Read BioFormatsImage from alabaster on disk representation

Reads the metadata and imgSource will point to the file within the on disk representation of SFE. The image itself should not be moved or the BioFormatsImabe object will no longer work.

Usage

readBioFormatsImage(path, metadata = NULL, ...)

Arguments

path

String containing a path to a directory, itself created with a saveObject method.

metadata

Named list containing metadata for the object - most importantly, the type field that controls dispatch to the correct loading function. If NULL, this is automatically read by readObjectFile(path).

...

Ignored, but used for other methods.

Value

A BioFormatsImage object for SFE.

See also

Other readObject-SFE-image: readExtImage(), readSpatRaster()

Examples

library(SFEData)
fp <- tempfile()
x1 <- XeniumOutput(dataset = "v1", file_path = file.path(fp, "xenium1"))
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
#> The downloaded files are in /tmp/RtmpfBErth/file2aa86af32cb1/xenium1/xenium_lr 
x2 <- XeniumOutput("v2", file_path = file.path(fp, "xenium2"))
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
#> The downloaded files are in /tmp/RtmpfBErth/file2aa86af32cb1/xenium2/xenium2 

# Single file OME-TIFF
fsave <- file.path(fp, "bfi1")
sfe <- readXenium(x1)
#> >>> Cell segmentations are found in `.csv` file(s)
#> >>> Reading cell and nucleus segmentations
#> >>> Making POLYGON geometries
#> >>> Checking polygon validity
#> >>> Saving geometries to parquet files
#> >>> Reading cell metadata -> `cells.csv`
#> >>> Reading h5 gene count matrix
#> >>> filtering cellSeg geometries to match 16324 cells with counts > 0
#> >>> filtering nucSeg geometries to match 16324 cells with counts > 0
bfi <- getImg(sfe)
bfi <- affineImg(bfi, M = matrix(c(cos(pi/6), sin(pi/6), -sin(pi/6), cos(pi/6)), nrow = 2), 
                 v = c(0,0))
saveObject(bfi, fsave)
bfi2 <- readObject(fsave)

unlink(fsave, recursive = TRUE)

# Multi file OME-TIFF
fsave <- file.path(fp, "bfi2")
sfe <- readXenium(x2)
#> >>> Cell segmentations are found in `.parquet` file(s)
#> >>> Reading cell and nucleus segmentations
#> >>> Making MULTIPOLYGON nuclei geometries
#> >>> Making POLYGON cell geometries
#> Sanity checks on cell segmentation polygons:
#> >>> ..found 132 cells with (nested) polygon lists
#> >>> ..applying filtering
#> >>> Checking polygon validity
#> >>> Saving geometries to parquet files
#> >>> Reading cell metadata -> `cells.parquet`
#> >>> Reading h5 gene count matrix
#> >>> filtering cellSeg geometries to match 6272 cells with counts > 0
#> >>> filtering nucSeg geometries to match 6158 cells with counts > 0
bfi <- getImg(sfe)
saveObject(bfi, fsave)
bfi2 <- readObject(fsave)
unlink(fsave, recursive = TRUE)