Delineating specific brain regions and counting nuclei with FIJI / ImageJ (Part 1)

In this video, I give tips on how to use counterstains such as DAPI or Nissl to delineate brain region boundaries in order to constrict cell/nuclei counting to just that brain region. The video is addressed to students that are helping me with research, but the info in here may be useful for you as well. The video is a bit lengthy, so feel free to skip through it as you need to. This video (Part 1) just focuses on the nucleus accumbens (Acb / NAc), the ventral pallidum (VP), the amygdala and its subregions (BLA, CeA, MeA), and the lateral habenula (LHb). Other parts that I am currently looking at will be addressed in the next video, which may include the LS, PAG, PVT, insula, S1, and area postrema. Timestamps: 0:00 - Intro and data entry setup 4:15 - Delineating the nucleus accumbens 19:10 - Example of thresholding and watershedding (and when not to watershed) 29:07 - Delineating the ventral pallidum 50:27 - Delineating major subregions of the amygdala 1:18:17 - Delineating the entire amygdala 1:21:43 - Delineating the lateral habenula (briefly)