As indicated in this file:
./src/caffe/layers/seg_accuracy_layer.cpp
in lines 102 to 104, you can see that
top[0]->mutable_cpu_data()[0] = (Dtype)confusion_matrix_.accuracy();
top[0]->mutable_cpu_data()[1] = (Dtype)confusion_matrix_.avgRecall(false);
top[0]->mutable_cpu_data()[2] = (Dtype)confusion_matrix_.avgJaccard();
they correspond to accuracy, average recall, and average Jaccard. You can google confusion matrix for their definitions.