Histopathology pairs of hematoxylin-eosin and Ki67 stainings of testicular seminoma
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About Dataset contains 77 pairs of stained sections of testicular seminoma. Each pair is produced from the neighbouring sections of the tissue to guarantee the most similarity possible of the stained tissue. HE and Ki67 images are registered and aligned. When used, please cite the following work: Petríková, D.; Cimrák, I.; Tobiášová, K. and Plank, L. (2024), Dataset of Hematoxylin-eosin and Ki67 histopathological image pairs complemented by algorithms providing Ki67 index, DATA, submitted. Data composition: Dataset is comprised of 154 PNG files. 77 files with prefix id_HE contain images of HE staining, and 77 files with prefix id_Ki67 contain images of Ki67 staining. Both files in each pair id_HE_string.png and id_Ki67_string.png have the same resolution with avarage value 35000px x 35000px. Data is available in 39 ZIP files each containig two HE. images and two of their Ki67 counterparts. For example, 03.zip contains the following files: 05_HE_slide-011-A1-S1-B11.png, 05_Ki67_slide-012-A1-S2-B12.png, 06_HE_slide-013-A1-S1-B13.png, 06_Ki67_slide-014-A1-S2-B14.png. Image names contain an additional random string. An example of a HE - Ki67 pair is in file HE-Ki67_pair.png. Data preprocessing: Original scans of tissues contained pairs of HE and Ki67 staining with rotated and shifted tissues. Therefore a preprocessing of image registration was performed to find an affine transformation for rotation and translation. The concrete steps of image registration was described in [Petrikova 2024]. Provided images are already aligned. Data usage: This dataset is aimed for AI models to predict the Ki67 index or even to generate Ki67 staining. Since one pair of HE and Ki67 images contain two physically different sections of tissue (although the neighbouring), there is no one-to-one correspondence on cellural level. However patches, created on the same locations from the images in one pair, containe similar quantitative characteristics, such as number of cells, number of Ki67 positive cells, averaged cell size, etc. In [Petrikova2024B] we elaborate the usage of the dataset by computing Ki67 index of HE patches evaluated from corresponding Ki67 patch. References: [Petrikova2024] Petríková, D.; Cimrák, I.; Tobiášová, K. and Plank, L. (2024). Ki67 Expression Classification from HE Images with Semi-Automated Computer-Generated Annotations. In Proceedings of the 17th International Joint Conference on Biomedical Engineering Systems and Technologies - BIOINFORMATICS; ISBN 978-989-758-688-0; ISSN 2184-4305, SciTePress, pages 536-544. DOI: 10.5220/0012535900003657 [Petrikova2024B] Petríková, D.; Cimrák, I.; Tobiášová, K. and Plank, L. (2024), Dataset of Hematoxylin-eosin and Ki67 histopathological image pairs complemented by algorithms providing Ki67 index, DATA, submitted.
数据集概述 本数据集包含77对睾丸精原细胞瘤的染色切片。每一对切片均取自相邻的组织切片，以确保染色后的组织具备最高的相似性。苏木精-伊红（Hematoxylin-eosin）染色图像与Ki67染色图像已完成配准与对齐。 使用本数据集时，请引用以下文献：Petríková, D.; Cimrák, I.; Tobiášová, K. and Plank, L. (2024), Dataset of Hematoxylin-eosin and Ki67 histopathological image pairs complemented by algorithms providing Ki67 index, DATA, submitted. 数据集构成 本数据集共包含154个PNG格式文件。其中77个文件前缀为id_HE，对应苏木精-伊红染色图像；77个文件前缀为id_Ki67，对应Ki67染色图像。每一对id_HE_string.png与id_Ki67_string.png文件具有相同的分辨率，平均尺寸为35000像素×35000像素。本数据集以39个ZIP压缩包形式分发，每个压缩包内含2张HE染色图像与2张对应的Ki67染色图像。例如，03.zip包含以下文件： 05_HE_slide-011-A1-S1-B11.png、 05_Ki67_slide-012-A1-S2-B12.png、 06_HE_slide-013-A1-S1-B13.png、 06_Ki67_slide-014-A1-S2-B14.png。 图像名称带有额外的随机字符串。一对HE-Ki67图像的示例存储于文件HE-Ki67_pair.png中。 数据预处理 原始组织扫描图像中的HE与Ki67染色切片存在旋转与位移偏差。因此我们通过图像配准流程计算了用于旋转与平移的仿射变换，具体的图像配准步骤详见[Petrikova 2024]。本数据集提供的图像均已完成对齐处理。 数据集用途 本数据集旨在用于人工智能模型预测Ki67指数，甚至可用于生成Ki67染色图像。由于每一对HE与Ki67图像取自物理上独立的相邻组织切片，二者在细胞层面不存在一一对应关系。不过，从每对图像的相同位置截取的图像块（patch）具备相似的量化特征，例如细胞总数、Ki67阳性细胞数、平均细胞尺寸等。在[Petrikova2024B]中，我们详细阐述了通过计算对应Ki67图像块的Ki67指数来评估HE图像块的数据集使用方法。 参考文献 [Petrikova2024] Petríková, D.; Cimrák, I.; Tobiášová, K. and Plank, L. (2024). Ki67 Expression Classification from HE Images with Semi-Automated Computer-Generated Annotations. In Proceedings of the 17th International Joint Conference on Biomedical Engineering Systems and Technologies - BIOINFORMATICS; ISBN 978-989-758-688-0; ISSN 2184-4305, SciTePress, pages 536-544. DOI: 10.5220/0012535900003657 [Petrikova2024B] Petríková, D.; Cimrák, I.; Tobiášová, K. and Plank, L. (2024), Dataset of Hematoxylin-eosin and Ki67 histopathological image pairs complemented by algorithms providing Ki67 index, DATA, submitted.
