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Cytometry Facility

FCS Renamer Help

Overview

With the FCS Renamer scrip you can easily rename the FCS files. For instance from Specimen_001_A01.fcs to YourPreferedName.fcs.

Note: Manually renaming the FCS files is not sufficient as the file name is also stored as keyword inside the FCS file itself. Opening a manually renamed FCS file in e.g. FlowJo will still display the original file name from the keyword.

The FCS Renamer script is installed on all VMs.

Preparation

Step 1) Create a folder with your fcs-files, that you want to rename.

Example of files that can be renamed.

Step 2) Create an excel list with two columns, called “original” and “name”

Example of the excel file needed for renaming.

Step 3) Type in the column “original” the current names of your fcs-files

Step 4) The "name" column should list the new names of the fcs-files without the suffix “.fcs“

 

Using the script

Double click the FCS Renamer icon on the VM desktop.

FCSRenamer icon.

 In the interface of the script:

  1. Select the Excel file with the new names.
  2. Select the folder with the original FCS files.
  3. Select the location to export the renamed files to.
  4. Click the Rename button to start the renaming process. Depending on the number of files and their sizes, the process can take a while.
  5. Check the message window for any issues.
Make sure that the paths start with a drive letter (e.g. Z:\) and not with a double backslash (e.g. \\homes.core.uzh.ch). The latter will not work and can happen if you select the file or folder via “Documents” and not via the files.core.uzh.ch drive.

 

FCSRenamer interface.

The script does not alter the original files, the renamed files are newly created copies.

Futher help

Please contact info@cytometry.uzh.ch if you encounter any issues with the script or have further question.