Introduction to Projects

What is a project?

In CellProfiler, a project is comprised of two elements:

The project is the container for image information associated with a CellProfiler analysis. It stores such details as:

By using projects, the above information is stored along with the analysis pipeline and is available on demand.

Working with projects

Creating a project

Upon starting CellProfiler, you will be presented with a new, blank project. At this point, you may start building your project by using the modules located in the "Input modules" panel on the upper-left. The modules are:

Detailed help for each module is provided by selecting the module and clicking the "?" button on the bottom of CellProfiler.

Saving a project

As you work in CellProfiler, the project is updated automatically, so there is no need to save it unless you are saving the project to a new name or location. You can always save your current work to a new project file by selecting File > Save Project As..., which will save your project, complete with the current image file list and pipeline, to a file with with the extension .cpproj.

You also have the option of automatically saving the associated pipeline file and the file list in addition to the project file. See File > Preferences... for more details.

For those interested, some technical details:

Legacy modules: LoadImages and LoadData

Historically, two modules were used for project creation: LoadImages and LoadData. While the approach described above partly supercedes these modules, you have the option of preserving these modules if you load old pipelines into CellProfiler that contain them; these pipelines will operate exactly as before.

Alternately, the user can choose to convert these modules into the project equivalent as closely as possible. Both LoadImages and LoadData remain accessible via the "Add module" and   buttons at the bottom of the pipeline panel.