A lightweight SpatialExperiment object
derived from a human hippocampus Visium sample, used for demonstrating
the SpatialArtifacts artifact detection workflow.
Format
A SpatialExperiment object with
12,971 genes and 4,965 spots, containing one sample (V11L05-335_C1).
The colData includes precomputed QC metrics (e.g., sum,
detected) from addPerCellQC.
Source
Derived from human hippocampus Visium data (sample V11L05-335_C1)
from Thompson et al. (2025). The raw Space Ranger output was accessed
internally via the spatialHPC project (LIBD4035) on the JHPCE cluster.
The same dataset is publicly available via the
humanHippocampus2024 Bioconductor ExperimentHub package
(https://bioconductor.org/packages/humanHippocampus2024).
A script to reproduce this object is provided in
inst/scripts/make-data.R.
Value
A SpatialExperiment object.
Details
The object was derived from human hippocampus Visium data (sample
V11L05-335_C1) from the spatialHPC project (LIBD4035). To meet
Bioconductor package size requirements (<5 MB), the object was subset
to highly variable genes using scran::getTopHVGs(), image data
was removed, and the counts matrix was stored as a sparse matrix with
XZ compression. QC metrics in colData were computed prior to
gene subsetting and remain accurate for the full spot set.
References
Thompson, J.R., Nelson, E.D., Tippani, M. et al. (2025). An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus. Nature Neuroscience 28, 1990–2004. doi:10.1038/s41593-025-02022-0
Examples
data(spe_vignette)
spe_vignette
#> class: SpatialExperiment
#> dim: 12971 4965
#> metadata(0):
#> assays(1): counts
#> rownames(12971): ENSG00000244734 ENSG00000123560 ... ENSG00000254089
#> ENSG00000125900
#> rowData names(1): symbol
#> colnames(4965): AAACAACGAATAGTTC-1 AAACAAGTATCTCCCA-1 ...
#> TTGTTTGTATTACACG-1 TTGTTTGTGTAAATTC-1
#> colData names(7): in_tissue array_row ... detected total
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres
#> imgData names(0):