Please note that the Default Output Folder will be deprecated in the future. The location of files written by the various output modules will be set to an absolute path in future versions of CellProfiler.
The Default Output Folder is accessible by pressing the "View output settings" button at the botton of the pipeline panel. The Default Output Folder is the folder that CellProfiler uses to store the output file it creates. Also, several File Processing modules (e.g., SaveImages or ExportToSpreadsheet) provide the option of saving analysis results to this folder on a default basis unless you specify, within the module, an alternate, specific folder on your computer. Within modules, we recommend selecting the Default Output Folder as much as possible, so that your pipeline will work even if you transfer your images and pipeline to a different computer. If, instead, you type specific folder path names into a module's settings, your pipeline will not work on someone else's computer until you adjust those pathnames within each module.
Use the Browse button (to the right of the text box) to specify the folder you would like to use as the Default Output Folder, or type the full folder path in the edit box. If you type a folder path that cannot be found, the message box below will indicate this fact until you correct the problem. If you want to specify a folder that does not yet exist, type the desired name and click on the New folder icon to the right of the Browse folder icon. The folder will be created according to the pathname you have typed.