rename_zeiss: Zeiss renamer

In hmbotelho/htmrenamer: File Renaming Tools for High Throughput Microscopy

Zeiss renamer

Description

Renaming of Zeiss TIF files exported with Zen Blue according to a microscope infile. See newinfile.df or newinfile.char for a description of the infile structure.

Usage

rename_zeiss(
  sourcefolder,
  targetfolder,
  infilepath,
  numrow,
  numcol,
  REGEXvalidimages = "^.*?s.*?t.*?\\.tif$",
  REGEXscenenum = "^.*/.*_s(.*)t.*\\.tif$",
  REGEXtimenum = "^.*/.*_s.*t(.*)\\.tif$",
  printMessages = TRUE,
  printFiles = TRUE,
  printToGUI = FALSE,
  move = FALSE
)

Arguments

sourcefolder	character, the folder with raw images.
targetfolder	character, folder where to place renamed files. A subfolder with the same name as the infile will be created by the function and must not exist previously.
infilepath	character, location of the microscope infile
numrow	integer, number of rows in the multi well plate
numcol	integer, number of columns in the multi well plate
REGEXvalidimages	character, regular expression matching all files which should be renamed
REGEXscenenum	character, regular expression capturing ((\1)) the scene number (i.e. well number)
REGEXtimenum	character, regular expression capturing ((\1)) the time number in a time lapse
printMessages	logical, print messages in the console?
printFiles	logical, print file-by-file progress in the console?
printToGUI	logical, print messages to the renamer GUI?
move	logical, move (rather than copy) raw images?

Value

Renamed files, metadata and log file

Null

See Also

rename_zeiss_gui for interacting with this function using a GUI.

hmbotelho/htmrenamer documentation built on April 11, 2025, 11:04 p.m.