convertCziToTif: Imports a czi file and saves it as a tif

In SFB-ELAINE/readCzi: Read CZI image files, convert them to tifs, and save metadata

Imports a czi file and saves it as a tif

Description

'convertCziToTif()' saves a multidimensional array (image) as tifs and stacks/edits the images if required.

Usage

convertCziToTif(
  input_file = NULL,
  output_dir = "output",
  convert_all_slices = FALSE,
  zstack_projection = TRUE,
  projection_method = "max",
  higher_contrast_layers = FALSE,
  higher_contrast_projection = TRUE,
  normalize_projection = TRUE,
  change_color_layers = "none",
  add_scale_bar = TRUE
)

Arguments

input_file	Path to a CZI file as a string.
output_dir	Path to a directory where the results are to be saved as a string.
convert_all_slices	A Boolean stating whether all z-stack layers of a CZI files are to be converted to tifs. (FALSE is the default value.)
zstack_projection	A Boolean stating whether the a projection of a z-stack image is to be calculated. (TRUE is the default value.)
projection_method	A character representing the method for calculating the image projection: mean or max (default value).
higher_contrast_layers	A Boolean stating wheterh the contrast of the z-stack layers should be enhanced using 'EBImage::clahe()'. (FALSE is the default value.)
higher_contrast_projection	A Boolean stating whether the contrast of the z-stack projection or the original image if it is not a z stack shall be enhanced using 'EBImage::clahe()'. (TRUE is the default value.)
normalize_projection	A Boolean statin whether the z-stack projection shall be normalized. (TRUE is the default value.)
change_color_layers	A character stating the color layers to be swuitched (either "none" or, e.g., "green<->red").
add_scale_bar	A Boolean stating whether to add scale bar to all images that are saved. (TRUE is the default value.)

Value

Nothing but saves the converted czi file as tif file(s).

SFB-ELAINE/readCzi documentation built on March 31, 2024, 4:50 a.m.