ilastik is a rich program useful for segmentation, feature extraction, and object classification! With pixel-based classification one can train a machine to identify cells of interest. A post on CellProfiler’s blog, describing use of ilastik to segment cells, was good for understanding how to segment images.
Feature selection used in ML training
You can chose to apply different convolution filters at different kernel sizes. I selected all features available, then trimmed the list to features that best highlighted, traced, or distinguished cells from the background. These features are part of the pixel-based training and classification.