zeyugao/RCCNucSeg

Nuclei Grading Dataset for ccRCC

License: Apache-2.0

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Overview

This dataset is designed for nuclei grading in clear cell renal cell carcinoma (ccRCC). It consists of 1000 H&E stained image patches with a resolution of 512 × 512.

In total, the dataset contains 70,945 labeled nuclei, each annotated with:

1. Instance segmentation masks
2. Classification masks

The original Whole Slide Images (WSIs) are sourced from the TCGA (The Cancer Genome Atlas) database.

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Data Splits

The dataset is divided into three subsets:

• Training: 700 patches
• Testing: 200 patches
• Validation: 100 patches

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Data Composition

Each sample in this dataset comprises two parts:

1. ROIs (image patches):
   • Saved as .png files under the corresponding folders.
2. Annotations:
   • Saved as .mat files under the corresponding folders.
   • Each .mat file contains the following three keys:

Key	Description
instance_map	A pixel matrix with values from 0 to N. 0 represents the background; 1-N are the instance numbers of each nucleus.
class_map	A pixel matrix with values from 0 to 4. 0: Background 1-3: Tumor nucleus grades 1 to 3 4: Endothelial nuclei
TCGA_file_name	The filename of the original TCGA WSI from which the image patch was cropped.

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Class Distribution

This dataset contains 70,945 annotated nuclei, distributed across four classes:

Class	Count	Color
Endothelial nuclei	16,652	Blue
Grade 1 tumor nuclei	45,108	Green
Grade 2 tumor nuclei	6,406	Yellow
Grade 3 tumor nuclei	2,779	Red

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Usage and Restrictions

• This dataset is for research purposes only.
• Commercial use is strictly prohibited.

If you use this dataset in your research, you must cite the following publication:

@inproceedings{gao2021nuclei,
  title={Nuclei grading of clear cell renal cell carcinoma in histopathological image by composite high-resolution network},
  author={Gao, Zeyu and Shi, Jiangbo and Zhang, Xianli and Li, Yang and Zhang, Haichuan and Wu, Jialun and Wang, Chunbao and Meng, Deyu and Li, Chen},
  booktitle={Medical Image Computing and Computer Assisted Intervention--MICCAI 2021: 24th International Conference, Strasbourg, France, September 27--October 1, 2021, Proceedings, Part VIII 24},
  pages={132--142},
  year={2021},
  organization={Springer}
}