# MIPHEI-ViT: Multiplex Immunofluorescence Prediction from H&E Images using ViT Foundation Models

arXiv: https://arxiv.org/abs/2505.10294 · HTML: https://mlsanity.com/paper/2505.10294/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 24 of its 62 references that are in the map.
- First posted on arXiv 15 May 2025.

## Builds on (most cited first, 24 of 24)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [High-Resolution Image Synthesis with Latent Diffusion Models](https://mlsanity.com/paper/2112.10752/) (2021)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Image-to-Image Translation with Conditional Adversarial Networks](https://mlsanity.com/paper/1611.07004/) (2016)
- [An Empirical Study of Training Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.02057/) (2021)
- [High-Resolution Image Synthesis and Semantic Manipulation with Conditional GANs](https://mlsanity.com/paper/1711.11585/) (2017)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [iBOT: Image BERT Pre-Training with Online Tokenizer](https://mlsanity.com/paper/2111.07832/) (2021)
- [ConvNeXt V2: Co-designing and Scaling ConvNets with Masked Autoencoders](https://mlsanity.com/paper/2301.00808/) (2023)
- [Vision Transformer Adapter for Dense Predictions](https://mlsanity.com/paper/2205.08534/) (2022)
- [CellViT: Vision Transformers for Precise Cell Segmentation and Classification](https://mlsanity.com/paper/2306.15350/) (2023)
- [Lizard: A Large-Scale Dataset for Colonic Nuclear Instance Segmentation and Classification](https://mlsanity.com/paper/2108.11195/) (2021)
- [Deep learning-based virtual histology staining using auto-fluorescence of label-free tissue](https://mlsanity.com/paper/1803.11293/) (2018)
- [ViT-CoMer: Vision Transformer with Convolutional Multi-scale Feature Interaction for Dense Predictions](https://mlsanity.com/paper/2403.07392/) (2024)
- [ViTMatte: Boosting Image Matting with Pretrained Plain Vision Transformers](https://mlsanity.com/paper/2305.15272/) (2023)
- [Deep Learning-enabled Virtual Histological Staining of Biological Samples](https://mlsanity.com/paper/2211.06822/) (2022)
- [Digital synthesis of histological stains using micro-structured and multiplexed virtual staining of label-free tissue](https://mlsanity.com/paper/2001.07267/) (2020)
- [Label-free virtual HER2 immunohistochemical staining of breast tissue using deep learning](https://mlsanity.com/paper/2112.05240/) (2021)
- [Cross-modality deep learning brings bright-field microscopy contrast to holography](https://mlsanity.com/paper/1811.07103/) (2018)
- [HEMIT: H&E to Multiplex-immunohistochemistry Image Translation with Dual-Branch Pix2pix Generator](https://mlsanity.com/paper/2403.18501/) (2024)
- [Batch Inverse-Variance Weighting: Deep Heteroscedastic Regression](https://mlsanity.com/paper/2107.04497/) (2021)
- [Random Multi-Channel Image Synthesis for Multiplexed Immunofluorescence Imaging](https://mlsanity.com/paper/2109.09004/) (2021)
- [Scalable, Trustworthy Generative Model for Virtual Multi-Staining from H&E Whole Slide Images](https://mlsanity.com/paper/2407.00098/) (2024)

## Built on by (most cited first, 2 of 2)

- [VitaminP: cross-modal learning enables whole-cell segmentation from routine histology](https://mlsanity.com/paper/2604.23799/) (2026)
- [Predicting Immune Biomarkers with MultiModal Mixture-of-Expert Pathology Foundation Models Empowers Precision Oncology](https://mlsanity.com/paper/2606.18123/) (2026)

## Abstract (arXiv)

Histopathological analysis is a cornerstone of cancer diagnosis, with Hematoxylin and Eosin (H&E) staining routinely acquired for every patient to visualize cell morphology and tissue architecture. On the other hand, multiplex immunofluorescence (mIF) enables more precise cell type identification via proteomic markers, but has yet to achieve widespread clinical adoption due to cost and logistical constraints. To bridge this gap, we introduce MIPHEI (Multiplex Immunofluorescence Prediction from H&E Images), a U-Net-inspired architecture that leverages a ViT pathology foundation model as encoder to predict mIF signals from H&E images using rich pretrained representations. MIPHEI targets a comprehensive panel of markers spanning nuclear content, immune lineages (T cells, B cells, myeloid), epithelium, stroma, vasculature, and proliferation. We train our model using the publicly available OrionCRC dataset of restained H&E and mIF images from colorectal cancer tissue, and validate it on five independent datasets: HEMIT, PathoCell, IMMUcan, Lizard and PanNuke. On OrionCRC test set, MIPHEI achieves accurate cell-type classification from H&E alone, with F1 scores of 0.93 for Pan-CK, 0.83 for alpha-SMA, 0.68 for CD3e, 0.36 for CD20, and 0.28 for CD68, substantially outperforming both a state-of-the-art baseline and a random classifier for most markers. Our results indicate that, for some molecular markers, our model captures the complex relationships between nuclear morphologies in their tissue context, as visible in H&E images and molecular markers defining specific cell types. MIPHEI offers a promising step toward enabling cell-type-aware analysis of large-scale H&E datasets, in view of uncovering relationships between spatial cellular organization and patient outcomes.