arXiv:2511.02142cs.CV2025-11

用视觉算法自动重建浮游有孔虫的生长轨迹,省去人工逐室标记。

From Instance Segmentation to 3D Growth Trajectory Reconstruction in Planktonic Foraminifera

  • 结合实例分割与专用排序算法,实现三维壳室生长路径自动重建。
  • 在专家标注数据上验证,显著减少人工工作量且保持生物合理性。
  • 对小壳室分割不全仍能稳定重建轨迹,适合大规模生态研究。

浮游有孔虫是具有复杂腔室结构的海洋原生生物,其壳室生长轨迹可反映环境变化下的发育与适应机制。然而,基于成像数据的自动追踪仍属空白,现有方法依赖人工逐室分割,耗时且主观。本文提出端到端流程,首次将实例分割技术应用于有孔虫分析,并结合专用腔室排序算法,从高分辨率断层扫描中重建三维生长轨迹。通过量化评估多种分割模型在不同空间特征上的表现,分析其对轨迹重建的影响。实验表明,该流程大幅降低人工成本,同时保持生物意义准确。尽管小腔室因体素精度低和连接微弱导致部分欠分割,但排序算法仍具鲁棒性,可稳定重建发育轨迹。本研究建立首个全自动、可复现的有孔虫数字化生长分析框架,为大规模数据驱动生态研究奠定基础。

原文摘要 · Abstract (English)

Planktonic foraminifera, marine protists characterized by their intricate chambered shells, serve as valuable indicators of past and present environmental conditions. Understanding their chamber growth trajectory provides crucial insights into organismal development and ecological adaptation under changing environments. However, automated tracing of chamber growth from imaging data remains largely unexplored, with existing approaches relying heavily on manual segmentation of each chamber, which is time-consuming and subjective. In this study, we propose an end-to-end pipeline that integrates instance segmentation, a computer vision technique not extensively explored in foraminifera, with a dedicated chamber ordering algorithm to automatically reconstruct three-dimensional growth trajectories from high-resolution computed tomography scans. We quantitatively and qualitatively evaluate multiple instance segmentation methods, each optimized for distinct spatial features of the chambers, and examine their downstream influence on growth-order reconstruction accuracy. Experimental results on expert-annotated datasets demonstrate that the proposed pipeline substantially reduces manual effort while maintaining biologically meaningful accuracy. Although segmentation models exhibit under-segmentation in smaller chambers due to reduced voxel fidelity and subtle inter-chamber connectivity, the chamber-ordering algorithm remains robust, achieving consistent reconstruction of developmental trajectories even under partial segmentation. This work provides the first fully automated and reproducible pipeline for digital foraminiferal growth analysis, establishing a foundation for large-scale, data-driven ecological studies.

实例分割3D重建古生态自动化分析

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