Welcome to 4D-Atlas

4D Spatiotemporal
Transcriptomics Database

A comprehensive platform for exploring four-dimensional spatial transcriptomic atlases across development, regeneration, and disease, enabling dynamic investigation of biological processes in both space and time.

15.6M+
Single Cells / Spots
1,580
Spatial Slices
81
Time Points
6
Species
4D Spatiotemporal Transcriptomics Concept 4D Spatiotemporal
4D-Atlas 4D Spatiotemporal Transcriptomics

Interactive Analysis Tools

Explore our suite of 7 interactive tools for spatiotemporal transcriptomics analysis

Analysis Tools

Integrated analytical tools for exploring four-dimensional spatial transcriptomic data

Spatial Map

Explore four-dimensional tissue architecture by visualizing cell types, tissues, and anatomical annotations across reconstructed 3D tissues and time.

Spatial Modules

Identify spatial hotspot modules and compare their tissue and cell-type enrichment across different developmental stages.

Pathway Activity

Explore pathway activities across tissues and cell types, and visualize their spatial distributions in reconstructed 3D tissues over time.

Regulatory Network

Explore transcription factor-centered regulatory networks and visualize dynamic transcription factor activities in reconstructed 3D tissues.

Cell-Cell Communication

Investigate dynamic ligand–receptor interactions and visualize how intercellular communication changes across space and time.

Developmental Trajectory

Explore cell-state transitions through transcriptomic trajectory reconstruction and cell fate inference across development, regeneration, and disease progression.

Gene Expression Trend

Identify gene clusters with distinct temporal expression patterns and visualize their expression trajectories across development, regeneration, and disease progression.

Contact & Citation

Get in touch or learn more about our platform

Visit
Contact Us
College of Bioinformatics Science and Technology
Harbin Medical University
Harbin, 150081, China
For questions, problems, or comments on the database, please send a mail to
wangli@hrbmu.edu.cn
Cite

4D-Atlas: A multi-species four-dimensional spatial transcriptomics database spanning development, regeneration, and disease