datasets
Training and evaluation data, with the modality, task and licence stated up front. Listed live from the Hugging Face Hub.
xenium_pan_datasetxenium_pandavid_datasetxenium_25_lung_dataset_update3xenium_5k_pandavid_dataset_v2xenium_25_lung_dataset_update4xenium_pandavid_dataset4xenium_25_lung_dataset_update1xenium_25_lung_datasetxenium_Xenium_V1_hLiver_nondiseased_section_FFPE_outs_pairxenium_25_lung_dataset_update2xenium_Xenium_V1_Human_Lung_Cancer_Addon_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_VUILD102MF_pairXenium_Prime_Ovarian_Cancer_FFPE_XRrun_outs_row-group-parquetData obtained from https://www.10xgenomics.com/datasets
celldega_Xenium_hCRCxenium_Xenium_V1_human_Pancreas_FFPE_outs_paircelldega_Xenium_human_Pancreas_FFPE_v2Xenium_V1_human_Pancreas_FFPE_outs_row_groupsData obtained from
10X Genomics
xenium-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_Prime_Ovarian_Cancer_FFPE_XRun_outs_row_groups_image_chunkxeniumrangerxenium-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_25_lung_dataset_frac10_trainxenium_TILD175_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.xenium_pandavid_dataset5xenium-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_25_lung_dataset_frac10_testxenium_VUHD113_pairxenium_25_lung_dataset_frac10_val