In-Context Adaptation of VLMs for Few-Shot Cell Detection in Optical Microscopy

Abstract

Foundation vision-language models (VLMs) excel on natural images, but their utility for biomedical microscopy remains underexplored. In this paper, we investigate how in-context learning enables state-of-the-art VLMs to perform few-shot object detection when large annotated datasets are unavailable, as is often the case with microscopic images. We introduce the Micro-OD benchmark, a curated collection of 252 images specifically curated for in-context learning, with bounding-box annotations spanning 11 cell types across four sources, including two in-lab expert-annotated sets. We systematically evaluate eight VLMs under few-shot conditions and compare variants with and without implicit test-time reasoning tokens. We further implement a hybrid Few-Shot Object Detection (FSOD) pipeline that combines a detection head with a VLM-based few-shot classifier, which enhances the few-shot performance of recent VLMs on our benchmark. Across datasets, we observe that zero-shot performance is weak due to the domain gap; however, few-shot support consistently improves detection, with marginal gains achieved after six shots. We observe that models with reasoning tokens are more effective for end-to-end localization, whereas simpler variants are more suitable for classifying pre-localized crops. Our results highlight in-context adaptation as a practical path for microscopy, and our benchmark provides a reproducible testbed for advancing open-vocabulary detection in biomedical imaging.