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Title: GitHub - ratschlab/DeepSpot: DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images

Open Graph Title: GitHub - ratschlab/DeepSpot: DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images

X Title: GitHub - ratschlab/DeepSpot: DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images

Description: DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images - ratschlab/DeepSpot

Open Graph Description: DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images - ratschlab/DeepSpot

X Description: DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images - ratschlab/DeepSpot

Opengraph URL: https://github.com/ratschlab/DeepSpot

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https://patch-diff.githubusercontent.com/ratschlab/DeepSpot#deepspot-leveraging-spatial-context-for-enhanced-spatial-transcriptomics-prediction-from-he-images
herehttps://www.medrxiv.org/content/10.1101/2025.02.09.25321567v1
https://patch-diff.githubusercontent.com/ratschlab/DeepSpot#news
NeurIPS 2025 Workshop on Multi-modal Foundation Models and Large Language Models for Life Scienceshttps://nips2025fm4ls.github.io/
DeepSpot2Cell: Predicting Virtual Single-Cell Spatial Transcriptomics from H&E images using Spot-Level Supervisionhttps://www.biorxiv.org/content/10.1101/2025.09.23.678121v1
Code.https://github.com/ratschlab/DeepSpot2Cell
"Machine Learning Teams Push the Boundaries of Virtual Spatial Biology in Global Autoimmune Disease Challenge."https://www.ericandwendyschmidtcenter.org/updates/machine-learning-teams-push-the-boundaries-of-virtual-spatial-biology-in-global-autoimmune-disease-challenge
linkhttps://www.medrxiv.org/content/10.1101/2025.02.09.25321567v2
linkhttps://bmi.inf.ethz.ch/news/article/kalin-nonchev-wins-autoimmune-ml-challenge
https://patch-diff.githubusercontent.com/ratschlab/DeepSpot#changelog
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8 TB of predicted TCGA spatial transcriptomics data - LUSC, LUAD, SKCM, KIRChttps://huggingface.co/datasets/nonchev/TCGA_digital_spatial_transcriptomics
more DeepSpot pretrained models on Visium and Xenium datahttps://zenodo.org/records/15322099
https://patch-diff.githubusercontent.com/ratschlab/DeepSpot#do-you-want-to-generate-spatial-transcriptomics-data-using-your-he-images
https://patch-diff.githubusercontent.com/ratschlab/DeepSpot/blob/main/figures/figure_2.png
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herehttps://github.com/ratschlab/he2st
https://patch-diff.githubusercontent.com/ratschlab/DeepSpot#contact
Kalin Nonchevhttps://bmi.inf.ethz.ch/people/person/kalin-nonchev
https://sis.id.ethz.ch/services/sensitiveresearchdata/https://sis.id.ethz.ch/services/sensitiveresearchdata/
https://patch-diff.githubusercontent.com/ratschlab/DeepSpot#nb-computational-data-analysis-was-performed-at-leonhard-med-httpssisidethzchservicessensitiveresearchdata-secure-trusted-research-environment-at-eth-zurich-our-pipeline-aligns-with-the-specific-cluster-requirements-and-resources
www.medrxiv.org/content/10.1101/2025.02.09.25321567v3https://www.medrxiv.org/content/10.1101/2025.02.09.25321567v3
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https://github.com/KalinNonchev
KalinNonchev Kalin Nonchev https://github.com/KalinNonchev
https://github.com/ivanmilevtues
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