Using the File Menu¶
The File menu provides options for loading and saving your pipelines and performing an analysis run.
New project: Clears the current project by removing all the analysis modules and resetting the input modules.
Open Project…: Open a previously saved CellProfiler project (.cpproj file) from your hard drive.
Open Recent: Displays a list of the most recent projects used. Select any one of these projects to load it.
Save Project: Save the current project to your hard drive as a .cpproj file. If it has not been saved previously, you will be asked for a file name to give the project. Thereafter, any changes to the project will be automatically saved to that filename unless you choose Save as….
Save Project As…: Save the project to a new file name.
Revert to Saved: Restore the currently open project to the settings it had when it was first opened.
Import…: Gives you the choice of importing a CellProfiler pipeline file from your hard drive (From file…) or from a web address (From URL…). In either case, you can import a pipeline from a pipeline (.cppipe) file or a project (.cpproj) file. Alternately, you can import an image file list.
Export…: You have the choice of exporting the pipeline you are currently working on as a CellProfiler .cppipe pipeline file (Pipeline), or the image set list as a CSV (Image set listing), or the pipeline notes as a text file (Pipeline notes).
Clear Pipeline: Removes all modules from the current pipeline, while keeping the image file list intact.
View Image: Opens a dialog box prompting you to select an image file for display. Images listed in the File list panel in the Images module can be also be displayed by double-clicking on the filename.
Analyze Images: Executes the current pipeline using the current pipeline and Default Input and Output folder settings.
Stop Analysis: Stop the current analysis run.
Open a New CP Window: (Mac only) You can run multiple instances of CellProfiler simultaneously; this is how you launch a new instance.
Preferences…: Displays the Preferences window, where you can change many options in CellProfiler.
Quit: End the current CellProfiler session. You will be given the option of saving your current pipeline if you have not done so.