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UnMICST:使用真实增强的深度学习方法对人类组织的高多重化图像进行鲁棒分割。

UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues.

机构信息

Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.

Image and Data Analysis Core, Harvard Medical School, Boston, MA, 02115, USA.

出版信息

Commun Biol. 2022 Nov 18;5(1):1263. doi: 10.1038/s42003-022-04076-3.

Abstract

Upcoming technologies enable routine collection of highly multiplexed (20-60 channel), subcellular resolution images of mammalian tissues for research and diagnosis. Extracting single cell data from such images requires accurate image segmentation, a challenging problem commonly tackled with deep learning. In this paper, we report two findings that substantially improve image segmentation of tissues using a range of machine learning architectures. First, we unexpectedly find that the inclusion of intentionally defocused and saturated images in training data substantially improves subsequent image segmentation. Such real augmentation outperforms computational augmentation (Gaussian blurring). In addition, we find that it is practical to image the nuclear envelope in multiple tissues using an antibody cocktail thereby better identifying nuclear outlines and improving segmentation. The two approaches cumulatively and substantially improve segmentation on a wide range of tissue types. We speculate that the use of real augmentations will have applications in image processing outside of microscopy.

摘要

未来的技术使人们能够常规地收集具有亚细胞分辨率的高度多重化(20-60 通道)的哺乳动物组织图像,用于研究和诊断。从这样的图像中提取单细胞数据需要精确的图像分割,这是一个通常使用深度学习来解决的具有挑战性的问题。在本文中,我们报告了两个发现,这些发现使用一系列机器学习架构极大地改善了组织的图像分割。首先,我们意外地发现,在训练数据中有意包含离焦和过饱和的图像会极大地改善后续的图像分割。这种真实的增强效果优于计算增强(高斯模糊)。此外,我们发现,使用抗体鸡尾酒在多种组织中成像核膜是可行的,从而更好地识别核轮廓并改善分割。这两种方法共同且显著地改善了广泛的组织类型的分割。我们推测,真实增强的使用将在显微镜以外的图像处理中有应用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b1ce/9674686/cb3b8d3d0047/42003_2022_4076_Fig1_HTML.jpg

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