datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
xenium_pan_datasetxenium_5k_pandavid_dataset_v2xenium_25_lung_dataset_update3xenium_pandavid_datasetxenium_Xenium_V1_hLiver_nondiseased_section_FFPE_outs_pairhumanbreast_xenium_janesick # Human Breast Cancer Xenium · Sample 1 Rep1+Rep2
Curated, ready-to-load spatial transcriptomics dataset.
## Source
- Paper: [Janesick et al., Nat. Commun. 2023](https://www.nature.com/articles/s41467-023-43458-x)
- Canonical download: cf.10xgenomics.com/samples/xenium/1.0.1/Xenium_FFPE_Human_Breast_Cancer_Rep{1,2}
## Scale
| Property | Value |
|---|---|
| Technology | 10x Genomics Xenium (313-gene panel) |
| Species | Homo sapiens |
| Tissue |… See the full description on the dataset page: https://huggingface.co/datasets/Shaow/humanbreast_xenium_janesick.Xenium_10xGenomicsxenium_25_lung_dataset_update4xenium_25_lung_dataset_update2xenium_pandavid_dataset4xenium_Xenium_V1_Human_Lung_Cancer_Addon_FFPE_outs_pairxenium_25_lung_dataset_update1xenium-senescence-demo
Xenium Senescence Benchmark (Demo Preview)
Note: This is a demo preview with 234 sample images. The full dataset (62K labeled cells across 2 tissue samples and 3 magnification scales) will be released upon paper publication.
Overview
A benchmark dataset for predicting cellular senescence from spatial transcriptomics (Xenium) cell images. Cell images are DAPI fluorescence microscopy captures at multiple magnification scales, labeled with senescence scores derived from… See the full description on the dataset page: https://huggingface.co/datasets/Xiang-zx-zx/xenium-senescence-demo.celldega_Xenium_hCRCXenium_Prime_Ovarian_Cancer_FFPE_XRrun_outs_row-group-parquetData obtained from https://www.10xgenomics.com/datasets
xenium_25_lung_datasetXenium_V1_human_Pancreas_FFPE_outs_row_groupsData obtained from
10X Genomics
xenium_VUILD102MF_pairHEST_Xenium_virtual_spatial_transcriptomics
HEST Xenium virtual spatial transcriptomics
This repository contains predicted spatial transcriptomics for HEST Xenium H&E
slides produced with DeepSpot-M.
Authors: Kalin Nonchev, Sebastian Dawo, Karina Silina, Viktor Hendrik
Koelzer, and Gunnar Rätsch.
Paper: DeepSpot-M: a multimodal foundation model for transcriptome-wide virtual spatial transcriptomics from histology (medRxiv, 2026; see the citation below).
Code: https://github.com/ratschlab/DeepSpotM.
News… See the full description on the dataset page: https://huggingface.co/datasets/ratschlab/HEST_Xenium_virtual_spatial_transcriptomics.xeniumrangerxenium-breast-cancer-split
Xenium Breast Cancer Dataset Split
Processed Xenium spatial transcriptomics data for 3D cell shape reconstruction.
Structure
test/ — test split (pkl, npy batches)
trainval/ — train/val split (pkl, npy batches)
split_info/ — cell type labels and original indices
xenium_Xenium_V1_human_Pancreas_FFPE_outs_pairCelldega_Xenium_Prime_Ovarian_Cancer_FFPE_XRun_outs_row_groups_image_chunkcelldega_Xenium_human_Pancreas_FFPE_v2xenium-senescence-data
Xenium Senescence Dataset
Cell morphology images (64x64 grayscale) from Xenium spatial transcriptomics, with senescence scores.
Structure
data_ccdm/
xenium_{tissue}_64x64_aligned.h5 # Images + senescence scores (aligned version)
checkpoints/
latents_{tissue}.npy # VAE-encoded latents (128-dim)
ot_pairs_{tissue}_typed.npy # Within-cell-type OT pairs (cosine cost)
celltype_ids_{tissue}.npy # Integer cell type IDs… See the full description on the dataset page: https://huggingface.co/datasets/Xiang-zx-zx/xenium-senescence-data.xenium_TILD175_pairxenium_25_lung_dataset_frac10_trainxenium_VUILD78LF_pairxenium_pandavid_dataset5xenium_von_10x
Dataset Card for SpatialRefinery Xenium
What is Xenium von 10x?
A collection of 31 spatial transcriptomic profiles, each linked and aligned to a Whole Slide Image (with pixel size < 0.3 µm/px) and metadata.
Xenium von 10x was assembled from the 10x website encompassing:
multiple tissues
1 species (Homo Sapiens)
31 cancer samples
This is a temporary dataset and can have bugs!!!
Instructions for Setting Up HuggingFace Account and Token
1.… See the full description on the dataset page: https://huggingface.co/datasets/rushin682/xenium_von_10x.