scholarly journals ALPACA: a fast and accurate approach for automated landmarking of three-dimensional biological structures

2020 ◽  
Author(s):  
Arthur Porto ◽  
Sara M. Rolfe ◽  
A. Murat Maga
Keyword(s):  
Geometric Morphometrics ◽  
Morphological Variation ◽  
Point Cloud ◽  
Three Dimensional ◽  
3D Slicer ◽  
Automated Method ◽  
Landmark Data ◽  
Biomedical Visualization ◽  
Wide Dissemination ◽  
3D Surfaces

AbstractLandmark-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 morphometric data is 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 wide dissemination.Here, we propose and implement a general and lightweight point cloud-based approach to automatically collect highdimensional 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 is performant such that it can be efficiently run on consumer-grade personal computers. Finally, it is general and can be applied to any biological structure of interest, regardless of whether anatomical atlases are available.Our validation procedures indicate that the method is capable of recovering multivariate patterns of morphological variation that are largely indistinguishable from 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 module as part of the SlicerMorph project. 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.

scholarly journals Measurement error in μ CT ‐based three‐dimensional geometric morphometrics introduced by surface generation and landmark data acquisition

2019 ◽  
Vol 235 (2) ◽  
pp. 357-378 ◽  
Author(s):  
Karolin Engelkes ◽  
Jennice Helfsgott ◽  
Jörg U. Hammel ◽  
Sebastian Büsse ◽  
Thomas Kleinteich ◽  
...  
Keyword(s):  
Measurement Error ◽  
Data Acquisition ◽  
Geometric Morphometrics ◽  
Three Dimensional ◽  
Surface Generation ◽  
Landmark Data

scholarly journals Morphological variation under domestication: how variable are chickens?

2018 ◽  
Vol 5 (8) ◽  
pp. 180993 ◽  
Author(s):  
Madlen Stange ◽  
Daniel Núñez-León ◽  
Marcelo R. Sánchez-Villagra ◽  
Per Jensen ◽  
Laura A. B. Wilson
Keyword(s):  
Neural Crest ◽  
Geometric Morphometrics ◽  
Multivariate Statistics ◽  
Morphological Variation ◽  
Three Dimensional ◽  
Cranial Vault ◽  
Shape Variation ◽  
Skull Morphology ◽  
Variable Part ◽  
Brain Shape

The process of domestication has long fascinated evolutionary biologists, yielding insights into the rapidity with which selection can alter behaviour and morphology. Previous studies on dogs, cattle and pigeons have demonstrated that domesticated forms show greater magnitudes of morphological variation than their wild ancestors. Here, we quantify variation in skull morphology, modularity and integration in chickens and compare those to the wild fowl using three-dimensional geometric morphometrics and multivariate statistics. Similar to other domesticated species, chickens exhibit a greater magnitude of variation in shape compared with their ancestors. The most variable part of the chicken skull is the cranial vault, being formed by dermal and neural crest-derived bones, its form possibly related to brain shape variation in chickens, especially in crested breeds. Neural crest-derived portions of the skull exhibit a higher amount of variation. Further, we find that the chicken skull is strongly integrated, confirming previous studies in birds, in contrast to the presence of modularity and decreased integration in mammals.

scholarly journals Morphological variation of the caudal fossa of domestic cat skulls assessed with CT and geometric morphometrics analysis

2017 ◽  
Vol 20 (8) ◽  
pp. 752-758 ◽  
Author(s):  
Caroline R Gordon ◽  
Thomas W Marchant ◽  
Joanna Lodzinska ◽  
Jeffrey J Schoenebeck ◽  
Tobias Schwarz
Keyword(s):  
Geometric Morphometrics ◽  
Morphological Variation ◽  
Three Dimensional ◽  
Internal Surface ◽  
Foramen Magnum ◽  
Domestic Cat ◽  
Bone Morphology ◽  
Normal Range ◽  
Advanced Imaging ◽  
Wide Range

Objectives This study aimed to investigate differences and demonstrate a normal range of morphological variation of the caudal fossa of the cranium of domestic cats. Methods CT scans of 32 domestic cat heads of 11 breeds were included. Isosurfaces from skulls were characterised through three-dimensional geometric morphometrics using geographical landmarks placed on the internal surface of the caudal fossa and foramen magnum. Raw data was transformed with a Procrustes fit and coordinate covariance was analysed by principal components to establish breed- and sex-level differences. Skulls were also classified according to the number of concavities along the mid-sagittal vermiform impression. Differences were investigated between breed groups and sex, and correlation was sought with age. Results Analyses revealed size-independent differences in occipital bone morphology across breeds and sex; however, no clustering was evident. Most variability was observed at the exoccipital bones, ventral portion of the supraoccipital bone, dorsum sellae of the basisphenoid and the osseous tentorium cerebelli. No statistically significant differences were identified via two-sample t-tests between breed groups or sexes. No statistically significant correlation using Spearman rho correlation coefficient was identified with age. Conclusions and relevance The feline caudal fossa displays a wide range of intra- and inter-breed variation, not linked to age or sex. Concavities along the vermiform impression have not previously been described. As advanced imaging modalities are becoming more frequently used for domestic felids, an established range of normality is important for discriminating pathological changes from anatomical variances.

