Introduction to Projects

What is a project?

In CellProfiler, a project is comprised of two elements:

• An image file list which is the list of files and their locations that are selected by the user as candidates for analysis.
• The pipeline, which is a series of modules put together used to analyze a set of images.
• Optionally, the associated information about the images (metadata). This information may be part of the images themselves, or imported externally by the user.

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

• What type of image(s) are the input files?
• Where are the input images located?
• What distinguishes multiple image channels from each other? How are these relationships represented?
• What information about the images and/or experiment is linked to the images, and how?
• Are certain groups of images to be processed differently from other groups?

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:

• Images: Assemble the relevant images for analysis (required).
• Metadata: Asociate metadata with the images (optional).
• NamesAndTypes: Assign names to channels and define their relationship (required).
• Groups: Define sub-divisions between groups of images for processing (optional).

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:

• The .cpproj file stores collected information using the HDF5 format. Documentation on how measurements are stored and handled in CellProfiler using this format can be found here.
• All information is cached in the project file after it is computed. It is either re-computed or retrieved from the cache when an analysis run is started, when entering Test mode, or when the user requests a refreshed view of the information (e.g., when a setting has been changed).

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.