用深度学习压缩高分辨率病理图像,体积缩小超40%且保持画质。
Deep learning-based compression of giga-resolution whole slide images

- 先用AI识别并移除玻璃区域,再用深度学习模型压缩图像。
- 相比JPEG,整体压缩率提升44%-80%,单张切片节省35%-40%空间。
- 适合需要高效存储病理数据的医院和研究机构使用。
数字病理学发展带来大量全切片图像(WSIs),其尺寸巨大,现有压缩方法如JPEG导致每张图像达数GB,浪费存储空间。本研究探索基于深度学习的组织分割去除玻璃区域,并对比JPEG、JPEG-2000和JPEG-XL等编码器。构建了包含21层金字塔的图像数据集,分别保留原始玻璃、用单色像素替代玻璃、用零字节瓦片替代玻璃。结果显示,移除玻璃后JPEG与JPEG-XL文件大小显著减小;深度学习压缩相比JPEG减少43%-72%体积,玻璃区域替换策略分别减少0.3%-33%和6%-62%。两者结合实现44%-80%总压缩率,表明深度学习能高效压缩玻璃区域,而传统编码器做不到。在组织切片数据集上,最优深度学习模型平均节省35%-40%空间,平均SSIM>0.95;JPEG-XL和JPEG-2000分别节省17%和14%,SSIM为0.96。但深度学习模型解压时间更长。
原文摘要 · Abstract (English)
Implementation of digital pathology leads to an increased number of whole slide images (WSIs). The large size of WSIs is challenging. Today, WSIs are compressed with codecs like JPEG resulting in several gigabytes per WSI, and large amounts of space are wasted storing glass. In this study, deep learning-based tissue segmentation for glass removal, and deep learning compression methods were explored and compared with JPEG, JPEG-2000 and JPEG-XL. Image pyramids (N=21) with intact glass, glass replaced by single-colored pixels, and glass replaced by zero-byte tiles were created and compressed with JPEG, JPEG-XL and a deep learning model. Additionally, several compression models were evaluated on a tissue patch dataset and compared with JPEG, JPEG-2000 and JPEG-XL. Removing glass reduced file sizes considerably for JPEG and JPEG-XL. Deep learning-based image compression reduced the WSI size by 43-72% compared to JPEG compression, whereas deep learning-based glass removal reduced the WSI size by 0.3-33%, and 6-62% using only single-colored pixels and removing all-glass tiles, respectively. Combining the two gave a small improvement to a 44-80% total size reduction which indicates that deep learning-based image compression is able to efficiently compress glass tiles, whereas JPEG is not. On the tissue patch dataset, the best deep learning-based compression models saved on average ~35-40% per patch compared to JPEG, while keeping an average SSIM above 0.95, whereas JPEG-XL and JPEG-2000 saved 17% and 14%, respectively while keeping an SSIM of 0.96. However, the deep learning models had higher decompression times than JPEG and JPEG-XL.
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