Any image analysis project using CellProfiler begins with providing the program with a set of image files to be analyzed. You can do this by clicking on the Images module to select it (located in the Input modules panel on the left); this module is responsible for collecting the names and locations of the files to be processed.
The most straightforward way to provide files to the Images module is to simply drag-and-drop them from your file manager tool (e.g., Windows Explorer, Finder) onto the file list panel (the blank space indicated by the text "Drop files and folders here"). Both individual files and entire folders can be dragged onto this panel, and as many folders and files can be placed onto this panel as needed. As you add files, you will see a listing of the files appear in the panel.
CellProfiler supports a wide variety of image formats, including most of those used in imaging, by using a library called Bio-Formats; see here for the formats available. Some image formats are better than others for image analysis. Some are "lossy" (information is lost in the conversion to the format) like most JPG/JPEG files; others are lossless (no image information is lost). For image analysis purposes, a lossless format like TIF or PNG is recommended.
If you have a subset of files that you want to analyze from the full list shown in the panel, you can also filter the files according to a set of rules that you specify. This is useful when, for example, you have dragged a folder of images onto the file list panel, but the folder contains the images from one experiment that you want to process along with images from another experiment that you want to ignore for now. You may specify as many rules as necessary to define the desired list of images.
For more information on this module and how to configure it for the best performance, please see the detailed help by selecting the module and clicking the button at the bottom of the pipeline panel, or check out the Input module tutorials on our Tutorials page.