Please note that the Default Input Folder will be deprecated in the future. The location of non-image files needed by some modules will be set to an absolute path in future versions of CellProfiler. For specifying the location of image files, please use the Input modules panel starting with the Images module.
The Default Input Folder is enabled only if a legacy pipeline is loaded into CellProfiler and is accessible by pressing the "View output settings" button at the botton of the pipeline panel. The folder designated as the Default Input Folder contains the input image or data files that you want to analyze. Several File Processing modules (e.g., LoadImages or LoadData) provide the option of retrieving images from 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 Input 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 specify the folder you would like to use as the Default Input 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 button . The folder will be created according to the pathname you have typed.