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How should I cite MorphoDig in scientific publications?

You may cite MorphoDig with the following reference:

Lebrun, R. MorphoDig, an open-source 3D freeware dedicated to biology. IPC5, Paris, France; 07/2018

Is MorphoDig a geometric morphometrics software ?

No. However, you can digitize 3D landmarks on complex 3D surfaces using MorphoDig, which you can use in other software.

Can I produce/extract 3D meshes out of CT/MRI data using MorphoDig ?

No. To extract 3D meshes CT/MRI data sets, you have to use another software. However, you can edit 3D Meshes in various ways using MorphoDig.

Is there a "CTRL-Z" functionality around ?

Yes, definitely. Most actions can be undone and redone.