And to emphasize what Dean said about SlicerMorph. If you collected your 3D data using SlicerMorph and run a GPA analysis, you can get the everything into geomorph with a single line of code from our SlicerMorphR package. Every GPA run will produce an *analysis.json *file that includes everything for you reconstruct the analysis in geomorph from scratch So if you enter:
*SM.output=parser2(PATH/TO/YOUR/GPA/OUTPUT/analysis.json , json=TRUE)* then the resultant object *SM.output$LMs *is the raw landmark coordinates in a 3D array that geomorph functions like gpagen expects, while *SM.output$ID* would be the filenames along with many other variables that give you the semi-landmarks indices etc... The brief tutorial that explains the rest of the variables in the SM.output object can be found here: https://github.com/SlicerMorph/Tutorials/blob/main/GPA_3/README.md On Sunday, March 15, 2026 at 10:44:24 AM UTC-7 Adams, Dean [EEOB] wrote: > Colleagues, > > > > We wish to announce a major update to geomorph, version 4.1.0, which is > now available on CRAN and github. > > The primary change is to remove all RGL-based 3D graphics, and replace > them with plotly-based graphics. This change was necessitated because under > the new MacOS operating system Tahoe, openGL graphics is no longer > supported, and the RGL library is no longer maintained on that system. That > change has cascaded to geomorph, and has forced us to pivot to other > packages for geomorph’s 3D graphics, so that all of our users may retain 3D > functionality. > > A secondary consequence of this change is that digitizing in geomorph is > no longer supported, as it relied on interactive RGL components. While > unfortunate, we note that when we released the original version of geomorph > fourteen years ago (2012), there were few freeware options available for 3D > digitizing. Thus, having these functions available in geomorph served an > important community need. Today in 2026 there are numerous options for 3D > data collection, including SlicerMorph which is freeware (and frankly quite > comprehensive). As such, the loss of digitizing capabilities within > geomorph should be of minimal impact. Nonetheless, for those users with > digitizing pipelines that use geomorph, we will add a repository for > version 4.0.9 of geomorph on github (on the ‘frozen’ branch), which will > retain the RGL-based digitizing functions. This branch and version are > considered frozen (and as RGL will no longer work on some OS platforms, its > use might require an older Mac OS or other OS). The geomorph team will not > maintain or update this frozen version in any way. We will simply retain it > in its current form for any users who wish to use the antiquated digitizing > functions. This version could also be discontinued in the future, pending > other R updates that might make it unfunctional. > > > > Regardless, we hope that the new 3D graphics via plotly will be suitable > for the geomorph community going forward, and we thank you for your > patience during this time of transition. > > All the best and happy GM-computing! > > Dean (on behalf of the geomorph team) > > > > Dr. Dean C. Adams > > Distinguished Professor > > Director, Ecology and Evolutionary Biology Graduate Program > > Department of Ecology, Evolution, and Organismal Biology > > Iowa State University > > *www.public.iastate.edu/~dcadams/ > <http://www.public.iastate.edu/~dcadams/>* > > phone: 515-294-3834 <(515)%20294-3834> > > > -- You received this message because you are subscribed to the Google Groups "Morphmet" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion visit https://groups.google.com/d/msgid/morphmet2/24d5fc5f-147d-41d2-a278-ae9eebd3e6c5n%40googlegroups.com.
