VISTACT: VIrtual histological STAining of micro-Computed Tomography

What is VISTACT dataset?

It is a set of phase-contrast micro-computed tomography volumes (PCμCT) of human lung tissue with corresponding serial histological sections stained with Elastin-van-Gieson (EvG), which is the gold-standard stain for pulmonary hypertension disease in the pathology workflow. Additionally, we also include a PCμCT dataset from mouse heart-lung tissue with corresponding H&E histological sections. Scan resolution: Human lung microCT scans: 1.63 μm/voxel ; Mouse lung microCT scan: 0.88 μm/voxel.

📄 Preprint

🤖 Codebase

Instructions for Setting Up HuggingFace Account and inspect the dataset

1. Create an Account on HuggingFace

Follow the instructions provided on the HuggingFace sign-up page.

2. Accept terms of use of VISTACT

1. On this page click request access (access will be automatically granted).

At this stage, you can already manually inspect the data by navigating in the Files and version.

Cite

If you find this dataset useful in your research, please cite our paper:

@article{almagro2025histology,
  title={Histology-guided 3D virtual staining of microCT-imaged lung tissue via deep learning},
  author={Almagro-P{\'e}rez, Cristina and Peruzzi, Niccol{\`o} and Galambos, Csaba and Song, Andrew H and Brunnstr{\"o}m, Hans and Gawlik, Kinga I and Stampanoni, Marco and Tran-Lundmark, Karin and Lovric, Goran},
  journal={bioRxiv},
  pages={2025--10},
  year={2025},
  publisher={Cold Spring Harbor Laboratory}
}