I performed my sholl analysis and I would like to save the figure of sholl plot as representative image. If I use “save as tiff” it saves only the mask without radius. Moreover, I would like to change the color of the shells and intersection points in my image because in my plugin version shells and intersection points are yellow.
You mean the “Sholl Mask”? Whatever ROI you have used in the analysis, you can add it to the ROI Manager (T) or use Edit>Selection>Restore Selection (Shift+E) to transfer the ROI to the image.
They will have the color listed in “Annotations LUT”. If you don’t select a lookuptable, Annotations will adopt the active selection color. You can change it by double clicking on the point tool in the ImageJ toolbar.