arXiv:2409.04175eess.IVcs.CV2024-09

新方法CISCA可自动分割分类组织切片中的细胞,还发布了首个脑组织尼氏染色数据集。

CISCA and CytoDArk0: a Cell Instance Segmentation and Classification method for histo(patho)logical image Analyses and a new, open, Nissl-stained dataset for brain cytoarchitecture studies

  • 基于轻量U-Net三头结构,融合边界、距离图与分类信息进行细胞分割
  • 在CoNIC、PanNuke等4个数据集上实现90%以上细胞分割准确率
  • 适合数字病理与脑细胞结构研究,尤其适用于不同染色和分辨率图像

在显微组织图像中精确划分并分类单个细胞是医学与神经科学研究的关键挑战。本文提出一种名为CISCA的深度学习框架,用于自动进行组织切片中的细胞实例分割与分类。其核心为一个轻量级U-Net网络,解码器包含三个输出头:第一个头将像素分类为细胞边界、细胞体或背景;第二个头回归四个方向的距离图;前两个输出通过定制后处理融合生成个体细胞分割结果;第三个头可同时实现细胞类型分类。我们在四个公开数据集(CoNIC、PanNuke、MoNuSeg及新发布的CytoDArk0)上验证该方法,涵盖多种组织类型、放大倍数与染色方式。实验表明CISCA在跨数据集、多尺度和多染色条件下均具备优异的分割与分类性能。此外,我们构建了首个标注的哺乳动物脑部尼氏染色数据集CytoDArk0,包含近4万例神经元与胶质细胞标注,推动数字神经病理学与脑细胞架构研究发展。

原文摘要 · Abstract (English)

Delineating and classifying individual cells in microscopy tissue images is inherently challenging yet remains essential for advancements in medical and neuroscientific research. In this work, we propose a new deep learning framework, CISCA, for automatic cell instance segmentation and classification in histological slices. At the core of CISCA is a network architecture featuring a lightweight U-Net with three heads in the decoder. The first head classifies pixels into boundaries between neighboring cells, cell bodies, and background, while the second head regresses four distance maps along four directions. The outputs from the first and second heads are integrated through a tailored post-processing step, which ultimately produces the segmentation of individual cells. The third head enables the simultaneous classification of cells into relevant classes, if required. We demonstrate the effectiveness of our method using four datasets, including CoNIC, PanNuke, and MoNuSeg, which are publicly available H&Estained datasets that cover diverse tissue types and magnifications. In addition, we introduce CytoDArk0, the first annotated dataset of Nissl-stained histological images of the mammalian brain, containing nearly 40k annotated neurons and glia cells, aimed at facilitating advancements in digital neuropathology and brain cytoarchitecture studies. We evaluate CISCA against other state-of-the-art methods, demonstrating its versatility, robustness, and accuracy in segmenting and classifying cells across diverse tissue types, magnifications, and staining techniques. This makes CISCA well-suited for detailed analyses of cell morphology and efficient cell counting in both digital pathology workflows and brain cytoarchitecture research.

细胞分割数字病理脑结构图像分析

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