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.
-  **Run Multiple Pipelines:** Execute multiple pipelines in sequential
   order. This option opens a dialog box allowing you to select the
   pipelines you would like to run, as well as the associated input and
   output folders. See the help in the *Run Multiple Pipelines* dialog
   for more details.
-  **Open a New CP Window:** You can run multiple instances of
   CellProfiler simultaneously; this is how you launch a new instance.
-  **Resume Pipeline:** Resume a partially completed analysis run from
   where it left off. You will be prompted to choose the output
   *.h5/.mat* file containing the partially complete measurements and
   the analysis run will pick up starting with the last cycle that was
   processed.
-  **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.