scholarly journals CONDITION ASSESSMENT OF RC BRIDGES. INTEGRATING MACHINE LEARNING, PHOTOGRAMMETRY AND BIM

2019 ◽  
Vol XLII-2/W15 ◽  
pp. 201-208 ◽  
Author(s):  
P. Borin ◽  
F. Cavazzini
Keyword(s):  
Neural Network ◽  
Point Cloud ◽  
Concrete Beam ◽  
Three Dimensional ◽  
Concrete Cover ◽  
Color Recognition ◽  
Automated Method ◽  
Beam Bridge

<p><strong>Abstract.</strong> The survey of building pathologies is focused on reading the state of conservation of the building, composed by the survey of constructive and decorative details, the masonry layering, the crack pattern, the degradation and the color recognition. The drawing of these representations is a time-consuming task, accomplished by manual work by skilled operators who often rely on in-situ analysis and on pictures. In this project three-dimensional an automated method for the condition survey of reinforced concrete spalling has been developed. To realize the automated image-based survey it has been exploited the Mask R-CNN neural network. The training phase has been executed over the original model, providing new examples of images with concrete cover detachments. At the same time, a photogrammetry process involved the images, in order to obtain a point cloud which acts as a reference to a Scan to BIM process. The BIM environment serves as a collector of information, as it owns the ontology to recreate entities and relationships. The information as extracted by neural network and photogrammetry serve to create the pictures which depict the concrete spalling in the BIM environment. A process of projecting information from the images to the BIM recreates the shapes of the pathology on the objects of the model, which becomes a decision support system for the built environment. A case study of a concrete beam bridge in northern Italy demonstrates the validity of the process.</p>

Handheld Laser Scanner Research

2019 ◽  
Vol 952 (10) ◽  
pp. 47-54
Author(s):  
A.V. Komissarov ◽  
A.V. Remizov ◽  
M.M. Shlyakhova ◽  
K.K. Yambaev
Keyword(s):  
Point Cloud ◽  
Three Dimensional ◽  
Laser Scanner ◽  
Test Site ◽  
Optical Systems ◽  
Advantages And Disadvantages ◽  
Site Survey ◽  
Laser Scanners ◽  
Three Dimensional Models ◽  
The Stability

The authors consider hand-held laser scanners, as a new photogrammetric tool for obtaining three-dimensional models of objects. The principle of their work and the newest optical systems based on various sensors measuring the depth of space are described in detail. The method of simultaneous navigation and mapping (SLAM) used for combining single scans into point cloud is outlined. The formulated tasks and methods for performing studies of the DotProduct (USA) hand-held laser scanner DPI?8X based on a test site survey are presented. The accuracy requirements for determining the coordinates of polygon points are given. The essence of the performed experimental research of the DPI?8X scanner is described, including scanning of a test object at various scanner distances, shooting a test polygon from various scanner positions and building point cloud, repeatedly shooting the same area of the polygon to check the stability of the scanner. The data on the assessment of accuracy and analysis of research results are given. Fields of applying hand-held laser scanners, their advantages and disadvantages are identified.

scholarly journals Three-dimensional segmentation and depth-encoded visualization of choroidal vasculature using swept-source optical coherence tomography

2021 ◽  
pp. 153537022110285
Author(s):  
Hao Zhou ◽  
Tommaso Bacci ◽  
K Bailey Freund ◽  
Ruikang K Wang
Keyword(s):  
Optical Coherence Tomography ◽  
Three Dimensional ◽  
Age Related Macular Degeneration ◽  
Optical Coherence ◽  
Full Thickness ◽  
Swept Source ◽  
Automated Method ◽  
Choroidal Imaging ◽  
Choroidal Vasculature ◽  
Choroidal Vessels

