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For quantification purposes, gain and offset settings were kept constant so that the average background pixel intensity was between 0 and 10 and the fluorescent signal coming from the cells was between 60 and 220 (0-255 scale for 8 bit images).
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Median foreground pixel intensities for spots were adjusted by subtracting median background pixel intensities.
A neighborhood region of interest (ROI) (11 × 11 pixels) is defined around each selected point, the boundary of which is used to estimate average background signal per pixel.
Immunostaining intensity higher than average background was set as pixel threshold for positive staining, which included both nuclear and cytoplasmic stainings.
For each genotype, the average, background-subtracted mean pixel intensity of PDF immuno-reactivity (IR) was calculated from five brains for each genotype, with four l- and s-vLNs measured in each brain.
Maximum DCF fluorescence intensity per neuronal cell body was determined on a pixel-by-pixel basis following background subtraction (average background of all images at t = 0 min for each condition) followed by erosion (2 pixels) and overlay with the original image (Zeiss imaging analysis software KS 300).
Only clusters with average pixel intensity 1.5 times greater than background pixel intensity were used for analysis.
The intensity at each point is the average (background corrected) unnormalized intensity over the 20 pixel strip along the Y T axis and averaged over 3 images, at the given time, plus the previous and next images.
Spill-in of signal from surrounding activity is derived by using an 'inverted' mask, i.e. setting the voxel values within the mask to zero and the surrounding pixels to the measured average background value, and following the same procedure.
Some features of foreground and background pixel values (e.g., mean and standard deviation) and average stroke width of the character are estimated from the background image and global output.
For calculation, the mean signal intensity (pixel) minus local background (pixel) of each spot was used.
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