DeepSpaceDB - Explore Spatial Transcriptomics
Welcome to DeepSpaceDB, a comprehensive spatial transcriptomics database hosting over 2,700 samples across human and mouse tissues. Our platform integrates high-resolution spatial data with powerful analysis tools, enabling researchers to explore gene expression patterns in their biological context.
Whether you're studying tissue development, disease progression, or cellular organization, DeepSpaceDB provides the tools and data you need to unlock spatial insights in your research. Learn more about DeepSpaceDB →
Visium Samples
2144
Visium Spots
5.4M
Xenium Samples
902
Xenium Cells
108M
Latest News
- Official release of DeepSpaceDB v2.0, including 628 Xenium samples and a new Xenium interface. Preprint on bioRxiv [2026 Jan 16]
- We added a new tutorial video about our Xenium interface [2026 Jan 15]
- Our manuscript introducing DeepSpaceDB was published in Nucleic Acids Research [2025 Oct 29]
- Our protocol paper was published in the Journal of Visualized Experiments (JoVE) [2025 Sep 5]
- We updated DeepSpaceDB. The current version (v1.1) contains 2144 Visium samples. [2025 Jun 3]
- We put our preprint about DeepSpaceDB on bioRxiv [2025 Jan 6]
- A short article about DeepSpaceDB was published in 客観日本 (Simplified Chinese and Traditional Chinese) [2024 Dec 13]
- A short article about DeepSpaceDB was published in JST News (Japanese) [2024 Dec 2]
We made DeepSpaceDB v1.0 public [2024 Sep 5]
Human Samples Distribution
Mouse Samples Distribution
Powerful Tools for Spatial Transcriptomics Research
Comprehensive analysis tools designed to accelerate your research from data exploration to discovery
Sample Analysis
Explore different comprehensive tools to analyze a tissue sample made by our scientists
See Sample page →
Tissue Explorer
Compare gene expression between manually selected parts of the tissue.
Try out the Tissue Explorer →
Gene/Pathway Search
Explore spatially variable genes and biological pathways
Search for a gene or pathway →
