# Pix2Rep-v2: Data-Efficient Representation Learning for Dense Medical Imaging Applications

arXiv: https://arxiv.org/abs/2609.01427 · HTML: https://mlsanity.com/paper/2609.01427/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 20 of its 29 references that are in the map.
- First posted on arXiv 1 Sep 2026.

## Builds on (most cited first, 20 of 20)

- [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)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [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)
- [Barlow Twins: Self-Supervised Learning via Redundancy Reduction](https://mlsanity.com/paper/2103.03230/) (2021)
- [SAM 3: Segment Anything with Concepts](https://mlsanity.com/paper/2511.16719/) (2025)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [The Faiss library](https://mlsanity.com/paper/2401.08281/) (2024)
- [AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://mlsanity.com/paper/2206.08023/) (2022)
- [Unsupervised Learning of Dense Visual Representations](https://mlsanity.com/paper/2011.05499/) (2020)
- [Causality-inspired Single-source Domain Generalization for Medical Image Segmentation](https://mlsanity.com/paper/2111.12525/) (2021)
- [MedSAM2: Segment Anything in 3D Medical Images and Videos](https://mlsanity.com/paper/2504.03600/) (2025)
- [vox2vec: A Framework for Self-supervised Contrastive Learning of Voxel-level Representations in Medical Images](https://mlsanity.com/paper/2307.14725/) (2023)
- [BT-Unet: A self-supervised learning framework for biomedical image segmentation using Barlow Twins with U-Net models](https://mlsanity.com/paper/2112.03916/) (2021)
- [S5CL: Unifying Fully-Supervised, Self-Supervised, and Semi-Supervised Learning Through Hierarchical Contrastive Learning](https://mlsanity.com/paper/2203.07307/) (2022)
- [Implicit U-Net for volumetric medical image segmentation](https://mlsanity.com/paper/2206.15217/) (2022)
- [Dense Self-Supervised Learning for Medical Image Segmentation](https://mlsanity.com/paper/2407.20395/) (2024)
- [Self-supervised Learning of Dense Hierarchical Representations for Medical Image Segmentation](https://mlsanity.com/paper/2401.06473/) (2024)

## Abstract (arXiv)

Dense self-supervised learning (SSL) is a powerful paradigm for learning without annotations the local descriptors required to solve dense medical imaging tasks. We present Pix2Rep-v2, a framework for SSL of pixel- and voxel-level representations suitable for few-shot downstream applications. Pix2Rep-v2 addresses the main challenges of dense SSL by leveraging a redundancy reduction objective at the pixel-level with a principle of equivariance of dense representations, that scales efficiently to 3D or wide field-of-view applications. We evaluate our method on four datasets, across multiple tasks, multiple modalities and anatomical structures using multiple backbones in 2D and 3D, and under various data regimes. As an alternative to linear probing or full fine-tuning on the downstream task, we also propose an in-context variant, without downstream training, based on a dense prototype approach. Pix2Rep-v2 shows substantially higher data-efficiency in few-shot scenarios compared to fully supervised baselines, and is competitive with the state-of-the-art e.g., +9.3 Dice points in one-shot segmentation on the M&Ms-2 dataset. Our code and pre-trained models are publicly available at https://github.com/BioMedTP/pix2rep-v2.