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MERFISH Colitis Query (Day 9 Colitis) Spatial Dataset

Source: R/dataDocumentation.R
merfish_query_data.Rd

This dataset contains a downsampled query (Day 9, DSS-induced colitis at peak inflammation) subset of the Cadinu et al. (2024) mouse colitis MERFISH dataset, for use alongside merfish_reference_data.

Usage

merfish_query_data

Format

An object of class SpatialExperiment with 943 rows and 1300 columns.

Source

Cadinu CA, et al. (2024), processed and hosted at https://doi.org/10.5281/zenodo.18274942.

Details

See merfish_reference_data for the shared processing steps. Cells are downsampled to at most 260 per cell type. The tier2_merged column retains the original fine-grained label (e.g. distinguishing "Fibroblast" from "Inflamed Fibroblast"), which is not passed to scDiagnostics functions directly but is useful for checking which cells a diagnostic actually flags.

References

Cadinu CA, et al. (2024). Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling. Cell 187(8):2010-2028.

See also

Use data("merfish_query_data") to load and access the resulting query dataset, and data("merfish_reference_data") for comparison with the reference dataset.

Examples

# Load and explore the MERFISH query dataset
data("merfish_query_data")