Dear Melanie Baker

To my knowledge neither PAST nor MorphoJ can estimate missing landmarks, in fact in theory MorphoJ does not allow the use of semilandmarks. From your question I understand you are using 2D landmarks obtained from 2D pictures using TPSDig. Thus, my recommendation is use two packages available in R which allow estimate missing landmarks. In the first one Geomorph there are two algorithms that can be used using the function estimate.missing:

The first approach (method="TPS") uses the thin-plate spline to interpolate landmarks on a reference specimen to estimate the locations of missing landmarks on a target specimen. Here, a reference specimen is obtained from the set of specimens for which all landmarks are present, Next, each incomplete specimen is aligned to the reference using the set of landmarks common to both. Finally, the thin-plate spline is used to estimate the locations of the missing landmarks in the target specimen (Gunz et al. 2009).

The second approach (method="Reg") is multivariate regression. Here each landmark with missing values is regressed on all other landmarks for the set of complete specimens, and the missing landmark values are then predicted by this linear regression model. Because the number of variables can exceed the number of specimens, the regression is implemented on scores along the first set of PLS axes for the complete and incomplete blocks of landmarks (see Gunz et al. 2009).

Please check the help file https://cran.r-project.org/web/packages/geomorph/geomorph.pdf

The second one named Morpho also uses two functions to estimate missing landmarks. The function fixLMmirror allow estimate missing landmarks from their bilateral counterparts and in the fixLMtps function the missing landmarks are estimated by deforming a sample average or a weighted estimate of the configurations most similar onto the deficient configuration. The deformation is performed by a Thin-plate-spline interpolation calculated by the available landmarks.

Please check the help file https://cran.r-project.org/web/packages/Morpho/Morpho.pdf

Please note that these methods have different requirements.

Both packages allow use files derived from TPSDig, thus you can use your files. These functions allow you read landmarks into R in Geomorph readland.tps and in Morpho readallTPS

I hope this helps!

Cheers,

Miguel

Why will one be forced to use sample(s) which landmarks are missing? Myself, to overcome this challenge, I usually take pictures of many samples. This allows me to only work on pictures were my landmarks of interest are preserved. For the pictures with missing landmarks, I usually discard them.

Dear Holger, thank you for that precision. I wasn't seeing it from that angle.

Best

Steve Baleba

Many of the tools use special values in the input files to denote "missing landmarks". Our Checkpoint software can be used to collect 3D landmark points and allows you to create templates that can be applied to subsequent specimen efficiently.

Further, when specimen are missing fragments and landmark points, Checkpoint allows you to mark those landmarks as "missing" while maintaining the ordering of the points.

The points can then be exported to common formats that are used by these other software tools.

https://www.stratovan.com/products/checkpoint?utm_source=rg&utm_medium=ans&utm_campaign=lm10