In the Output Filename box in the Folder panel, you can specify the name of the output file where all information about the analysis as well as any measurements will be stored to the hard drive. The output file is a .mat file, which is readable by CellProfiler and by MATLAB. Results in the output file can be accessed or exported using Data Tools from the main menu of CellProfiler. The pipeline with its settings can be be loaded from an output file using File > Load Pipeline..., or by double-clicking the output file in the file list panel (located in the lower left corner of the CellProfiler main window).
The output file will be saved in the Default Output Folder unless you type a full path and file name into the output file name box. The path must not have spaces or characters disallowed by your computer's platform.
If the output filename ends in OUT.mat (the typical text appended to an output filename), CellProfiler will prevent you from overwriting this file on a subsequent run by generating a new file name and asking if you want to use it instead. You can override this behavior by checking the Allow overwrite? box to the right.