After importing a model, the next step is to import an image of the compartments in the model. To do this, go to Import->Geometry from image, or choose one of the built-in example images from Import->Example geometry image.
The image should be segmented such that each compartment has a unique colour.
For each compartment in the model:
click on the compartment name
click on “Select compartment geometry…”
then click on the desired part of the image.