Fig. 3: Image acquisition and 3D-stacks of aligned sections.
From: Cellular 3D-reconstruction and analysis in the human cerebral cortex using automatic serial sections
A Overview of a microscopic glass slide with the commercial Leica software. Systematic sampling of every third section was manually marked with three local points for the autofocus calibration. B In MATLAB, a TIF image was loaded where each second was of interest, which is different from (A) but easier to visualize as an example (i). Next, we used an entropy filter to detect sections of interest (ii). Binary masks have been computed for each section of interest and the images are ready for export (iii). The output of each exported section (iv). C Individual sections were aligned and stacked on top of each other. The stacked block of sections was then cropped down to a specific ROI (1.05 × 1.05 mm) which only contains tissue.
