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Chunk #67 — STAR★METHODS — QUANTIFICATION AND STATISTICAL ANALYSIS — FISH image quantification

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Transcriptional and anatomical diversity of medium spiny neurons in the primate striatum.
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To quantify DRD1 and DRD2 grains in D1/D2-hybrid cells, D1- and D2- MSNs (Figure 4H), we scanned high resolution images for RXFP1-positive cells in triple stained DRD1, DRD2, and RXFP1 sections. The majority of RXFP1-positive cells expressed both DRD1 and DRD2 in dorsal striatum. We quantified the number of grains for DRD1 and DRD2 in these D1/D2-hybrid cells as well as adjacent normal D1 and D2 MSNs in ImageJ using similar methods as above except that we quantified the total grains in the cells instead of nuclei. To quantify DRD1 and DRD2 grains in D1/D2-hybrid cells, we first draw ROIs for RXFP1 expressing cells and added the ROIs to the “ROI Manager” based on the RXFP1 signal. We then opened the DRD1 and DRD2 images and identified the DRD1 and DRD2 grains using the “Find Maxima” function in ImageJ and then output binary images with a single pixel for each local maxima by choosing an output type of “Single points”. We measured the integrated intensity and calculated the number of grains for each ROI using the “Measure” function within the