Document

In FCSalyzer, the document is the canvas onto which plots, statistics, and so on are painted on. You can place objects by selecting the respective object-icon in the menu bar and then creating the object by clicking and dragging on the document.

The document can be saved, of course. The document is stored in XML format with the ending .FCX. If you want to, you can change the document in a good text editor (keep the format UTF-8, please) to adjust minor things - like the position of objects on the pages.

The saved file does not contain the FCS data files used in the analysis, only links to them. The links are stored absolute (i. e. with the full path pointing to the FCS file). When loading a data file, FCSalyzer first looks for it in a relative location, then in the same directory as the document is stored in, and as a last resort in the absolute location stored in the document file. It tries to first find the data file in a relative location so that the document can be properly opened even if the folder containing document and data files is moved after the document was saved.

Importantly: XML files are human readable text documents. This means that all information in the .FCX document are in clear text that can be read in any text editor. All file paths, file names, comments, custom parameter descriptions and so on can be extracted directly from the .FCX data file. An example would be the file path of a FCS data file, which could be "c:\users\secret_user_name\secret_project_name\secret_secret.fcs"
Please make sure that the FCX document file only contains information as permitted by your organization.