Count graphics are named according to transporter(s) (e.g. "vmat2" or "vmat2 and vgat"). Note that these are not markings of cell types, rather just transporter expression. For example, neurons labeled "vmat2" belong to all cell types with VMAT2: vmat2 only, vmat2 + vgat only, vmat2 + vglut2 only, and triple. Sometimes multiple count graphics for a single transporter show up (e.g. "vmat2 part2" or "vmat2 addition". The additional graphics are for neurons that were missed in the initial count due to accidental exiting of the Count tool. Sometimes an extra event counter was created or placed in the wrong location. In these cases the graphic will have a note saying how many miscounts there are (e.g. "VMAT2 -1" for one miscount). There will be a correction graphic (a black rectangle) after covering the miscount (e.g. "VMAT2 correction"). T1: VMAT2T2: VGATT3: VGLUT2T4: DAPI Animals alpha, epsilon, and mu are male; beta, sigma, and delta are female. All were 8-9 weeks old at time of sacrifice. Fiber regions:ml: medial lemiscusfr: fasciculus retroflexusmt: medial terminal nucleus of the accessory optic tractpm: principal mammilary tract vtgx: ventral tegmental decussation Cellular regions:CLi: Caudal linear nucleus DR: Dorsal rapheIF: Interfascicular nucleus IPN: Interpeduncular nucleusPBP: Parabrachial pigmented nucleus PIF: Parainterfascicular nucleusPN: Paranigral nucleus RLi: Rostral linear nucleusRN: red nucleus SNCD: SNc, dorsalSNCL: SNc, lateral SNCM: SNc, medialSNCV: SNc, ventral VTAR: VTA, rostral

48 coronal sections from 3 male and 3 female C57Bl/6J mice were labeled for mRNAs encoding the canonical vesicular transporters for dopamine (VMAT2), GABA (VGAT), and glutamate (VGLUT2). These sections were then imaged via confocal microscopy and saved as CZI files, editable with Zeiss Zen software. These image files include 'event marker' graphics, indicating where neurons positive for one or more of the above transporters are. The protocols used for sample preparation, labeling, imaging, and counting are linked in the Related Works section. Cell count data are organized by subregion (SUBREGION counts for R.csv), anterior-posterior (e.g. VGATVTA.csv), or anterior-posterior and medial-lateral distribution (e.g. 'snc triple.csv' or 'snc vmat2 AP and ML.csv'). The R code provided uses these csv files to visualize expression patterns across VTA and SNc.