颜林林
(2022-06-30 00:17):
#paper doi:10.1038/s41597-022-01450-y Scientific Data, 2022, HunCRC: annotated pathological slides to enhance deep learning applications in colorectal cancer screening. 《Nature》子刊《Scientific Data》确实是宝藏。这篇来自匈牙利的论文,就分享了一组很有用的数据。取材了200张H&E染色的结直肠癌的肿瘤组织切片,使用40倍高分辨率扫描全片,然后由病理医生进行标注,从中切分出多个不同类别的图像块,可用于后续结直肠癌的各类病理图像分析研究。值得夸赞的是,从样本采集到数据处理,整个过程有详细描述,数据处理代码、带标注的原始图像、处理后的带分类信息的图像块,全部都开放供直接下载使用。
代码地址:
https://github.com/qbeer/qupath-binarymask-extension
https://github.com/patbaa/crc_data_paper
原始图像数据:
https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=91357370
处理后数据:
https://figshare.com/articles/dataset/patches_and_local_annotations_slide_200_zoom_124x124_um2/19500266
HunCRC: annotated pathological slides to enhance deep learning applications in colorectal cancer screening
翻译
Abstract:
Histopathology is the gold standard method for staging and grading human tumors and provides critical information for the oncoteam's decision making. Highly-trained pathologists are needed for careful microscopic analysis of the slides produced from tissue taken from biopsy. This is a time-consuming process. A reliable decision support system would assist healthcare systems that often suffer from a shortage of pathologists. Recent advances in digital pathology allow for high-resolution digitalization of pathological slides. Digital slide scanners combined with modern computer vision models, such as convolutional neural networks, can help pathologists in their everyday work, resulting in shortened diagnosis times. In this study, 200 digital whole-slide images are published which were collected via hematoxylin-eosin stained colorectal biopsy. Alongside the whole-slide images, detailed region level annotations are also provided for ten relevant pathological classes. The 200 digital slides, after pre-processing, resulted in 101,389 patches. A single patch is a 512 × 512 pixel image, covering 248 × 248 μm tissue area. Versions at higher resolution are available as well. Hopefully, HunCRC, this widely accessible dataset will aid future colorectal cancer computer-aided diagnosis and research.
翻译
Related Links:
- https://www.nature.com/articles/s41597-022-01450-y.pdf
- https://www.nature.com/articles/s41597-022-01450-y
- https://github.com/qbeer/qupath-binarymask-extension
- https://github.com/patbaa/crc_data_paper
- https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=91357370
- https://figshare.com/articles/dataset/patches_and_local_annotations_slide_200_zoom_124x124_um2/19500266