Abstract: Neurons have incredibly diverse properties that underlie their distinct functions. Proper classification is challenging as neurons can be defined by many different criteria, including anatomy, molecular identity, and electrophysiology. Moving forward, it’ll be fundamentally important to perform multi-modal measurements of neuron properties to ameliorate conflicting definitions of cell types. To address this correspondence problem, we have developed a Multi-Round immunostaining expansion microscopy (MiRiEx) strategy that can be combined with multicolor genetic labeling strategies (Brainbow) to simultaneously interrogate morphology, molecular identity, and connectivity in brain sections. The capacity for 3-4x linear expansion of the tissue specimen gives us the ability to perform “super-resolution” imaging to untangle densely labeled neurons and trace their neurites using nTracer, a custom ImageJ software. By optimizing the preservation of antigens in a hydrogel, we are able to carry out multiple rounds of immunostaining for Brainbow fluorophores and cell type markers. As a proof of concept, we demonstrate that MiRiEx can be applied to Brainbow labeled inhibitory neurons in the basolateral amygdala to correlate inhibitory neuron cell types with their morphologies and local anatomy network. Furthermore we show that Brainbow immunostaining can be combined with synaptic markers to count inhibitory and excitatory inputs on interneurons. We envision MiRiEx combined with Brainbow to be a powerful tool researchers can use to perform multi-modal analysis of neuronal structure, molecular identity, and connectivity.