Visualization of BDNF mRNA with Htt and dynein in vibratome sections of a rat brain cortex. White arrow indicates co-localization of BDNF mRNA with Htt and dynein in the images, while yellow arrow indicates co-localization of BDNF mRNA with Htt and dynein in the diagram. Co-localized spots appear white in the merged panel. N: Nucleus. (a) An optic slice from confocal microscopy. BDNF mRNA, Htt and dynein are shown in red, green and blue, respectively. Scale bar: 10 μm. (b) A diagram showing intensity profile of pixels underlying the white line drawn in the merged panel in (a). (c) Co-localization analysis of BDNF mRNA and dynein using the LSM software. (d) 3D projection of image stack of 37 optical slices. Reconstruction method: LSM software, optical slice interval: 0.5 μm, stack size: 18.0 μm, rotation angle: 0°. (e) Intensity profile of pixels underlying the white line drawn in the merged panel in (d). (f) 3D co-localization analysis of mRNA and dynein in image stack. The pixels in red channel (mRNA) and blue channel (dynein) were segmented using a 2D thresholding approach of the whole stack and segmented stacks were reconstructed using the LSM software. One projection at rotation angle 0°is shown. (g) Percent co-localization of BDNF mRNA (exon 2c, 4, 6, 8, 9) with Htt and dynein.