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The global background method uses a common background value for each ROI.
Average fluorescence intensities were logged into Excel files, after subtraction of the local background value for each spot.
The background value for each image was set using the "threshold" function of the program to a level that would exclude all pixels in control tissues stained with secondary antibody alone.
A background-subtracted image of the radioactivity was then obtained by subtracting the background value for each pixel from the original image.
Images were also processed using SPOT (CSIRO, New South Wales, Australia)[ 32], an R-based implementation which uses seeded region growing to determine the foreground pixels for each spot and morphological opening to determine the background value for each spot.
Example image captures from a female sample co-hybridised with the male reference are shown in Figure 2. Captured images were then loaded into PamChip Analyser (V.4) which was set to record values for median spot intensity minus a background value for each spot using the 'local corners' method.
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To determine peaks above BCHAR, we first applied a Lowess smoother robust to outliers, within a 500-year window width and then subtracted background values for each time interval from the total CHAR accumulation (for each interval) (Higuera et al. 2010).
With this subset of data, the quasi-background value for each RNA-seq protocol as a whole was represented by the median of 99th percentiles of raw counts in the 3 RNA samples.
Due to the origin of the soil samples, the obtained results helped determine the background value for the magnetic susceptibility of the forest topsoil in Polish lowlands and uplands.
Our extension is twofold: first, the object boundaries are determined directly in the PET data and second, for each voxel in the spill-out region a local background is computed independently instead of using a common background value for the complete ROI.
To determine a background value for Δψm, cells were incubated with 1 µM CCCP (Calbiochem, La Jolla, CA, USA), which is sufficient to completely abrogate Δψm.
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