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. Author manuscript; available in PMC: 2022 Jul 5.
Published in final edited form as: Science. 2022 Jan 7;375(6576):eabl5981. doi: 10.1126/science.abl5981

Fig. 1. Multiplexed identification of transcriptomic cell subclasses and types in functionally imaged neurons.

Fig. 1.

(A) Schematic of the CRACK platform. (B) Expression patterns of genes selected to identify L2/3 S1 excitatory (blue) and inhibitory (green) cell subclasses and types. (C) Barcode scheme for multiplexed HCR-FISH of selected genes. (D) Registration of in vivo calcium-imaged neurons to ex vivo tissue section across multiple rounds of HCR-FISH. (Top left) In vivo two-photon images of RCaMP1.07+ neurons. (Top right) Ex vivo confocal images of reidentified RCaMP1.07+ neurons showing endogeneous protein (green) followed by HCR-FISH staining transcripts (magenta). (Bottom) Overlays of (left) B2-488 and (right) B1-647 readout channels across all HCR-FISH barcode rounds. (E) Decoding of in vivo imaged neuron [(D), dotted rectangle] identified as an Adamts2 cell type expressing Fst and Slc17a7. Positive readouts are identified with green rectangles. Scale bars, (D) 50 μm; (E) 20 μm.