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To distinguish between the grains and the dyed resin-filled pore space, a binary image was calculated, with white pixels representing the grains and black pixels the pore space.
Brightness, contrast and threshold was adjusted identically for all sections and the "area fraction" occupied by Aβ staining in the binary image was calculated.
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After user determination of the AIS start point, connected components of the binary image were calculated and the single connected element closest to the AIS start isolated.
The percentage of pixels with binary value of 1s versus pixel numbers of the whole image was calculated as the estimation of vessel density.
The mean fluorescence from each image was calculated with ImageJ.
If such a valley is found, C V =1; else 0. iv) Player location condition ( C P ): From the video frame, a binary edge image is calculated using the 'sobel' method and image dilation [37] is performed.
If such a valley is found, C V =1; else 0. Player location condition ( C P ): From the video frame, a binary edge image is calculated using the 'sobel' method and image dilation [37] is performed.
Average intensity in these images was calculated over areas marked by the binary masks corresponding to chloroplasts.
Fluorescence ratios of scanned images were calculated as the average of two paired arrays (dye swap), and the raw profiles were processed to identify statistically significant transitions in copy number using Circular Binary Segmentation [11], [12].
A binary image was obtained by threshold function.
The ATase positive binary image was added to the propidium iodide positive binary image and the total nuclear area recorded.
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