I’m sorry to hear that you are having trouble downloading my images. Please follow this link to find the full-sized cortical slices we’re looking at (on the left hand viewer), and I also will attach the cropped sample I’m using above: http://human.brain-map.org/ish/specimen/show/79947031?gene=2050
The reason I mentioned wanting “something more quantitative” is because the schematic image I uploaded earlier went about this process differently. It was taken from a figure in the following paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5113791/
They used the following methods: “Neuronal somata were automatically identified using Surface Module of IMARIS software (IMARIS 7.71; Bitplane) and extracted to a table of [x,y,z] coordinates. Laminar boundaries were automatically identified based on density of cell bodies with custom routines written in Matlab. For this calculation, soma locations from two to three consecutive 50‐μm sections were aligned and collapsed across the z‐plane (coronal) using the pial surface as a reference. The local density in a sliding 25‐μm window was computed to generate a density image. The stereotypical changes in density, alternating low–high from layers 1–6 were identified by finding the peaks in the derivative of the density in 25‐μm sliding windows, corresponding to the transitions from high‐to‐low or low‐to‐high density.”
While I don’t have access to IMARIS and I’m not using z-stacks (at the moment), I had initially hoped to use a sliding window to generate a cell density plot, as described above. I am, however, nescient as to whether this method is better than using projections. Please forgive me if I have misunderstood anything.