[FieldTrip] How make a heat map on a skull using 3D landmark-based geometric morphometrics?

Savriama, Yoland F yoland.savriama at helsinki.fi
Mon Oct 30 12:47:27 CET 2017

Dear colleagues,

I use 3D landmark-based geometric morphometrics for statistical analyses of morphological variation in vertebrate skulls. I would like to know how I could create a heat map of a skull that will show the deviations from the mean shape for a given effect around each landmark.

For instance, the patterns of shape changes associated with a given Principal Component that would be mapped on a 3D skull representing the average mean shape. In this case, the visualisations of these deviations will be restricted and associated only with the local landmark coordinates as opposed to a full heat map that would cover the entire skull.

In fact, the exact thing I would like to achieve had been done in Figure 4A of this publication:

Maga, A. M., Navarro, N., Cunningham, M. L., & Cox, T. C. (2015). Quantitative trait loci affecting the 3D skull shape and size in mouse and prioritization of candidate genes in-silico. Frontiers in physiology, 6.


I would greatly appreciate your feedback on this matter.

Best wishes,


Institute of Biotechnology
P.O. Box 56 (Viikinkaari 5)
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