基于星凸性与空间关联性,单次完成多类生物对象的实例分割。
Single-shot Star-convex Polygon-based Instance Segmentation for Spatially-correlated Biomedical Objects
- 利用星凸形状先验和交互约束,构建双架构实现多类别对象联合分割。
- 在IoU_R、AP和新指标JTPR上均优于基线模型,支持嵌套结构识别。
- 适用于荧光/明场显微图像中的部分包含/排除关系,计算高效易扩展。
生物医学图像中常存在因固有属性而具有空间相关或嵌套关系的对象,如细胞核嵌于真核细胞内、菌落仅生长于培养皿中。这类语义关系至关重要,但现有检测方法通常独立处理,依赖多阶段分析流程。我们提出,可利用空间相关性作为基础先验,提升实例分割等任务的表征能力。为此,我们基于广泛使用的StarDist(SD)框架,设计了HydraStarDist(HSD)与新型改进版HSD-WBR,充分利用目标对象的星凸特性,并通过联合编码器隐式引入对象间交互约束。HSD-WBR进一步在正则化层中加入自研的“边界内正则化惩罚”(WBR),显式强化空间先验。两者均能在单次推理中实现嵌套实例分割。实验表明,在IoU_R、AP指标上表现竞争力,且在新提出的任务相关指标——联合真阳性率(JTPR)上显著更优。该方法还可拓展用于捕捉荧光或明场显微图像中的部分包含/排除关系,具备单次学习、计算高效的优点。
原文摘要 · Abstract (English)
Biomedical images often contain objects known to be spatially correlated or nested due to their inherent properties, leading to semantic relations. Examples include cell nuclei being nested within eukaryotic cells and colonies growing exclusively within their culture dishes. While these semantic relations bear key importance, detection tasks are often formulated independently, requiring multi-shot analysis pipelines. Importantly, spatial correlation could constitute a fundamental prior facilitating learning of more meaningful representations for tasks like instance segmentation. This knowledge has, thus far, not been utilised by the biomedical computer vision community. We argue that the instance segmentation of two or more categories of objects can be achieved in parallel. We achieve this via two architectures HydraStarDist (HSD) and the novel (HSD-WBR) based on the widely-used StarDist (SD), to take advantage of the star-convexity of our target objects. HSD and HSD-WBR are constructed to be capable of incorporating their interactions as constraints into account. HSD implicitly incorporates spatial correlation priors based on object interaction through a joint encoder. HSD-WBR further enforces the prior in a regularisation layer with the penalty we proposed named Within Boundary Regularisation Penalty (WBR). Both architectures achieve nested instance segmentation in a single shot. We demonstrate their competitiveness based on $IoU_R$ and AP and superiority in a new, task-relevant criteria, Joint TP rate (JTPR) compared to their baseline SD and Cellpose. Our approach can be further modified to capture partial-inclusion/-exclusion in multi-object interactions in fluorescent or brightfield microscopy or digital imaging. Finally, our strategy suggests gains by making this learning single-shot and computationally efficient.
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