Any suggestions on using lights of different wavelengths, polarization microscopy techniques? I am imaging my particles under conventional light microscopy and can obtain width and length of the particles.
you will need to calibrate your scale on the focus, by measuring something with a known thickness (focusing top and bottom and reading the number of focus steps that corresponds to).
Then you measure top and bottom focus of your particles and convert that to thickness. If the thickness is below 5 microns the technique is very imprecise.
Use maximum magnification and the thickness standard should be measured in the same immersion media for your thickness standard. Also use top lens to reduce the depth focus.
An alternative method is to use a universal stage to tilt your particles and measure their three dimensional shape. That has been applied to fluid inclusions in minerals. If you have access to a spindle stage that is the most accurate way, and it does not depend on any calibrations or assumptions.