A flexible image segmentation pipeline for heterogneous multiplexed tissue images based on pixel classification. The pipeline is based on CellProfiler (http://cellprofiler.org/, v1.3.5) for segmentation and Ilastik (http://ilastik.org/) for for pixel classification. It is streamlined by using the specially developped imctools python package (https://github.com/BodenmillerGroup/imctools) package as well as custom CellProfiler modules (https://github.com/BodenmillerGroup/ImcPluginsCP).