`SpatialData.data`
Helena Lucia Crowell
Artür Manukyan
Hugo Gruson
Vince Carey
October 08, 2026
Source:vignettes/SpatialData.data.Rmd
SpatialData.data.RmdSpatialData.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
- biocOSN: Bioc’s NSF OSN bucket,
- sandbox: scverse’s spatialdata-sandbox (https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html)
Installation
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:
if(!requireNamespace("pak"))
install.packages("pak")
pak::pak("HelenaLC/SpatialData.data")To interrogate our S3 bucket you will need paws.storage installed.
library(spatialdataR)
library(SpatialData.data)
library(paws.storage)
Sys.setenv(AWS_REGION = "us-east-1") Load SpatialData (.zarr) from Archives
Any SpatialData dataset can be retrieved (once) into some location, and read into R.
(x <- SD.data_load("ColorectalCarcinomaMIBITOF"))## 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.
(x <- SD.data_load("ColorectalCarcinomaMIBITOF", src ="sandbox"))## 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:
View(SD.data_list(metadata = TRUE))You can also interrogate the sources (S3 buckets) for available (zipped) .zarr archives:
SD.data_available("biocOSN")## [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"Session info
## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.5 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-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
## [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
## [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
##
## time zone: 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_0.99.44
## [4] BiocStyle_2.41.0
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.2.1 blob_1.3.0
## [3] dplyr_1.2.1 filelock_1.0.3
## [5] R.utils_2.13.0 fastmap_1.2.0
## [7] SingleCellExperiment_1.35.2 BiocFileCache_3.3.0
## [9] digest_0.6.39 lifecycle_1.0.5
## [11] sf_1.1-3 RSQLite_3.53.3
## [13] magrittr_2.0.5 compiler_4.6.1
## [15] rlang_1.3.0 sass_0.4.10
## [17] tools_4.6.1 yaml_2.3.12
## [19] knitr_1.52 S4Arrays_1.13.2
## [21] htmlwidgets_1.6.4 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_2.23-26 withr_3.0.3
## [31] purrr_1.2.2 BiocGenerics_0.59.12
## [33] desc_1.4.3 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 ragg_1.5.2
## [43] generics_0.1.4 otel_0.2.0
## [45] DBI_1.3.0 cachem_1.1.0
## [47] proxy_0.4-29 BiocManager_1.30.27
## [49] XVector_0.53.0 matrixStats_1.5.0
## [51] vctrs_0.7.3 Matrix_1.7-5
## [53] jsonlite_2.0.0 bookdown_0.48
## [55] IRanges_2.47.5 S4Vectors_0.51.10
## [57] bit64_4.8.6 RBGL_1.89.0
## [59] systemfonts_1.3.2 jquerylib_0.1.4
## [61] units_1.0-1 glue_1.8.1
## [63] pkgdown_2.2.1 ZarrArray_1.0.1
## [65] Rarr_2.0.1 GenomicRanges_1.65.4
## [67] tibble_3.3.1 pillar_1.11.1
## [69] htmltools_0.5.9 Seqinfo_1.3.2
## [71] graph_1.91.0 dbplyr_2.6.0
## [73] R6_2.6.1 httr2_1.3.0
## [75] textshaping_1.0.5 evaluate_1.0.5
## [77] lattice_0.22-9 Biobase_2.73.2
## [79] R.methodsS3_1.8.2 png_0.1-9
## [81] duckspatial_1.2.1 memoise_2.0.1
## [83] paws.common_0.9.0 bslib_0.12.0
## [85] class_7.3-23 Rcpp_1.1.2
## [87] SparseArray_1.13.4 anndataR_1.2.2
## [89] xfun_0.61 fs_2.1.0
## [91] MatrixGenerics_1.25.0 pkgconfig_2.0.3