Use Python's 'spatialdata-io' to transform manufacturer output to .zarr with specific folder structure.
Source:R/sdio.R
use_sdio.Rd
Use Python's 'spatialdata-io' to transform manufacturer output to .zarr with specific folder structure.
Examples
pa <- path_to_10x_xen_demo()
#> returning path to cached zip
td <- tempfile()
dir.create(td)
unzip(pa, exdir=td)
target <- tempfile()
use_sdio("xenium", srcdir=td, dest=target)
#> NULL
br2fov <- readSpatialData(target)
br2fov
#> class: SpatialData
#> - images(1):
#> - morphology_focus (5,3529,5792)
#> - labels(2):
#> - cell_labels (3529,5792)
#> - nucleus_labels (3529,5792)
#> - points(1):
#> - transcripts (1113950)
#> - shapes(3):
#> - cell_boundaries (7275,circle)
#> - cell_circles (7275,circle)
#> - nucleus_boundaries (7020,circle)
#> - tables(1):
#> - table (280,7275)
#> coordinate systems:
#> - global(7): morphology_focus cell_labels ... nucleus_boundaries
#> transcripts