SpatialData.dataSpatialData.data
package provides utilities for accessing, reading and generating
SpatialData datasets. Data from a variety of spatial omics technologies
has been made available as SpatialData (zipped) .zarr
stores.
These scverse SpatialData examples are available through sources
You can install SpatialData.data using:
if(!requireNamespace("spatialdataR"))
BiocManager::install("spatialdataR")
if(!requireNamespace("SpatialData.data"))
BiocManager::install("SpatialData.data")You can also install the development version like so:
To interrogate our S3 bucket you will need paws.storage installed.
Any SpatialData dataset can be retrieved (once) into some location, and read into R.
## class: SpatialData
## - images(3):
## - point16_image (3,1024,1024)
## - point23_image (3,1024,1024)
## - point8_image (3,1024,1024)
## - labels(3):
## - point16_labels (1024,1024)
## - point23_labels (1024,1024)
## - point8_labels (1024,1024)
## - points(0):
## - shapes(0):
## - tables(1):
## - table (36,3309) [point8_labels,point16_labels,point23_labels]
## coordinate systems(3):
## - point16(2): point16_image point16_labels
## - point23(2): point23_image point23_labels
## - point8(2): point8_image point8_labelsYou can also install the same data from different sources, including
the scverse’s spatialdata sandbox where SpatialData stores
are saved as Zarr v3.
## class: SpatialData
## - images(3):
## - point16_image (3,1024,1024)
## - point23_image (3,1024,1024)
## - point8_image (3,1024,1024)
## - labels(3):
## - point16_labels (1024,1024)
## - point23_labels (1024,1024)
## - point8_labels (1024,1024)
## - points(0):
## - shapes(0):
## - tables(1):
## - table (36,3309) [point8_labels,point16_labels,point23_labels]
## coordinate systems(3):
## - point16(2): point16_image point16_labels
## - point23(2): point23_image point23_labels
## - point8(2): point8_image point8_labelsWe can check all available datasets and their sources with:
## [1] "MouseIntestineVisHD" "MouseBrainVisHD"
## [3] "MouseBrainVis" "LungAdenocarcinomaMCMICRO"
## [5] "MouseBrainMERFISH" "MouseLiverMERFISH"
## [7] "ColorectalCarcinomaMIBITOF" "MulticancerSteinbock"
## [9] "JanesickBreastVisiumEnh" "JanesickBreastXeniumRep1"
## [11] "JanesickBreastXeniumRep2" "HumanLungMulti_10x"
## [13] "SpaceMHelaniH3T3"or as below for a detailed overview and metadata on all datasets:
You can also interrogate the sources (S3 buckets) for available (zipped) .zarr archives:
## [1] "HuLungXenmulti.zip"
## [2] "mcmicro_io.zip"
## [3] "merfish.zarr.zip"
## [4] "mibitof.zip"
## [5] "steinbock_io.zip"
## [6] "visium_associated_xenium_io_aligned.zip"
## [7] "visium_hd_3.0.0_io.zip"
## [8] "xenium_rep1_io_aligned.zip"
## [9] "xenium_rep2_io_aligned.zip"## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] paws.storage_0.11.0 SpatialData.data_0.99.10 spatialdataR_0.99.45
## [4] BiocStyle_2.41.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.1 grumpy_0.1.1
## [3] dplyr_1.2.1 blob_1.3.0
## [5] filelock_1.0.3 R.utils_2.13.0
## [7] fastmap_1.2.0 SingleCellExperiment_1.35.2
## [9] BiocFileCache_3.3.0 digest_0.6.39
## [11] lifecycle_1.0.5 sf_1.1-3
## [13] RSQLite_3.53.3 magrittr_2.0.5
## [15] compiler_4.6.1 rlang_1.3.0
## [17] sass_0.4.10 tools_4.6.1
## [19] yaml_2.3.12 knitr_1.52
## [21] S4Arrays_1.13.2 bit_4.6.0
## [23] classInt_0.4-11 curl_8.0.0
## [25] reticulate_1.47.0 DelayedArray_0.39.8
## [27] xml2_1.6.0 abind_1.4-8
## [29] KernSmooth_2.23-27 withr_3.0.3
## [31] purrr_1.2.2 BiocGenerics_0.59.12
## [33] sys_3.4.3 R.oo_1.27.1
## [35] grid_4.6.1 stats4_4.6.1
## [37] e1071_1.7-17 SummarizedExperiment_1.43.0
## [39] cli_3.6.6 rmarkdown_2.32
## [41] crayon_1.5.3 generics_0.1.4
## [43] otel_0.2.0 DBI_1.3.0
## [45] cachem_1.1.0 proxy_0.4-29
## [47] BiocManager_1.30.27 XVector_0.53.0
## [49] matrixStats_1.5.0 vctrs_0.7.3
## [51] Matrix_1.7-6 jsonlite_2.0.0
## [53] IRanges_2.47.5 S4Vectors_0.51.10
## [55] bit64_4.8.6 RBGL_1.89.0
## [57] maketools_1.3.2 jquerylib_0.1.4
## [59] units_1.0-1 glue_1.8.1
## [61] ZarrArray_1.1.7 Rarr_2.1.45
## [63] GenomicRanges_1.65.4 tibble_3.3.1
## [65] pillar_1.11.1 htmltools_0.5.9
## [67] Seqinfo_1.3.2 graph_1.91.0
## [69] dbplyr_2.6.0 R6_2.6.1
## [71] httr2_1.3.0 evaluate_1.0.5
## [73] lattice_0.23-1 Biobase_2.73.2
## [75] R.methodsS3_1.8.2 png_0.1-9
## [77] duckspatial_1.3.0 memoise_2.0.1
## [79] paws.common_0.9.0 bslib_0.12.0
## [81] class_7.3-24 Rcpp_1.1.2
## [83] SparseArray_1.13.4 anndataR_1.3.2
## [85] xfun_0.61 MatrixGenerics_1.25.0
## [87] buildtools_1.0.0 pkgconfig_2.0.3