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The amygdala is the neural structure that acts as an evaluator of potentially threatening stimuli. We present a biologically plausible model of the visual fear conditioning pathways leading to the amygdala, using a topographic conditioning map (TCM). To evaluate the model, we first use abstract stimuli to understand its ability to form topographic representations, and subsequently to condition on arbitrary stimuli.We then present results on facial emotion recognition using the sub-cortical pathway of the model. Compared to other emotion classification approaches, ourmodel performswell, but does not have the need to pre-specify features. This generic ability to organise visual stimuli is enhanced through conditioning, which also improves classification performance. Our approach demonstrates that a biologically motivated model can be applied to real-world tasks, while allowing us to explore biological hypotheses.