The choroid provides nutritional support for the retinal pigment epithelium and photoreceptors. Choroidal dysfunction plays a major role in several of the most important causes of vision loss including age-related macular degeneration, myopic degeneration, and pachychoroid diseases such as central serous chorioretinopathy and polypoidal choroidal vasculopathy. We describe an imaging technique using depth-resolved swept-source optical coherence tomography (SS-OCT) that provides full-thickness three-dimensional (3D) visualization of choroidal anatomy including topographical features of individual vessels. Enrolled subjects with different clinical manifestations within the pachychoroid disease spectrum underwent 15 mm × 9 mm volume scans centered on the fovea. A fully automated method segmented the choroidal vessels using their hyporeflective lumens. Binarized choroidal vessels were rendered in a 3D viewer as a vascular network within a choroidal slab. The network of choroidal vessels was color depth-encoded with a reference to the Bruch’s membrane segmentation. Topographical features of the choroidal vasculature were characterized and compared with choroidal imaging obtained with indocyanine green angiography (ICGA) from the same subject. The en face SS-OCT projections of the larger choroid vessels closely resembled to that obtained with ICGA, with the automated SS-OCT approach proving additional depth-encoded 3D information. In 16 eyes with pachychoroid disease, the SS-OCT approach added clinically relevant structural details, including choroidal thickness and vessel depth, which the ICGA studies could not provide. Our technique appears to advance the in vivo visualization of the full-thickness choroid, successfully reveals the topographical features of choroidal vasculature, and shows potential for further quantitative analysis when compared with other choroidal imaging techniques. This improved visualization of choroidal vasculature and its 3D structure should provide an insight into choroid-related disease mechanisms as well as their responses to treatment.

scholarly journals Automated Segmentation of Infarct Lesions in T1-Weighted MRI Scans Using Variational Mode Decomposition and Deep Learning

Sensors ◽  
2021 ◽  
Vol 21 (6) ◽  
pp. 1952
Author(s):  
May Phu Paing ◽  
Supan Tungjitkusolmun ◽  
Toan Huy Bui ◽  
Sarinporn Visitsattapongse ◽  
Chuchart Pintavirooj
Keyword(s):  
Deep Learning ◽  
Brain Infarction ◽  
Three Dimensional ◽  
Dice Similarity Coefficient ◽  
Automated Segmentation ◽  
Variational Mode Decomposition ◽  
Brain Scans ◽  
Automated Method ◽  
Mode Decomposition ◽  
Segmentation Task

Automated segmentation methods are critical for early detection, prompt actions, and immediate treatments in reducing disability and death risks of brain infarction. This paper aims to develop a fully automated method to segment the infarct lesions from T1-weighted brain scans. As a key novelty, the proposed method combines variational mode decomposition and deep learning-based segmentation to take advantages of both methods and provide better results. There are three main technical contributions in this paper. First, variational mode decomposition is applied as a pre-processing to discriminate the infarct lesions from unwanted non-infarct tissues. Second, overlapped patches strategy is proposed to reduce the workload of the deep-learning-based segmentation task. Finally, a three-dimensional U-Net model is developed to perform patch-wise segmentation of infarct lesions. A total of 239 brain scans from a public dataset is utilized to develop and evaluate the proposed method. Empirical results reveal that the proposed automated segmentation can provide promising performances with an average dice similarity coefficient (DSC) of 0.6684, intersection over union (IoU) of 0.5022, and average symmetric surface distance (ASSD) of 0.3932, respectively.

scholarly journals 3D-Volume Rendering of the Pelvis with Emphasis on Paraurethral Structures Based on MRI Scans and Comparisons between 3D Slicer and OsiriX®

2021 ◽  
Vol 45 (3) ◽  
Author(s):  
C. M. Durnea ◽  
S. Siddiqi ◽  
D. Nazarian ◽  
G. Munneke ◽  
P. M. Sedgwick ◽  
...  
Keyword(s):  
Image Processing ◽  
Secondary Analysis ◽  
Three Dimensional ◽  
3D Models ◽  
Clinical Role ◽  
Cross Sectional ◽  
3D Slicer ◽  
Mri Scans ◽  
3D Volume ◽  
Good Agreement

AbstractThe feasibility of rendering three dimensional (3D) pelvic models of vaginal, urethral and paraurethral lesions from 2D MRI has been demonstrated previously. To quantitatively compare 3D models using two different image processing applications: 3D Slicer and OsiriX. Secondary analysis and processing of five MRI scan based image sets from female patients aged 29–43 years old with vaginal or paraurethral lesions. Cross sectional image sets were used to create 3D models of the pelvic structures with 3D Slicer and OsiriX image processing applications. The linear dimensions of the models created using the two different methods were compared using Bland-Altman plots. The comparisons demonstrated good agreement between measurements from the two applications. The two data sets obtained from different image processing methods demonstrated good agreement. Both 3D Slicer and OsiriX can be used interchangeably and produce almost similar results. The clinical role of this investigation modality remains to be further evaluated.

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