In the demo code above I show processing results using small images (512 x 512). However, you can process the whole section of the mouse brain in “one shot”, as it is shown in the slide above. Processing of one image 15,000 x 9,000 pixels takes ~ 4 minutes(4-core i7-3770S CPU@3.1GHz).
As it seems (Fig.4, below), this algorithm produces quite acceptable result in different cortical areas of the brain with quite different neuronal density, as well as in the hippocampus, where the neuronal density is much higher.
Fig.3: Segmentation results in different brain regions
In different brain resions, including cortex, hyppocampus and subcortical areas, segmentation results consistently show correct outline of cell bodies.