Re: Getting the scale

Posted by Cspr on
URL: http://imagej.273.s1.nabble.com/Getting-the-scale-tp3686642p3686650.html

I thought it might be better if I stated the problem in its complete form.

So I have an LIF file. In such a file is number of series and each series consists of a number of slices and each slice consist of three images. Each slice in each series are taken with the same micron resolution, but slices in other series within the same LIF file might have a different micron resolution.

What i've been doing in my, admittedly naive, approach was to use ImageJ Fiji to get the scale for the first series (using Analyze -> Set scale...), and just hardcode that value in Java and on each image using the IJ.run(image, "Set scale", "bla bla") where "bla bla would be something like "distance=14.591" etc.

This works for the series from which I used ImageJ Fiji to get the scale. However obviously when chaging series the scale is NOT necessarily correct anymore. So the problem is how to calculate the distance/scale on a series to series basis?