Orchestrated neuronal migration and cortical folding: A computational and experimental study
Fig 3
Workflow of cell density calculation.
The ferret brain sections could be divided into five anatomical zones: marginal zone (MZ), cortical plate (CP), intermediate zone (IZ), outer subventricular zone (OSVZ), and inner subventricular zone (ISVZ). First, we select an ROI aligned radially, such that cell migration along radial glial fibers consistently occurs along the length of the domain. Secondly, the high-resolution image is imported into ImageJ [44] and neurons are segmented based on the color threshold. Each neuron and its coordinates are then labeled and recorded automatically. Thirdly, we post-process the data in Matlab to generate a neuron density plot by counting neurons in each subcell. Finally, the cell density profile along the y-axis is generated by averaging the data in the x-axis direction. Here we note that the small peak seen in the OSVZ represents GFP-positive fibers, not neurons. Scale bar, 500 μm. For detailed methods on the image analysis, please refer to Section 4.3.