bfconvert: Convert Bio-Format

In neuroconductor/bftools: BioFormats Tools

Convert Bio-Format

Description

Convert Bio-Format

Usage

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
outfile	Output filename
series	All images in the input file are converted by default. To convert only one series, set this to a numeric
timepoint	To convert only one timepoint, set this to a numeric
channel	To convert only one channel, set this to a numeric
z	To convert only z section, set this to a numeric
range	To convert images between certain indices (inclusive), set 0 to first
tilex	width in pixels of each tile
tiley	height in pixels of each tile.
crop	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.
compression	By default, all images will be written uncompressed. This is the type of compression done, like LZW.
overwrite	Should the file be overwritten
lookup	To disable the conversion of lookup tables, leaving the output file without any lookup tables, set this to FALSE
bigtiff	This option forces the writing of a BigTiff file
opts	Additional options to pass to bfconvert
verbose	Should the command be printed
run	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
}

neuroconductor/bftools documentation built on Feb. 7, 2023, 12:52 a.m.