Shape changes from analyses of 3D data are difficult with MorphoJ. The most intuitive way to visualize such shape changes is by warping surfaces (Wiley et al. 2005; Klingenberg 2013). MorphoJ can produce files for input into the Landmark software (Wiley et al. 2005) to deform surfaces (imported from .PLY files, from optical surface scans or CT scans) using the thin-plate spline.
First, download the Landmark software and install it (available for Windows only), and also download the PDF documentation.
Second, load your .PLY file with your surface data into Landmark and place the landmarks on it in the same sequence as they appear in the MorphoJ dataset on which your analyses are based. For how to do these things, see the PDF documentation for Landmark.
In MorphoJ, go to the graph from which you want to make a visualization and select Export Coordinate File from the pop-up menu (see screen shot above).
This will invoke a dialog box where you can specify the name and location for a file with the information about the shape change in the graph. The default file name extension for the file is .dta, which is a file type that can be read by the Landmark software. Save the file in a convenient location with this file name extension.
In Landmark, open the project containing the surface corresponding to the dataset analyzed in MorphoJ. The interface should show a folder icon for the project and an icon for the surface in the Database Contents area on the left side, as well as three windows labeled A, B, and C.
Right-click the icon of the surface in the Database Contents area in Landmark and select Load into A.
Landmark will display the surface in window A and a red letter A will appear in the icon of the surface in the area to the left.
To open the file with the shape changes, select Import > Into project from the File menu.
A dialog box will appear in which you can seect the .dta file you saved in MorphoJ for import into the Landmark project.
As a result, the contents of the file will be displayed as a folder icon in the Database Contents area of Landmark. The name of the folder icon contains information about the origin of the information in MorphoJ.
Two icons are attached to this folder icon: one is named according to the shape change you saved in MorphoJ ("PC2" in the screen shot below, as the information was exported from a graph showing the shape change for a principal component) and the other is names "starting_shape". This starting shape is usually the mean shape in the MorphoJ dataset (e.g. for graphs of principal components, canonical variates or regression), but it can be something else (e.g. in shape changes mapped onto phylogenies, where the user can select the starting and target shape separately).
To load the shape that is to visualized into window B, right-click on the icon of the shape (e.g. PC2 in the screen shot above) and select Load into B from the popup menu that appears. As a result, the landmarks will be loaded into window B and appear as faint dots in it.
The next step is to match the coordinates of the landmarks in the newly imported information to the landmark coordinates of the surface in window A. Select Correspondences... from the View menu, and the following dialog box will appear:
The two lists A and B contain the landmarks in the two windows (note that counting starts with 0, not 1). Select s0 (the first landmark) in the lists for both windows, and then click on the button marked >>. This will move the two landmarks into the list of correspondences, on the right side of the dialog box. Click the >> button for every landmark, until no more are left in lists A and B.
When this is done, click on the slider bar below window C. A dialog box like the following will appear:
Click the OK button. A surface will appear in window C. Then move the slider all the way to the right, to the 100% position. At this position, the surface shows the shape specified by the information imported from MorphoJ, which may look like this:
To improve the appearance of the surface, click on the following three buttons to remove the bounding box, the axes and to make the surface opaque (remove transparency).
To eliminate the set of axes that pierce the surface, select Data bounds from the View menu and click on PCA Axes to remove the tick mark to the left of it.
For further information on manipulation of the new surface and export to graphics files, see the PDF documentation of the Landmark software.
Klingenberg, C. P. 2013. Visualizations in geometric morphometrics: how to read and how to make graphs showing shape changes. Hystrix 24:15–24.
Wiley, D. F., N. Amenta, D. A. Alcantara, D. Ghosh, Y. J. Kil, E. Delson, W. Harcourt-Smith, F. J. Rohlf, K. St. John, and B. Hamann. 2005. Evolutionary morphing. Proceedings of the IEEE Visualization 2005 (VIS'05):431–438.