# Self-supervised Pretraining of Cell Segmentation Models

arXiv: https://arxiv.org/abs/2604.10609 · HTML: https://mlsanity.com/paper/2604.10609/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 13 of its 52 references that are in the map.
- First posted on arXiv 12 Apr 2026.

## Builds on (most cited first, 13 of 13)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [iBOT: Image BERT Pre-Training with Online Tokenizer](https://mlsanity.com/paper/2111.07832/) (2021)
- [Surgical-DINO: Adapter Learning of Foundation Models for Depth Estimation in Endoscopic Surgery](https://mlsanity.com/paper/2401.06013/) (2024)
- [Evaluating General Purpose Vision Foundation Models for Medical Image Analysis: An Experimental Study of DINOv2 on Radiology Benchmarks](https://mlsanity.com/paper/2312.02366/) (2023)
- [MorphoSeg: An Uncertainty-Aware Deep Learning Method for Biomedical Segmentation of Complex Cellular Morphologies](https://mlsanity.com/paper/2409.17110/) (2024)
- [UINO-FSS: Unifying Representation Learning and Few-shot Segmentation via Hierarchical Distillation and Mamba-HyperCorrelation](https://mlsanity.com/paper/2504.15669/) (2025)
- [SelfAdapt: Unsupervised Domain Adaptation of Cell Segmentation Models](https://mlsanity.com/paper/2508.11411/) (2025)
- [Glioma C6: A Novel Dataset for Training and Benchmarking Cell Segmentation](https://mlsanity.com/paper/2511.07286/) (2025)

## Built on by (most cited first, 1 of 1)

- [Maximum Matching Accuracy: An Instance Segmentation Evaluation Metric Utilizing Globally Optimal Matching](https://mlsanity.com/paper/2606.10107/) (2026)

## Abstract (arXiv)

Instance segmentation enables the analysis of spatial and temporal properties of cells in microscopy images by identifying the pixels belonging to each cell. However, progress is constrained by the scarcity of high-quality labeled microscopy datasets. Many recent approaches address this challenge by initializing models with segmentation-pretrained weights from large-scale natural-image models such as Segment Anything Model (SAM). However, representations learned from natural images often encode objectness and texture priors that are poorly aligned with microscopy data, leading to degraded performance under domain shift. We propose DINOCell, a self-supervised framework for cell instance segmentation that leverages representations from DINOv2 and adapts them to microscopy through continued self-supervised training on unlabeled cell images prior to supervised fine-tuning. On the LIVECell benchmark, DINOCell achieves a SEG score of 0.784, improving by 10.42% over leading SAM-based models, and demonstrates strong zero-shot performance on three out-of-distribution microscopy datasets. These results highlight the benefits of domain-adapted self-supervised pretraining for robust cell segmentation.