# An Active Learning Pipeline for Biomedical Image Instance Segmentation with Minimal Human Intervention

arXiv: https://arxiv.org/abs/2511.04811 · HTML: https://mlsanity.com/paper/2511.04811/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 6 of its 12 references that are in the map.
- First posted on arXiv 6 Nov 2025.

## Builds on (most cited first, 6 of 6)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [SAM 2: Segment Anything in Images and Videos](https://mlsanity.com/paper/2408.00714/) (2024)
- [Deep Batch Active Learning by Diverse, Uncertain Gradient Lower Bounds](https://mlsanity.com/paper/1906.03671/) (2019)
- [Suggestive Annotation: A Deep Active Learning Framework for Biomedical Image Segmentation](https://mlsanity.com/paper/1706.04737/) (2017)
- [Self Pre-training with Masked Autoencoders for Medical Image Classification and Segmentation](https://mlsanity.com/paper/2203.05573/) (2022)

## Abstract (arXiv)

Biomedical image segmentation is critical for precise structure delineation and downstream analysis. Traditional methods often struggle with noisy data, while deep learning models such as U-Net have set new benchmarks in segmentation performance. nnU-Net further automates model configuration, making it adaptable across datasets without extensive tuning. However, it requires a substantial amount of annotated data for cross-validation, posing a challenge when only raw images but no labels are available. Large foundation models offer zero-shot generalizability, but may underperform on specific datasets with unique characteristics, limiting their direct use for analysis. This work addresses these bottlenecks by proposing a data-centric AI workflow that leverages active learning and pseudo-labeling to combine the strengths of traditional neural networks and large foundation models while minimizing human intervention. The pipeline starts by generating pseudo-labels from a foundation model, which are then used for nnU-Net's self-configuration. Subsequently, a representative core-set is selected for minimal manual annotation, enabling effective fine-tuning of the nnU-Net model. This approach significantly reduces the need for manual annotations while maintaining competitive performance, providing an accessible solution for biomedical researchers to apply state-of-the-art AI techniques in their segmentation tasks. The code is available at https://github.com/MMV-Lab/AL_BioMed_img_seg.