PixCell: A generative foundation model for digital histopathology images
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2025
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| author | Yellapragada, Srikar Graikos, Alexandros Li, Zilinghan Triaridis, Kostas Belagali, Varun Nandi, Tarak Nath Bai, Karen Knudsen, Beatrice S. Kurc, Tahsin Gupta, Rajarsi R. Prasanna, Prateek Madduri, Ravi K Saltz, Joel Samaras, Dimitris |
| author_facet | Yellapragada, Srikar Graikos, Alexandros Li, Zilinghan Triaridis, Kostas Belagali, Varun Nandi, Tarak Nath Bai, Karen Knudsen, Beatrice S. Kurc, Tahsin Gupta, Rajarsi R. Prasanna, Prateek Madduri, Ravi K Saltz, Joel Samaras, Dimitris |
| contents | The digitization of histology slides has revolutionized pathology, providing massive datasets for cancer diagnosis and research. Self-supervised and vision-language models have been shown to effectively mine large pathology datasets to learn discriminative representations. On the other hand, there are unique problems in pathology, such as annotated data scarcity, privacy regulations in data sharing, and inherently generative tasks like virtual staining. Generative models, capable of synthesizing realistic and diverse images, present a compelling solution to address these problems through image synthesis. We introduce PixCell, the first generative foundation model for histopathology images. PixCell is a diffusion model trained on PanCan-30M, a large, diverse dataset derived from 69,184 H&E-stained whole slide images of various cancer types. We employ a progressive training strategy and a self-supervision-based conditioning that allows us to scale up training without any human-annotated data. By conditioning on real slides, the synthetic images capture the properties of the real data and can be used as data augmentation for small-scale datasets to boost classification performance. We prove the foundational versatility of PixCell by applying it to two generative downstream tasks: privacy-preserving synthetic data generation and virtual IHC staining. PixCell's high-fidelity conditional generation enables institutions to use their private data to synthesize highly realistic, site-specific surrogate images that can be shared in place of raw patient data. Furthermore, using datasets of roughly paired H&E-IHC tiles, we learn to translate PixCell's conditioning from H&E to multiple IHC stains, allowing the generation of IHC images from H&E inputs. Our trained models are publicly released to accelerate research in computational pathology. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2506_05127 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | PixCell: A generative foundation model for digital histopathology images Yellapragada, Srikar Graikos, Alexandros Li, Zilinghan Triaridis, Kostas Belagali, Varun Nandi, Tarak Nath Bai, Karen Knudsen, Beatrice S. Kurc, Tahsin Gupta, Rajarsi R. Prasanna, Prateek Madduri, Ravi K Saltz, Joel Samaras, Dimitris Image and Video Processing Computer Vision and Pattern Recognition Quantitative Methods The digitization of histology slides has revolutionized pathology, providing massive datasets for cancer diagnosis and research. Self-supervised and vision-language models have been shown to effectively mine large pathology datasets to learn discriminative representations. On the other hand, there are unique problems in pathology, such as annotated data scarcity, privacy regulations in data sharing, and inherently generative tasks like virtual staining. Generative models, capable of synthesizing realistic and diverse images, present a compelling solution to address these problems through image synthesis. We introduce PixCell, the first generative foundation model for histopathology images. PixCell is a diffusion model trained on PanCan-30M, a large, diverse dataset derived from 69,184 H&E-stained whole slide images of various cancer types. We employ a progressive training strategy and a self-supervision-based conditioning that allows us to scale up training without any human-annotated data. By conditioning on real slides, the synthetic images capture the properties of the real data and can be used as data augmentation for small-scale datasets to boost classification performance. We prove the foundational versatility of PixCell by applying it to two generative downstream tasks: privacy-preserving synthetic data generation and virtual IHC staining. PixCell's high-fidelity conditional generation enables institutions to use their private data to synthesize highly realistic, site-specific surrogate images that can be shared in place of raw patient data. Furthermore, using datasets of roughly paired H&E-IHC tiles, we learn to translate PixCell's conditioning from H&E to multiple IHC stains, allowing the generation of IHC images from H&E inputs. Our trained models are publicly released to accelerate research in computational pathology. |
| title | PixCell: A generative foundation model for digital histopathology images |
| topic | Image and Video Processing Computer Vision and Pattern Recognition Quantitative Methods |
| url | https://arxiv.org/abs/2506.05127 |