Digital images of the Nissl sections were taken with a 25× objective on a Zeiss Axio Observer VivaTome microscope. Co-registration of the fluorescence and light microscopic images was achieved using gross morphology, pial surface shape, cutting and other artefacts, and blood vessels as fiduciary marks. The depths – in microns from the pial surface – of layers 4a, 4b, 4c, 5, and 6 (V1), or layers 4, 5, and 6 (MT) were recorded on the reference images. These measurements were then converted to the magnification of the data images and the layer boundaries drawn with a ±10 μm confidence boundary Inhibitors,research,lifescience,medical onto TIFF image files using Photoshop (Adobe). The

depth of the boundary between layers 1 and 2 was determined by eye, based on the sharp increase in the density of cell somata at the layer transition. Counting cells Once the layer boundaries had been drawn, counting

was done from TIFF image files using custom software written in Matlab (Mathworks, Natick, MA). Data channels (red and green) were isolated and immunopositive somata counted Inhibitors,research,lifescience,medical in each channel separately from gray-scale images. Only Inhibitors,research,lifescience,medical wholly selleck kinase inhibitor visible, in focus, immunolabeled somata were counted. Somata that crossed the left image boundary or the 20 μm confidence boundary around layer borders were excluded, as were objects smaller than 5 μm along their long axis. The x and y co-ordinates of the center of the cell body were recorded manually. Quantification of single and dual labeling was made from small shapes (equivalent to a five micron Inhibitors,research,lifescience,medical object) centered at these x/y co-ordinates in a new image frame, i.e., in the same frame size as the original TIFF image, but with the data channels turned off. The counting objects had to overlap to be considered dually labeled. In cases where the markings touched but did not overlap, the data channels

were inspected and a qualitative determination was made. Roughly 0.5% of the sample required this additional step. Qualitative data collection Qualitative observations were made from the same data Inhibitors,research,lifescience,medical images used for quantitative data collection. In describing this “neuropil” (i.e., nonsomatic) staining, we classified Megestrol Acetate the neuropil immunoreactivity as dendritic, axonal, or punctate. Varicose processes with collaterals emerging at right angles were classified as axonal. Dendrites were identified as larger caliber processes of a slightly varicose or nonvaricose nature (i.e., not characterized by the classic “beads-on-a-string” appearance of axons), from which branches emerged at angles of less than 90°. In addition to labeled somata, dendrites, and axons; we defined as “puncta” small spots – approximately 1 micron in diameter or less – that were not visibly attached to any process. These puncta could represent spines, axon terminals, or “islands” of immunoreactivity along larger structure such as a dendrite or axon. Photomicrograph production Confocal images were captured using the Zeiss Zen 2010 software.