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 you select as candidates for analysis.
  • The pipeline, which is a series of modules put together to analyze a set of images.
  • Optionally, the associated information about the images (metadata). This information may be part of the images themselves, or you may import them from an external file.

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?

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 pipeline window on the upper-left. The modules are:

  • Images: Assemble the relevant images for analysis (required).
  • Metadata: Associate 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.

Rather than the four input modules, you may alternatively use the LoadData module to associate images with your project. LoadData allows you to upload a spreadsheet to provide the same location, metadata, channel, and grouping information as the four input modules. See the help for that module for more information.

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 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).