Dendritic spines have been proposed to transform synaptic signals through chemical and electrical compartmentalization. However, the quantitative contribution of spine morphology to synapse compartmentalization and its dynamic regulation are still poorly understood.We used time-lapse superresolution STED imaging in combination with FRAP measurements, 2-photon glutamate uncaging, electrophysiology and simulations to investigate the dynamic link between nanoscale anatomy and compartmentalization in live spines of CA1 neurons in mouse brain slices.We report a diversity of spine morphologies that argues against common categorization schemes, and establish a close link between compartmentalization and spine morphology, where spine neck width is the most critical morphological parameter. We demonstrate that spine necks are plastic structures that become wider and shorter after LTP. These morphological changes are predicted to lead to a substantial drop in spine head EPSP, while leaving overall biochemical compartmentalization preserved. 3 Dendritic spines form the postsynaptic component of most excitatory synapses, whose plasticity is essential for brain development and higher brain functions 1,2 . In addition to the molecular composition of the synapse, the morphology of spines is thought to be critical for synaptic function, as spine head size correlates with synaptic strength 3,4 and undergoes changes during synaptic plasticity [5][6][7][8] . Even so, our understanding of how spine structure shapes synapse function remains fragmented.It is well established that spines compartmentalize biochemical signals 9 . By contrast, the quantitative contribution of spine morphology to compartmentalization is still unknown, and only moderate correlations between spine neck length or head volume and chemical diffusion have been reported [9][10][11] . It is an open question to what extent biochemical compartmentalization is determined primarily by spine geometry or intracellular factors such as organelles or protein assemblies.Concerning electrical compartmentalization, it is not clear how electrical signals are transformed by the spine neck 9,[12][13][14] . This is an important question because synaptic strength may be adjusted through structural changes in spine necks, which has been a long-standing hypothesis 15,16 . An early electron microscopy study reported that the average spine head becomes larger and the neck wider and shorter after the induction of long-term plasticity (LTP) 17 , which was corroborated more recently by work based on 2-photon microscopy 6,18,19 . However, it is not known how these structural changes might affect biochemical and electrical compartmentalization, because 2-photon microscopy does not have sufficient spatial resolution to properly resolve spines and electron microscopy cannot be combined with functional assays. 4 Here, we combined stimulated emission depletion (STED) microscopy, fluorescence recovery after photo-bleaching (FRAP) experiments, 2-photon glutamate uncaging, and patch-clam...