Use Python's 'spatialdata-io' to transform manufacturer output to .zarr with specific folder structure.

Usage

use_sdio(platform = "xenium", srcdir, dest)

Arguments

platform: character(1) must be an element of `available_sdio()` output
srcdir: character(1) path to folder holding manufacturer output files
dest: character(1) a path to a desired destination for zarr representation

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