DINO-Nucleus: Multi-Level Self-Supervised Features for Nucleus Instance Segmentation

Mohammad Sarhangzadeh, Elyar Esmaeilzadeh, Doruk Oner

Nucleus instance segmentation and counting are essential for quantitative microscopy, enabling reliable analysis of cell populations, tissue organization, and disease-related changes. However, accurately separating touching nuclei remains difficult, and many existing approaches rely on complex models or sensitive post-processing procedures. We present DINO-Nucleus, a parameter-efficient framework that leverages multi-level self-supervised DINOv2 representations for nucleus instance segmentation and counting. The model jointly predicts nucleus regions, pixel-wise instance flows, and explicit nucleus centers, while a consistency objective encourages the predicted flows to converge toward their corresponding centers. Multi-level transformer features provide complementary spatial and semantic information, and the pretrained backbone is adapted using lightweight LoRA modules to reduce fine-tuning cost. Experimental results show that DINO-Nucleus achieves strong segmentation and counting performance with parameter-efficient backbone adaptation. These findings demonstrate that parameter-efficient adaptation of multi-level self-supervised features can provide an effective solution for…