transcriptomics
TCGA_virtual_spatial_transcriptomics_atlas
TCGA virtual spatial transcriptomics atlas
This repository contains predicted spatial transcriptomics for TCGA H&E slides,
both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE), produced
with DeepSpot-M.
Authors: Kalin Nonchev, Sebastian Dawo, Karina Silina, Viktor Hendrik
Koelzer, and Gunnar Rätsch.
Model: ratschlab/DeepSpotM · Code: github.com/ratschlab/DeepSpotM · Paper: medRxiv 2026.06.19.26356060.
News
[09.2026] Introducing Aurora - a no-code… See the full description on the dataset page: https://huggingface.co/datasets/ratschlab/TCGA_virtual_spatial_transcriptomics_atlas.TCGA_virtual_spatial_transcriptomics
Dataset card for TCGA digital spatial transcriptomics data
This repository contains results from the paper "DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images".
Authors: Kalin Nonchev, Sebastian Dawo, Karina Selina, Holger Moch, Sonali Andani, Tumor Profiler Consortium, Viktor Hendrik Koelzer, and Gunnar Rätsch
The preprint is available here.
What is TCGA digital spatial transcriptomics?
We trained a model using… See the full description on the dataset page: https://huggingface.co/datasets/nonchev/TCGA_virtual_spatial_transcriptomics.spatial-transcriptomics-atlas-demo
Spatial Transcriptomics Atlas: Human Lymph Node Architecture and Immune Microenvironment
Integrated multi-modal analysis of spatial gene expression in human lymph node tissue. Panels depict high-resolution histology (A), annotated tissue domains (B), gene detection density (C), expression patterns of top spatially variable genes (D--F), and neighborhood enrichment statistics (G).
Abstract
This repository presents a reproducible computational… See the full description on the dataset page: https://huggingface.co/datasets/QasimHussain/spatial-transcriptomics-atlas-demo.HEST_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.HEST_Visium_virtual_single_cell_transcriptomics
HEST-1k Visium virtual single-cell spatial transcriptomics
Predicted virtual single-cell gene expression for HEST-1k Visium samples,
produced with DeepSpot2Cell. DeepSpot2Cell is a Deep Sets model that predicts
transcriptomic profiles at single-cell resolution from H&E images and CellViT cell
segmentations, trained with spot-level Visium supervision only (no single-cell
ground truth). At inference every detected cell in each Visium spot receives its
own predicted expression… See the full description on the dataset page: https://huggingface.co/datasets/ratschlab/HEST_Visium_virtual_single_cell_transcriptomics.human_spatial_transcriptomics
Human Spatial Transcriptomics Multi-organ Multi-platform Collection
This dataset provides a cleaned human spatial transcriptomics collection in .h5ad format. The released archive, Homo_sapiens_h5ad_flat.zip, contains 1,155 .h5ad files gathered into a flat archive for convenient download and reuse.
Dataset Summary
The collection covers Homo sapiens spatial transcriptomics data across multiple organs and experimental platforms. According to the accompanying internal… See the full description on the dataset page: https://huggingface.co/datasets/Bgoood/human_spatial_transcriptomics.