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Abstract Geometric morphometrics is used in the biological sciences to quantify morphological traits. However, the need for manual landmark placement hampers scalability, which is both time‐consuming, labor‐intensive, and open to human error. The selected landmarks embody a specific hypothesis regarding the critical geometry relevant to the biological question. Any adjustment to this hypothesis necessitates acquiring a new set of landmarks or revising them significantly, which can be impractical for large datasets. There is a pressing need for more efficient and flexible methods for landmark placement that can adapt to different hypotheses without requiring extensive human effort. This study investigates the precision and accuracy of landmarks derived from functional correspondences obtained through the functional map framework of geometry processing. We utilize a deep functional map network to learn shape descriptors, which enable us to achieve functional map‐based and point‐to‐point correspondences between specimens in our dataset. Our methodology involves automating the landmarking process by interrogating these maps to identify corresponding landmarks, using manually placed landmarks from the entire dataset as a reference. We apply our method to a dataset of rodent mandibles and compare its performance to MALPACA's, a standard tool for automatic landmark placement. Our model demonstrates a speed improvement compared to MALPACA while maintaining a competitive level of accuracy. Although MALPACA typically shows the lowest RMSE, our models perform comparably well, particularly with smaller training datasets, indicating strong generalizability. Visual assessments confirm the precision of our automated landmark placements, with deviations consistently falling within an acceptable range for MALPACA estimates. Our results underscore the potential of unsupervised learning models in anatomical landmark placement, presenting a practical and efficient alternative to traditional methods. Our approach saves significant time and effort and provides the flexibility to adapt to different hypotheses about critical geometrical features without the need for manual re‐acquisition of landmarks. This advancement can significantly enhance the scalability and applicability of geometric morphometrics, making it more feasible for large datasets and diverse biological studies. 

Abstract Landmark‐based geometric morphometrics has emerged as an essential discipline for the quantitative analysis of size and shape in ecology and evolution. With the ever‐increasing density of digitized landmarks, the possible development of a fully automated method of landmark placement has attracted considerable attention. Despite the recent progress in image registration techniques, which could provide a pathway to automation, three‐dimensional (3D) morphometric data are still mainly gathered by trained experts. For the most part, the large infrastructure requirements necessary to perform image‐based registration, together with its system specificity and its overall speed, have prevented its wide dissemination.Here, we propose and implement a general and lightweight point cloud‐based approach to automatically collect high‐dimensional landmark data in 3D surfaces (Automated Landmarking through Point cloud Alignment and Correspondence Analysis). Our framework possesses several advantages compared with image‐based approaches. First, it presents comparable landmarking accuracy, despite relying on a single, random reference specimen and much sparser sampling of the structure's surface. Second, it can be efficiently run on consumer‐grade personal computers. Finally, it is general and can be applied at the intraspecific level to any biological structure of interest, regardless of whether anatomical atlases are available.Our validation procedures indicate that the method can recover intraspecific patterns of morphological variation that are largely comparable to those obtained by manual digitization, indicating that the use of an automated landmarking approach should not result in different conclusions regarding the nature of multivariate patterns of morphological variation.The proposed point cloud‐based approach has the potential to increase the scale and reproducibility of morphometrics research. To allow ALPACA to be used out‐of‐the‐box by users with no prior programming experience, we implemented it as a SlicerMorph module. SlicerMorph is an extension that enables geometric morphometrics data collection and 3D specimen analysis within the open‐source 3D Slicer biomedical visualization ecosystem. We expect that convenient access to this platform will make ALPACA broadly applicable within ecology and evolution. 

Abstract Large‐scale digitization projects such as#ScanAllFishesandoVertare generating high‐resolution microCT scans of vertebrates by the thousands. Data from these projects are shared with the community using aggregate 3D specimen repositories like MorphoSource through various open licenses. We anticipate an explosion of quantitative research in organismal biology with the convergence of available data and the methodologies to analyse them.Though the data are available, the road from a series of images to analysis is fraught with challenges for most biologists. It involves tedious tasks of data format conversions, preserving spatial scale of the data accurately, 3D visualization and segmentations, and acquiring measurements and annotations. When scientists use commercial software with proprietary formats, a roadblock for data exchange, collaboration and reproducibility is erected that hurts the efforts of the scientific community to broaden participation in research.We developed SlicerMorph as an extension of 3D Slicer, a biomedical visualization and analysis ecosystem with extensive visualization and segmentation capabilities built on proven python‐scriptable open‐source libraries such as Visualization Toolkit and Insight Toolkit. In addition to the core functionalities of Slicer, SlicerMorph provides users with modules to conveniently retrieve open‐access 3D models or import users own 3D volumes, to annotate 3D curve and patch‐based landmarks, generate landmark templates, conduct geometric morphometric analyses of 3D organismal form using both landmark‐driven and landmark‐free approaches, and create 3D animations from their results. We highlight how these individual modules can be tied together to establish complete workflow(s) from image sequence to morphospace. Our software development efforts were supplemented with short courses and workshops that cover the fundamentals of 3D imaging and morphometric analyses as it applies to study of organismal form and shape in evolutionary biology.Our goal is to establish a community of organismal biologists centred around Slicer and SlicerMorph to facilitate easy exchange of data and results and collaborations using 3D specimens. Our proposition to our colleagues is that using a common open platform supported by a large user and developer community ensures the longevity and sustainability of the tools beyond the initial development effort.