Convert Bio-Format

bfconvert(
file,
outfile = tempfile(fileext = ".tiff"),
series = NULL,
timepoint = NULL,
channel = NULL,
z = NULL,
range = NULL,
tilex = NULL,
tiley = tilex,
crop = NULL,
compression = NULL,
overwrite = TRUE,
lookup = TRUE,
bigtiff = FALSE,
opts = "",
verbose = TRUE,
run = TRUE
)

bf_convert(
file,
outfile = tempfile(fileext = ".tiff"),
series = NULL,
timepoint = NULL,
channel = NULL,
z = NULL,
range = NULL,
tilex = NULL,
tiley = tilex,
crop = NULL,
compression = NULL,
overwrite = TRUE,
lookup = TRUE,
bigtiff = FALSE,
opts = "",
verbose = TRUE,
run = TRUE
)

bfconvert_version()

## Arguments

file File to Convert Output filename All images in the input file are converted by default. To convert only one series, set this to a numeric To convert only one timepoint, set this to a numeric To convert only one channel, set this to a numeric To convert only z section, set this to a numeric To convert images between certain indices (inclusive), set 0 to first width in pixels of each tile height in pixels of each tile. of the format x,y,width,height. The (x, y) coordinate (0, 0) is the upper-left corner of the image; x + width must be less than or equal to the image width and y + height must be less than or equal to the image height. By default, all images will be written uncompressed. This is the type of compression done, like LZW. Should the file be overwritten To disable the conversion of lookup tables, leaving the output file without any lookup tables, set this to FALSE This option forces the writing of a BigTiff file Additional options to pass to bfconvert Should the command be printed Should the command be run? Useful for diagnostics.

## Value

The output file name

## Examples

file = "~/Downloads/2017_08_03__0006.czi"
if (file.exists(file)) {
res = bfconvert(file = file, run = FALSE)
res
}