FCS file concatenation tool


Cytobank offers a standalone tool for concatenating multiple FCS files into a single FCS file. Currently, FCS files cannot be properly concatenated inside of Cytobank.


How to use the tool

Download the correct tool for your operating system from the links below.

To concatenate files, click the "Add" button and select the files you’d like to combine from the file chooser. Edit the channel names to ensure they match in the resulting combined file, select the output options desired such as file number channel (see important note below), ordering the files by time (convenient for visualizing the data once concatenated), select a file name and a save location, and then hit the "Merge Files" button. The concatenated file will appear in the specified location and you’ll then be able to upload it to Cytobank or analyze it in another software of your choice.


Important notes about the file number channel option:

By default, the concatenation tool is configured to add a "file number channel". This feature adds an extra channel into the concatenated product file which allows the tracking of which original file contributed to the events in the final product. Each event contributed from file number 1, for example, will have a value of ~1 in the file number channel. Each event contributed from file number 2 will have a value of ~2 in the file number channel. The values are not exactly the respective integer, but instead are randomly "jittered" and assigned decimal values close to the correct integer. This is for visual purposes when looking at the file number channel in a plot, in order to make the values more visually detectable. The file number channel can be used for downstream workflows similar to the cluster channel added during clustering.

When working with different groups of concatenated files from different sessions, consistency is recommended with use of the file number channel, otherwise panel conflicts may occur in Cytobank.

When doing serial concatenations (i.e. concatenating concatenated files) the file number channel should be included in a maximum of one concatenation. Otherwise, multiple file number channels will result with potential problematic effects.


Mac users:

Download the tool from this link: FCSConcat_81.zip

If a warning message is displayed about a damaged file, you may need to adjust your system preferences to allow programs from external developers to be run. To do this, navigate to System Preferences, Security & Privacy, and then choose "Anywhere" option under the section for "Allow apps downloaded from:"


Windows users:

Download the tool from this link: fcs_concat_81.zip

For large concatenations, there is sometimes an error on Windows that says "ERROR: Map failed". If you encounter this error, use this version of the concatenation tool: fcs-concat-081-installer.zip





Have more questions? Submit a request