Four square regions of interest (ROIs) were randomly defined within the stratum radiatum of CA1 and the mean pixel intensity computed for each ROI.
For analysis, the midpoint coordinates for all regenerated bone segments were manually identified and the corresponding calcein intensities were used to compute mean intensity, standard deviation of intensity, and coefficient of variation for each fish.
Median pixel intensities computed from spot regions were used to represent spot intensity in subsequent analyses.
We extracted the raw (unnormalized) intensity values for all probes in each significant region, and computed a mean intensity for serpentine and granitic populations.
The intraarray replicates were merged by computing their mean intensity.
An additional method to reduce the impact of a highly fluctuating light source is to scale each frame (before subtracting) by computing the mean intensity over the entire field and normalize the frame to the mean of means.
The transformed VOIs, which were subsequently aligned with the original data and were applied to the original data to compute the mean intensity.
The mask for the photoconverted region of the nuclear envelope was used to compute the mean intensity in this region in both red and green channels at each time point.
That is for each ellipse centered about (x(p), y(p)) with skew σ p (p)/σ m (p) and angle θ(p), we compute the mean intensity along this ellipse.
The total activity in a sphere was computed as the mean intensity of all voxels within the volume of interest (VOI) corresponding to the sphere.
