For Figure 2 figure supplement 2B, localization of PDGFRα+ and PDGFRβ+ cells was measured using the profile option where fluorescent intensities are graphed along a line drawn across the XY-plane of a confocal image.
In the following, LM models with MD, HD, and SEQ data were designated LMMD, LMHD, and LMSEQ; BVS models with MD, HD, and SEQ data were designated BVSMD, BVSHD, and BVSSEQ; and BVS models using the QTL intensity profile with MD, HD, and SEQ data were designated BVSINTMD, BVSINTHD, and BVSINTSEQ, respectively.
Marziliano et al. [29] calculated the sharpness value using the edge-intensity profiles after Sobel filtering.
Using the line intensity-profile tool, 10 µm wide lines were constructed centrally through each nephron segment and the maximum pixel value was determined along the line at each z-plane.
A further major benefit of using this comprehensive array platform rather than a targeted gene panel is the ability to generate genome-wide copy-number profiles using the intensity measures of the methylation probes, with a good concordance to other copy-number platforms such as CGH or SNP arrays, as we have recently described [ 14].
Using the Plot Profile function, the pixel intensity along the line was measured and plotted against distance along the line.
Intensity profile measurements were done using the "plot profile" tool in ImageJ, using a line with a 20 or 30-pixel width.
By solving the focused transport equation described in the previous section using the injection profile equation, we can simulate the SEP event intensity and anisotropy profile.
Spindles were analysed using Image J software, by creating a region of interest and using the 'plot profile' plugin to capture the tubulin and H2B intensity along the long axis of the spindle.
Histograms of fluorescence intensity were generated from ventral z-stacks, using the 'Plot Profile' tool in ImageJ.
