![]() ![]() Select Ellipses from the Show: drop-down menu in the particle analyzer (Analyze▷ Analyze Particles…↑) and it will draw the ellipse for each particle in a separate window. ![]() The DrawEllipse macro draws (destructively) the best fit ellipse and the major and minor axis.Mean - Average gray value within the selection. The Edit▷Selection▷ Fit Ellipse↑ command replaces an area selection with the best fit ellipse. Area is in calibrated units, such as square millimeters, if Set Scale has been used to spatially calibrate the image.There are several ways to view the fitted ellipse: Mean Gray Value - Average gray value within the selection. i1 experimental image i2 flat-field image k1 mean flat-field intensity k2 0. Use the Image Calculator plus plugin (Analyze Tools Calculator plus). This value, the k1 value, will appear in the results window. Click the Select all button on the flat-field image and measure the average intensity. Next select the right stacks for the analysis in Channel1 and Channel2. Area is in calibrated units, such as square millimeters, if Analyze>Set Scale was used to spatially calibrate the image. Open both the experimental image and the flat-field image. With the green and red stacks of the colocsample1bRGBBG.tif dataset open and the channels split (see above) choose the menu item Analyze-Colocalization-Colocalization Threshold. Note that ImageJ cannot calculate the major and minor axis lengths if Pixel Aspect Ratio in the Analyze▷ Set Scale…↓ dialog is not 1.0. The Colocalization Threshold plugin performs several functions for you in one go. Purpose: This protocol describes how to quantify any type of cellular foci, such as phosphorylated Ser139 on histone variant H2A.X (H2AX) stained images of tissue or cells, using the free NIH Image Processing and Analysis in Java software called Fiji or ImageJ. The coordinates of the center of the ellipse are displayed as X and Y if Centroid is checked. Quantification of foci using Fiji or ImageJ. Angle is the angle between the primary axis and a line parallel to the X-axis of the image. Major and Minor are the primary and secondary axis of the best fitting ellipse. Uses the headings Major, Minor and Angle. Fit ellipse Fits an ellipse to the selection.
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