Automated Landmarking via Multiple Templates

• Published in: bioRxiv
• Main Authors: Zhang, Chi, Porto, Arthur, Rolfe, Sara, Altan Kocatulum, Maga, A Murat
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 25.01.2022; Cold Spring Harbor Laboratory
• Edition: 1.2
• Subjects: Animal models; Automation; Evolutionary Biology; Morphology; Morphometry; Phenotypes; phenotype; Geometric morphometrics; craniofacial variation; automated landmarking
• ISSN: 2692-8205; 2692-8205
• DOI: 10.1101/2022.01.04.474967

Geometric morphometrics based on landmark data has been increasingly used in biomedical and biological researchers for quantifying complex phenotypes. However, manual landmarking can be laborious and subject to intra and interobserver errors. This has motivated the development of automated landmarking methods. We have recently introduced ALPACA (Automated Landmarking through Point cloud Alignment and Correspondence), a fast method to automatically annotate landmarks via use of a landmark template as part of the SlicerMorph toolkit. Yet, using a single template may not consistently perform well for large study samples, especially when the sample consists of specimen with highly variable morphology, as it is common evolutionary studies. In this study, we introduce a variation on our ALPACA pipeline that supports multiple specimen templates, which we call MALPACA. We show that MALPACA outperforms ALPACA consistently by testing on two different datasets. We also introduce a method of choosing the templates that can be used in conjunction with MALPACA, when no prior information is available. This K-means method uses an approximation of the total morphological variation in the dataset to suggest samples within the population to be used as landmark templates. While we advise investigators to pay careful attention to the template selection process in any of the template-based automated landmarking approaches, our analyses show that the introduced K-means based method of templates selection is better than randomly choosing the templates. In summary, MALPACA can accommodate larger morphological disparity commonly found in evolutionary studies with performance comparable to human observer. Competing Interest Statement The authors have declared no competing interest. Footnotes * Correct typos. * https://github.com/SlicerMorph/mouse_models