Comparison between 3D mesh plots
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I have been working on Digital holographic microscopy (DHM). It is a well-established imaging modality to visualize a microscopic object (say a red blood cell) in 3D. I have reconstructed 3-D profiles of these micro objects using the unwrapped phase maps of these micro objects using the mesh function. Now I want to compare these 3D mesh plots with the other mesh plots (of the same micro object), is SSIM a viable option in this situation? Also, what other comparison methods can I use?
Div Tiwari on 8 Aug 2016
Since the third dimension of a grayscale image matrix can correspond with the depth data of your 3D profiles, SSIM is a reasonable approach for a similarity comparison. However, you must make sure you specify the 'DynamicRange' name-value pair argument appropriately or normalize your data along the Z-axis.
Additionally, you may modify the 'Exponents' name-value pair argument to affect sensitivity towards the correlation of local means, standard-deviations, and cross-covariances respectively (a higher exponent means greater sensitivity). For example, if the mean thickness is more important and the shape is not as much for a particular comparison, you can increase the value of alpha (first element of 'Exponent' vector) and decrease the value of gamma (third element of 'Exponent' vector). The documentation page describes the mathematical background for this: http://www.mathworks.com/help/images/ref/ssim.html#bt5rm3r-1
Finally, some other methods of comparison are element-wise difference (with optional normalization against the data), 2-D cross correlation using 'xcorr2' (requires the Signal Processing Toolbox), or implementing a simple script for cosine similarity.