I am doing research on mCT 2D images of human teeth. The scans are firstly manipulated with Avizo software, but I prefer to do the actual measurements in ImageJ, which is much easier to use. I save a tiff snapshot of the image together with scale bars, and then import the image into ImageJ. I then set the scale by drawing a line across the scale bars. Usually, 1mm = 50-60 pixels. The problem is that this is never sufficiently accurate, no matter how carefully I try to draw the line. I have noticed that there is always a small discrepency between measurements taken in Avizo and measurements taken in ImageJ. Is there any way round this problem?
If you find a way to read out the pixel size in the Avizo software, you can set the exact value in ImageJ using the pixel width and pixel height fields in Image Properties…, see also the documentation.