Defining a complete set of cell types within the cortex requires reconciling disparate results achieved through diverging methodologies. To address this correspondence problem, multiple methodologies must be applied to the same cells in multiple single-cell experiments. Here we present an approach in which spatial transcriptomics using multiplexed fluorescence in situ hybridization (mFISH) on tissue previously interrogated through two-photon optogenetic mapping of synaptic connectivity can resolve the anatomical, transcriptomic, connectomic, electrophysiological, and morphological characteristics of single cells within the mouse cortex.
MainThe parable of the Blind Men and the Elephant tells the story of a group of blind men, naïve to the nature of an elephant, presented with such a creature to try to conceptualize while observing only through touch ( Figure 1A, upper). The men are each concerned with a single area and draw a conclusion for the whole based on their limited perspective. As scientists, we are similarly a group of observers each indirectly observing one portion of a large, hidden, and complex problem. The parable's moral is that these challenging concepts may have many facets individually revealed to those with diverging perspectives. To strive towards a comprehensive description, we must be able to synthesize these unique perspectives into a consistent whole.This challenge of differing perspectives leading to seemingly conflicting outcomes is exemplified in attempts to understand the number and features of cell types within the mouse cortex (Fig 1A, lower). Recent studies report self-consistent outcomes based on anatomy 1 , transcriptomics 2,3 , electrophysiology 4 , morphology 4 , long-range 5 and local connectomics 6 , and in vivo recordings 7 . However, these studies markedly disagree on the number of underlying cell types. Even if they did agree on the number of types, how results from one study map to those of another is not obvious. To reconcile this problem of cell type correspondence, single-cells must traverse multiple modalities.Each of these modalities, save transcriptomics, explicitly or implicitly carries spatial information within the specimen at single-cell resolution. Multiplexed fluorescence in situ hybridization (mFISH) enables a transcriptomic readout with this same single-cell spatial resolution. We have extended the hairpin