Separating synapses into different classes based on their appearance in EM images has many applications in biology. Examples may include assigning a neurotransmitter to a particular class, or separating synapses whose strength can be modulated from those whose strength is fixed. Traditionally, this has been done in a supervised manner, giving the classification algorithm examples of the different classes. Here we instead separate synapses into classes based only on the observation that nearby synapses in the same neuron are likely more similar than synapses chosen randomly from different cells. We apply our methodology to data from {\it Drosophila}. Our approach has the advantage that the number of synapse types does not need to be known in advance. It may also provide a principled way to select ground-truth that spans the range of synapse structure.