Object detection on labeled images only

edit

I want to train a vertebra classifier (in magnetic resonance images).

I was wondering if there is a tool which uses labeled images only, that is images with objects labeled by rectangles? Instead of creating a vector of positive samples which are to be placed at random locations in supplied background images, is there a tool to use labeled images?

Use already existing image, just knowing where the objects are and consider everything else as background. Would this way have some advantages over the classic way?

Example images: