Figure 1.

Workflow of cell segmentation and feature extraction. A, Workflow implemented in PaCeQuant for automatic detection of cell outlines (part 1, light gray) and extraction of shape features (part 2, dark gray). In the first part, input images are processed in four basic stages (image quality improvement [I] to region filtering [IV], left column) via nine individual processing steps (panels on the right). In the second part, the feature extraction (step 10) is performed. B, Example of an input image (step 0), the processed image after outline extraction (step 7), and an image containing identified and filtered regions (step 9) used for feature extraction. For an overview of all image-processing steps, see Supplemental Figure S1.