bf_import(uri::AbstractString; order::AbstractString="TZYXC", squeeze::Bool=false, subset=nothing, subidx=nothing)

Import all images and metadata in the file using Bio-Formats.

The order keyword argument is the output order of dimensions, allowing you to reshuffle the dimensions of the images or skip singleton dimensions. Providing "CYX" for order gives you three-dimensional images in a "channels-first" data format but will fail with an error if any of the images in the file has a size greater than one in the T or Z dimension.

By setting the squeeze keyword argument to true all singleton dimensions in the images will be dropped (even if they are in the order argument).

The keyword argument subset allows to only import one or multiple specific sets (for datasets with multiple sets) and the keyword argument subidx allows to import specific ranges of the data (in the order as given by the user).

bf_import_http(url::AbstractString, [ filename::AbstractString ]; kwargs...)

Download and import an image using Bio-Formats.


returns the number of series present in the file as given by filename. Currently URLs are not allowed to avoid multiple downloads.

openbytes(oxr::OMEXMLReader, index::Int, x::Int, y::Int, w::Int, h::Int)

returns a byte[] of the current dataset in the reader oxr and frame index index starting at x-position x and y-position y (1-based indexing) with a width w and height h.