Understanding the immune system in solid tissues requires highplex staining, imaging, and analysis for multi-marker cellular phenotypes. We present a comprehensive workflow for highplex images, covering tissue and cell segmentation and cellular phenotyping in a single software package. Visualization templates for marker subsets and pre-trained nuclear segmentation algorithms are reusable and paint-to-train tissue segmentation is easy to perform. Spatial biodistribution metrics, heatmaps and interactive partitioned t-SNE plots can be generated for each tissue type with a minimum of work. This workflow for highplex image analysis enables biologists and immunologists by circumventing the need for expert programming for each specific application.
