how can I change the background colour in individual cells in a matrix?
This depends on the specific cell class you are using. If this supports the setting of the background colour, than you just ask the matrix fro the specific cell and set that colour.
how could I change the selection behaviour (to remplace the gray dotted line?
You need to tell a bit more, what you want to achive. If you don't want the dotted border at all, than there may be a problem as this is hard coded fro most cell classes, when they become frist responder.
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