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Datasets:
Cilem
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histopathology-1024

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image
imagewidth (px)
224
224
slide_name
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20 values
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y
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level
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Dataset Card for Histopathology Dataset

Dataset Summary

This dataset contains 1024x1024 patches of a group of histopathology images taken from the CAMELYON16 dataset and embedding vectors extracted from these patches using the Google Path Foundation model.

Data Processing

Thumbnail of Main Slide

Main Slide Thumbnail

Usage

  • CAMELYON16: List of images taken from CAMELYON16 dataset:
    • test_001.tif
    • test_002.tif
    • test_003.tif
    • test_004.tif
    • test_005.tif
    • test_006.tif
    • test_007.tif
    • test_008.tif
    • test_009.tif
    • test_010.tif
    • test_011.tif
    • test_012.tif
    • test_013.tif
    • test_014.tif
    • test_015.tif
    • test_016.tif
    • test_017.tif
    • test_018.tif
    • test_019.tif
    • test_020.tif
  • Create a folder named wsi and download the images given in the list. Then:
from datasets import load_dataset
import openslide as ops


dataset = load_dataset("Cilem/histopathology-1024")
slide_name = dataset['train'][0]['slide_name']
resize = dataset['train'][0]['resize']
path = os.path.join('wsi', slide_name)
slide = ops.OpenSlide(path)
patch = slide.read_region((x, y), 0, patch_size)
patch = patch.resize(resize)
display(patch)

Supported Tasks

Machine learning applications that can be performed using this dataset:

  • Classification
  • Segmentation
  • Image generation

Languages

  • English

Dataset Structure

Data Fields

  • image: Patch image.
  • slide_name: Main slide name of the patch.
  • x: X coordinate of the patch.
  • y: Y coordinate of the patch.
  • level: Level of the main slide.
  • patch_size: Size of the patch.
  • resize: Image size used to obtain embedding vector with Path foundation model.
  • embedding_vector: Embedding vector of the patch extracted using Path foundation model.

Dataset Creation

Source Data

  • Original Sources
    • CAMELYON16: List of images taken from CAMELYON16 dataset:
      • test_001.tif
      • test_002.tif
      • test_003.tif
      • test_004.tif
      • test_005.tif
      • test_006.tif
      • test_007.tif
      • test_008.tif
      • test_009.tif
      • test_010.tif
      • test_011.tif
      • test_012.tif
      • test_013.tif
      • test_014.tif
      • test_015.tif
      • test_016.tif
      • test_017.tif
      • test_018.tif
      • test_019.tif
      • test_020.tif
    • Google Path Foundation: Embedding vectors extracted from the patches using the Path Foundation model.

Considerations for Using the Data

Social Impact and Bias

Attention should be paid to the Path Foundation model licenses provided by Google.
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Number of rows:
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Total file size:
4.29 GB