# Extending 2D foundational DINOv3 representations to 3D segmentation of neonatal brain MR images

arXiv: https://arxiv.org/abs/2602.23962 · HTML: https://mlsanity.com/paper/2602.23962/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 5 of its 19 references that are in the map.
- First posted on arXiv 27 Feb 2026.

## Builds on (most cited first, 5 of 5)

- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [Vision Transformers for Dense Prediction](https://mlsanity.com/paper/2103.13413/) (2021)
- [DINOv3](https://mlsanity.com/paper/2508.10104/) (2025)
- [Customized Segment Anything Model for Medical Image Segmentation](https://mlsanity.com/paper/2304.13785/) (2023)
- [3DSAM-adapter: Holistic adaptation of SAM from 2D to 3D for promptable tumor segmentation](https://mlsanity.com/paper/2306.13465/) (2023)

## Abstract (arXiv)

Precise volumetric delineation of hippocampal structures is essential for quantifying neurodevelopmental trajectories in pre-term and term infants, where subtle morphological variations may carry prognostic significance. While foundation encoders trained on large-scale visual data offer discriminative representations, their 2D formulation is a limitation with respect to the 3D organization of brain anatomy. We propose a volumetric segmentation strategy that reconciles this tension through a structured window-based disassembly-reassembly mechanism: the global MRI volume is decomposed into non-overlapping 3D windows or sub-cubes, each processed via a separate decoding arm built upon frozen high-fidelity features, and subsequently reassembled prior to a ground-truth correspendence using a dense-prediction head. This architecture preserves constant a decoder memory footprint while forcing predictions to lie within an anatomically consistent geometry. Evaluated on the ALBERT dataset for hippocampal segmentation, the proposed approach achieves a Dice score of 0.65 for a single 3D window. The method demonstrates that volumetric anatomical structure could be recovered from frozen 2D foundation representations through structured compositional decoding, and offers a principled and generalizable extension for foundation models for 3D medical applications.