Module: RenameOrRenumberFiles

Rename or Renumber Files renames or renumbers files on the hard drive.
This file-renaming utility adjusts text within image file names. Be very careful with this module because its purpose is to rename (and overwrite) files! You will have the opportunity to confirm the name change for the first cycle only. If the folder containing the files contains subfolders, the subfolders and their contents will also be renamed. The module will not rename the file in test mode, so you should use test mode to ensure that the settings are correct.

You can use this module to standardize the number of characters in your file names and to remove unwanted characters from your file names. This is especially useful if you want file names that have numbers in them to appear in numerical order when processed by NamesAndTypes.

While this module performs basic renaming operations, if you can extract metadata from your images using the Metadata module, you may find using metadata substitution in SaveImages to be more flexible. Please refer to metadata handling for those modules and in Help for more details.


Renumbering can be useful when numbers within image filenames do not have a minimum number of digits and thus appear out of order when listed in some Unix/Mac OSX systems. For example, on some systems, files would appear like this and thus be measured differently from the expected sequence by CellProfiler:


To renumber the files in the expected order, the numeric digits need to be padded with zeros to the same length. In this case, you would want to:

Original nameNew name
1DrosophilaDAPI_1.tif 1DrosophilaDAPI_001.tif
1DrosophilaDAPI_10.tif 1DrosophilaDAPI_010.tif

Renaming can be useful when file names are too long or have characters that interfere with other software or file systems. To accomplish the following, you would want to:

Original nameNew name
1DrosophilaDAPI_001.tif 1DrosDP_001.tif
1DrosophilaDAPI_010.tif 1DrosDP_010.tif
1DrosophilaDAPI_100.tif 1DrosDP_100.tif

See also: NamesAndTypes, SaveImages


Select the input image

Select the images associated with the files you want to rename. This should be an image loaded by the Input modules. Be very careful because you will be renaming these files!

Number of characters to retain at start of file name

Number of characters at the start of the old file name that will be copied over verbatim to the new file name. For instance, if this setting is "6" and the file name is "Image-734.tif", the output file name will also start with "Image-".

Number of characters to retain at the end of file name

Number of characters at the end of the old file name that will be copied over verbatim to the new file name. For instance, if this setting is "4" and the file name is "Image-734.tif", the output file name will also end with ".tif".

Handling of remaining characters

You can either treat the characters between the start and end as numbers or you can delete them. If you treat them as numbers, you will be given the opportunity to pad the numbers with zeros so that all of your file names will have a uniform length. For instance, if you were to renumber the highlighted portion of the file "Image-734.tif" using four digits, the result would be "Image-0734.tif".

Number of digits for numbers

(Used only if Renumber is selected)
Use this setting to pad numbers with zeros so that they all have a uniform number of characters. For instance, padding with four digits has the following result:

Add text to the file name?

Select Yes if you want to add text to the file name. If you had chosen Renumber above, the module will add the text after your number. If you had chosen Delete, the module will replace the deleted text with the text you enter here.

Replacement text

(Used only if you chose to add text to the file name)
Enter the text that you want to add to each file name.

Replace spaces?

Select Yes to replace spaces in the final version of the file name with some other text.

Select No if the file name can have spaces or if none of the file names have spaces.

Space replacement

This is the text that will be substituted for spaces in your file name.