here we provide the data sets supporting the experiments in our publication Normalization of HE-Stained Histological Images using Cycle Consistent Generative Adversarial Networks, which were collected at the Institute of Pathology, Medical Faculty Mannheim, Heidelberg University.

The HE-Staining Variation (HEV) data set offers serial sections of a follicular thyroid carcinoma, stained with different HE-staining protocols (including name of [stainVariant]):

  1. stained with HE with the standard protocol of the Institute of Pathology, Mannheim (HE)
  2. stained too long with HE (longHE)
  3. stained too short with HE (shortHE)
  4. stained only with Hematoxylin (onlyH)
  5. stained only with Eosin (onlyE)
  6. stained too long with Hematoxylin (longH)
  7. stained too long with Eosin (longE)
  8. stained too short with Hematoxylin (shortH)
  9. stained too short with Eosin (shortE)

We provided the original whole-slide-images (WSI) in the folder HEV_wsi.zip for each stain-variant.

wsi_example

In addition, for the stain-variants 1-5 we provide patches (n ~40,000 for each set) of size 256x256 pixels and split them into 60% train (train_[stainVariant].zip) and 40% test (test_[stainVariant].zip) sets .

stain_normalization_example

Patches from our TumorLymphnode data set for image classification are provided inside tumorLymphnode_patches.zip. It contains ~3,600 patches of size 165x165 pixels for each class normal lymph nodes (normal) and carcinoma infiltration (tumor).

The code for our models is available at Gitlab.

Subject Computer and Information Science; Medicine, Health and Life Sciences
Keyword Stain Normalization
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This dataset is made available under the following terms. Please confirm and/or complete the information needed below in order to continue.

Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation shown on the dataset page.

Custom Dataset Terms — the following Custom Dataset Terms have been defined for this dataset.

Licensed under a Creative Commons Attribution 4.0 International License.  CC by
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