Serial 2D Spatial Transcriptomics for Isotropic 3D Reconstruction of Multiple Tissues

Preprocessed serial 2D spatial transcriptomics sections for mouse brain, embryo, kidney, spinal cord, and human gastrula tissue, designed for isotropic-resolution 3D reconstruction tasks. The 1.6 GB dataset, authored by Bohan Li and last updated in April 2026, includes auxiliary structural features from the Allen Mouse Brain CCFv3 reference. All data is normalized and stored as .pt files with spatial coordinates and the top 50 principal components of gene expression.

Use Cases

• Train 3D reconstruction models based on serial 2D spatial transcriptomics sections.
• Analyze continuous spatial gene expression variation across tissue depth based on normalized principal components.
• Incorporate structural priors for modeling based on auxiliary point cloud and image-derived features from the Allen Mouse Brain CCFv3.
• Benchmark isotropic scaling methods for spatial coordinates in the xy-plane.

Strengths

• Includes data from five distinct biological systems: mouse brain (two variants), embryo, kidney, spinal cord, and human gastrula (Carnegie stage 7).
• All data is preprocessed with consistent normalization, including min-max scaling for features and isotropic scaling for spatial coordinates.
• Provides auxiliary structural features from the authoritative Allen Mouse Brain CCFv3 reference dataset.
• Includes normalization metadata (min_dic.csv, scale_dic.csv) and a shared PCA model for exact reconstruction and inverse transformation.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment for specific model training needs.
• Data may reflect bias inherent to the specific biological samples and profiling technologies used.

Provenance

Source

figshare

Collection Method

Aggregation and preprocessing of serial 2D spatial transcriptomics sections from multiple studies.

Time Range

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Freshness

Last updated 2026-04-27 10:47:13

Geography

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