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Cynomolgus Monkey Embryo CS9/CS10 Spatial Atlas
Welcome
This interactive web application allows you to explore the 3D spatial transcriptome atlas of cynomolgus monkey embryos at Carnegie Stages 9 and 10.
- 22 major lineage clusters identified across CS9 and CS10
- 3D spatial reconstruction with Spateo alignment
- Gene expression visualization across UMAP and spatial coordinates
- Interactive data exploration and download capabilities
Use the sidebar menu to navigate between different features:
22
Lineage Clusters
2
Developmental Stages
3D
Spatial Reconstruction
Interactive
Data Explorer
Getting Started
1. Navigate to Cluster Explorer to visualize the 22 lineage clusters
2. Use Gene Expression to search and visualize specific genes
3. Explore the Spatial Viewer for 3D tissue organization
4. Download data and plots from the Download Data section
Cluster Explorer
Stage Selection
Cluster Selection
Select a cluster from the dropdown or click on the UMAP plot.
Cluster Statistics
Cell Count
Percentage
UMAP Visualization
Top Marker Genes
Gene Expression Viewer
Gene Selection
Search for any of the 4,663 genes in the dataset.
Display Options
Expression Statistics
UMAP Expression
CS9
CS10
Expression by Cluster
Spatial Expression (3D)
3D Spatial Viewer
Stage Selection
View Mode
Overlay Options
Spatial Information
3D Spatial Visualization
Download Data
Download from Zenodo
The complete dataset is available for download from Zenodo.
Download Dataset from Zenodo
Dataset Contents
| File | Description | Format |
|---|---|---|
| metadata.rds | Cell annotations, QC metrics, cluster assignments (93,888 cells) | RDS |
| umap_coords.rds | UMAP dimensional reduction coordinates | RDS |
| spatial_coords.rds | 3D spatial coordinates from Spateo alignment (20 slices) | RDS |
| expression_data.rds | Sparse gene expression matrix (4,663 genes × 93,888 cells) | RDS |
| marker_genes_combined.rds | Cell type identity markers (combined CS9 + CS10) | RDS |
| marker_genes_cs9.rds | CS9-specific developmental markers | RDS |
| marker_genes_cs10.rds | CS10-specific developmental markers | RDS |
Loading Data in R
# Download and unzip from Zenodo, then:
library(Matrix)
metadata <- readRDS('MonkeyEmbryo_CS910_Atlas_Data/metadata.rds')
umap <- readRDS('MonkeyEmbryo_CS910_Atlas_Data/umap_coords.rds')
spatial <- readRDS('MonkeyEmbryo_CS910_Atlas_Data/spatial_coords.rds')
expr <- readRDS('MonkeyEmbryo_CS910_Atlas_Data/expression_data.rds')
markers <- readRDS('MonkeyEmbryo_CS910_Atlas_Data/marker_genes_combined.rds')
About
Project Information
Cynomolgus Monkey Embryo CS9/CS10 Spatial Atlas
This web application provides interactive access to spatial transcriptomics data from cynomolgus monkey embryos at Carnegie Stages 9 and 10, capturing key events of early organogenesis.
License
This application is released under the MIT License.