arXiv:2604.09370q-bio.QMcs.CV2026-04

自动标注组织切片中的细胞结构,人工标注量减少数倍。

Cluster-First Labelling: An Automated Pipeline for Segmentation and Morphological Clustering in Histology Whole Slide Images

  • 先聚类后标注,用深度学习分割+聚类分组对象
  • 在13种组织类型上达到96.8%的聚类标签准确率
  • 适合病理学研究者快速构建标注数据集

组织切片图像(WSI)中识别组织成分极耗人力:单张切片含数万计细胞、细胞核及其他形态各异的结构,每项均需手动勾画边界并分类。我们提出一个云端部署的端到端自动化流程,采用‘先聚类后标注’范式。系统将切片分块,剔除低信息量区域,使用Cellpose-SAM分割细胞、细胞核等结构,通过预训练ResNet-50提取神经嵌入,经UMAP降维后用DBSCAN进行形态聚类。人类标注员仅需标注代表性聚类而非个体对象,使标注工作量降低数个数量级。我们在来自人、大鼠、兔三种物种的13种组织类型中共评估3,696个组织成分,通过逐块匈牙利匹配评估无监督聚类与独立人工标注的一致性。系统整体加权聚类标签对齐准确率达96.8%,其中7种组织类型达完美一致。该流程、配套标注网页应用及全部评估代码均已开源。

原文摘要 · Abstract (English)

Labelling tissue components in histology whole slide images (WSIs) is prohibitively labour-intensive: a single slide may contain tens of thousands of structures--cells, nuclei, and other morphologically distinct objects--each requiring manual boundary delineation and classification. We present a cloudnative, end-to-end pipeline that automates this process through a cluster-first paradigm. Our system tiles WSIs, filters out tiles deemed unlikely to contain valuable information, segments tissue components with Cellpose-SAM (including cells, nuclei, and other morphologically similar structures), extracts neural embeddings via a pretrained ResNet-50, reduces dimensionality with UMAP, and groups morphologically similar objects using DBSCAN clustering. Under this paradigm, a human annotator labels representative clusters rather than individual objects, reducing annotation effort by orders of magnitude. We evaluate the pipeline on 3,696 tissue components across 13 diverse tissue types from three species (human, rat, rabbit), measuring how well unsupervised clusters align with independent human labels via per-tile Hungarian-algorithm matching. Our system achieves a weighted cluster-label alignment accuracy of 96.8%, with 7 of 13 tissue types reaching perfect agreement. The pipeline, a companion labelling web application, and all evaluation code are released as open-source software.

组织切片自动标注聚类分析病理图像

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