Leveraging Cell-level Spatial Transcriptomics as Weak Supervision for Nuclei Classification

Abstract:Deep learning-based nuclei analysis in histopathology relies heavily on large-scale, expert-curated datasets that are costly and difficult to scale across organs. To address this, we propose a scalable framework leveraging cell-level spatial transcriptomics (ST) as an alternative supervision source for nuclei classification. Cell-level ST provides both gene expression profiles and nucleus masks, enabling automatic generation of image-label pairs without manual annotation. We convert gene expression into cell-type labels and introduce an image-oriented classification strategy to effectively transfer these identities to histopathology images. Evaluated on unseen tissues, our framework achieves comparable segmentation and classification performance compared with conventional supervised approaches, despite using fewer manually annotated datasets.

Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG)

arXiv:2604.23481 [cs.CV]

(or arXiv:2604.23481v2 [cs.CV] for this version)

https://doi.org/10.48550/arXiv.2604.23481 Focus to learn more arXiv-issued DOI via DataCite

arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website.

Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them.

Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs.