Setting the Output Filename

Please note that the output file will be deprecated in the future. This setting is temporarily present for those needing HDF5 or MATLAB formats, and will be moved to Export modules in future versions of CellProfiler.

The output file is a file where all information about the analysis as well as any measurements will be stored to the hard drive. Important note: This file does not provide the same functionality as the Export modules. If you want to produce a spreadsheet of measurements easily readable by Excel or a database viewer (or similar programs), please refer to the ExportToSpreadsheet or ExportToDatabase modules and the associated help.

The options associated with the output file are accessible by pressing the “View output settings” button at the bottom of the pipeline panel. In the settings panel to the left, in the Output Filename box, you can specify the name of the output file.

The output file can be written in one of two formats:

  • A .mat file which is readable by CellProfiler and by MATLAB (Mathworks).
  • An .h5 file which is readable by CellProfiler, MATLAB and any other program capable of reading the HDF5 data format. Documentation on how measurements are stored and handled in CellProfiler using this format can be found here.

Results in the output file can also 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…

The output file will be saved in the Default Output Folder unless you type a full path and file name into the 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.

For analysis runs that generate a large number of measurements, you may notice that even though the analysis completes, CellProfiler continues to use an inordinate amount of your CPU and RAM. This is because the output file is written after the analysis is completed and can take a very long time for a lot of measurements. If you do not need this file, select “Do not write measurements” from the “Measurements file format” drop-down box.