Extended Data Fig. 6: TH⁺ AC ROI selection and signal.

(a) TH IF of a TH⁺ AC imaged on a confocal microscope with a 40× objective with barcoding ROI overlaid (magenta, left). Fluorescent image of the barcoded region (right). Pixel value set to 0–400. (b) Profile scan performed on the 50 × 5 µm rectangle across the fluorescent barcode signal (dotted box in panel a). Dashed vertical lines indicate ROI boundary. (c) Selected images of single TH⁺ amacrine cells stained with IF (top), with the ROIs overlaid (magenta, bottom). ROIs were drawn slightly inside the cell bodies to account for light-scattering at the ROI boundary. Scale bars are 10 µm. Panels (a) and (c) are representative images from n = 5 technical replicates. (d) A single sequencing run depth at 3.7 million read depth from a representative experimental condition was selected for subsampling without replacement illustrating UMI scaling by fraction of reads for the genes Th, Cartpt, and total UMIs. Mean + /- standard deviation of 5 simulations (cyan) are plotted, with full dataset represented as a single point (magenta).