Dataset Information

Shape-changing chains for morphometric analysis of 2D and 3D, open or closed outlines

ABSTRACT: Morphometrics is a multivariate technique for shape analysis widely employed in biological, medical, and paleoanthropological applications. Commonly used morphometric methods require analyzing a huge amount of variables for problems involving a large number of specimens or complex shapes. Moreover, the analysis results are sometimes difficult to interpret and assess. This paper presents a methodology to synthesize a shape-changing chain for 2D or 3D curve fitting and to employ the chain parameters in stepwise discriminant analysis (DA). The shape-changing chain is comprised of three types of segments, including rigid segments that have fixed length and shape, scalable segments with a fixed shape, and extendible segments with constant curvature and torsion. Three examples are presented, including 2D mandible profiles of fossil hominin, 2D leaf outlines, and 3D suture curves on infant skulls. The results demonstrate that the shape-changing chain has several advantages over common morphometric methods. Specifically, it can be applied to a wide range of 2D or 3D profiles, including open or closed curves, and smooth or serrated curves. Additionally, the segmentation of profiles is a flexible and automatic protocol that can consider both biological and geometric features, the number of variables obtained from the fitting results for statistical analysis is modest, and the chain parameters that characterize the profiles can have physical meaning.

SUBMITTER: Li B

PROVIDER: S-EPMC8563779 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:Mitochondrial morphology and function are coupled in healthy cells, during pathological conditions and (adaptation to) endogenous and exogenous stress. In this sense mitochondrial shape can range from small globular compartments to complex filamentous networks, even within the same cell. Understanding how mitochondrial morphological changes (i.e. "mitochondrial dynamics") are linked to cellular (patho) physiology is currently the subject of intense study and requires detailed quantitative information. During the last decade, various computational approaches have been developed for automated 2-dimensional (2D) analysis of mitochondrial morphology and number in microscopy images. Although these strategies are well suited for analysis of adhering cells with a flat morphology they are not applicable for thicker cells, which require a three-dimensional (3D) image acquisition and analysis procedure. Here we developed and validated an automated image analysis algorithm allowing simultaneous 3D quantification of mitochondrial morphology and network properties in human endothelial cells (HUVECs). Cells expressing a mitochondria-targeted green fluorescence protein (mitoGFP) were visualized by 3D confocal microscopy and mitochondrial morphology was quantified using both the established 2D method and the new 3D strategy. We demonstrate that both analyses can be used to characterize and discriminate between various mitochondrial morphologies and network properties. However, the results from 2D and 3D analysis were not equivalent when filamentous mitochondria in normal HUVECs were compared with circular/spherical mitochondria in metabolically stressed HUVECs treated with rotenone (ROT). 2D quantification suggested that metabolic stress induced mitochondrial fragmentation and loss of biomass. In contrast, 3D analysis revealed that the mitochondrial network structure was dissolved without affecting the amount and size of the organelles. Thus, our results demonstrate that 3D imaging and quantification are crucial for proper understanding of mitochondrial shape and topology in non-flat cells. In summary, we here present an integrative method for unbiased 3D quantification of mitochondrial shape and network properties in mammalian cells.

Project description:PurposeTotal and regional body composition are important indicators of health and mortality risk, but their measurement is usually restricted to controlled environments in clinical settings with expensive and specialized equipment. A method that approaches the accuracy of the current gold standard method, dual-energy x-ray absorptiometry (DXA), while only requiring input from widely available consumer grade equipment, would enable the measurement of these important biometrics in the wild, enabling data collection at a scale that would have previously been prohibitive in time and expense. We describe an algorithm for predicting three-dimensional (3D) body shape and composition from a single frontal 2-dimensional image acquired with a digital consumer camera.MethodsDuplicate 3D optical scans, two-dimensional (2D) optical images, and DXA whole-body scans were available for 183 men and 233 women from the Shape Up! Adults Study. A principal component analysis vector basis was fit to 3D point clouds of a training subset of 152 men and 194 women. The relationship between this vector space and DXA-derived body composition was modeled with linear regression. The principal component 3D shape was then fitted to match a silhouette extracted from a 2D photograph of a novel body. Body composition was predicted from the resulting 3D shape match using the linear mapping between the principal component parameters and the DXA metrics. Accuracy of body composition estimates from the silhouette method was evaluated against a simple model using height and weight as a baseline, and against DXA measurements as ground truth. Test-retest precision of the silhouette method was evaluated using the duplicate 2D optical images and compared against precision of the duplicate DXA scans. Paired t-tests were performed to detect significant differences between the sets.ResultsResults were reported on a held-out set. Body composition prediction achieved R2 s of 0.81 and 0.74 for percent fat prediction of males and females, respectively, on a held-out test set consisting of 31 males and 39 females. Precision estimates for fat mass were 2.31% and 2.06% for males and females, respectively, compared to 1.26% and 0.68% for DXA scans. The t-tests revealed no statistically significant differences between the silhouette method measurements and DXA measurements, or between retests.ConclusionTotal and regional body composition measures can be estimated from a single frontal photograph of a human body. Body composition prediction using consumer level photography can enable early screening and monitoring of possible physiological indicators of metabolic disease in regions where medical imagery or clinical assessment is inaccessible.

Dataset Information

Shape-changing chains for morphometric analysis of 2D and 3D, open or closed outlines

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets