Fig. 2

Workflow for isolation of glomeruli from other vascular structures in the renal cortex. A series of erosion, dilation, and component labeling and extraction procedures were used to separate perfused glomeruli from afferent and efferent vasculature. Representative images from each step are shown as both 2-dimensional single slide cross sections (top) and anterior views of a portion of the 3-dimensional objects (bottom). Beginning with the binarized 3-dimensional representation of the cortical vasculature (a), three voxels (15 μm) were removed from all surfaces in a 3-dimensional manner using an erosion function resulting in the complete removal of any parts of the object with thickness ≤30 μm, effectively removing any detected capillaries or arterioles connected to the glomeruli (b). c The original thickness of the now eroded vascular components (b) was restored by applying a 3-dimensional dilation of 3 voxels. d All individual, disconnected, components of the image in (c) were labeled according to the total number of voxels in each object. All objects <45 or >1000 total voxels were removed from the image. The total number of objects remaining, representing the glomeruli, was quantified