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.