Read VisiumHD output into spe

Read VisiumHD output into spe

Usage

readVisiumHD(dir, bin = c("016um", "008um", "002um", "segmented"), ...)

Arguments

dir

directory containing the VisiumHD files

bin

Which output to read. Bin sizes "016um", "008um", "002um" read the corresponding 'binned_outputs/square_*' folder. "segmented" reads the cell-segmentation results in 'segmented_outputs': the count matrix 'filtered_feature_cell_matrix.h5', with per-cell coordinates taken from the centroids of 'cell_segmentations.geojson'.

...

Parameters for readVisium

Details

For "segmented", cells have no array_row/array_col grid, so the result is cell-level (like Xenium) and is not compatible with the Visium spot-grid options of gridDensity() / trimEdge().