stVirtual: Mouse Brain Spatial Transcriptomics and IMC Data for Cross-Slice Simulation

Processed mouse brain spatial transcriptomics and Imaging Mass Cytometry spatial omics data used to demonstrate the stVirtual tool. The dataset includes an example route between slices T170 and T171 and a compact demo for the workflow. It was last updated on 2026-05-23 by author Yijin Zhou and is provided under a CC-BY-4.0 license for demonstration and reproducibility.

Use Cases

• Demonstrating cross-slice simulation based on the example route between slices T170 and T171.
• Performing virtual intermediate tissue reconstruction based on the provided spatial-domain annotations.
• Creating 3D/4D tissue representations based on the processed spatial transcriptomics and IMC data.
• Reproducing the stVirtual workflow based on the compact IMC demo included in the dataset.

Strengths

• Includes processed data from two spatial omics modalities: spatial transcriptomics and Imaging Mass Cytometry.
• Spatial-domain annotations for the IMC data were generated using the GASTON method.
• Dataset size is 400.0 MB, indicating a medium-scale, downloadable resource.
• Associated code repository is provided for full reproducibility of the stVirtual demo.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment for large-scale modeling.
• Dataset is explicitly for demonstration purposes and may not be suitable for primary research.

Provenance

Source

Yijin Zhou

Collection Method

Processed from original spatial omics experiments for use in the stVirtual demo.

Freshness

Last updated 2026-05-23 08:23:28.