无需调参,一键分割细胞结构,加速药物筛选
subCellSAM: Zero-Shot (Sub-)Cellular Segmentation for Hit Validation in Drug Discovery
- 用自提示机制结合形态先验,零样本完成细胞分割
- 在标准数据集和真实药物筛选中准确识别关键结构
- 适合药企快速验证候选药物,无需额外训练
高通量显微成像是生物制药药物发现的关键驱动力,可并行评估数千种药物候选物。传统图像分析与深度学习方法虽被用于处理此类大规模复杂数据,但通常需大量手动调参或领域特定模型微调。本文提出一种新方法,利用分割基础模型在零样本设置下进行细胞、亚细胞结构分割,通过上下文学习策略实现。该方法采用三步流程,引入自提示机制,利用生长掩码和有策略的前景/背景点编码形态与拓扑先验。我们在标准细胞分割基准和行业相关的药物靶点验证任务上验证了该方法,结果表明其无需特定数据集调优即可准确分割生物学相关结构。
原文摘要 · Abstract (English)
High-throughput screening using automated microscopes is a key driver in biopharma drug discovery, enabling the parallel evaluation of thousands of drug candidates for diseases such as cancer. Traditional image analysis and deep learning approaches have been employed to analyze these complex, large-scale datasets, with cell segmentation serving as a critical step for extracting relevant structures. However, both strategies typically require extensive manual parameter tuning or domain-specific model fine-tuning. We present a novel method that applies a segmentation foundation model in a zero-shot setting (i.e., without fine-tuning), guided by an in-context learning strategy. Our approach employs a three-step process for nuclei, cell, and subcellular segmentation, introducing a self-prompting mechanism that encodes morphological and topological priors using growing masks and strategically placed foreground/background points. We validate our method on both standard cell segmentation benchmarks and industry-relevant hit validation assays, demonstrating that it accurately segments biologically relevant structures without the need for dataset-specific tuning.
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