This research was supported by the Intramural Research Program of the National Institute of Dental and Craniofacial Research (NIDCR) of the National Institutes of Health (NIH), and the Advanced Education in Orthodontics and Dentofacial Orthopedics program of Roseman University College of Dental Medicine.

3D Cephalometric Landmark Annotation Demonstration on Human CBCT Scans

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K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Craniofacial+analysis+may+indicate+co-occurrence+of+skeletal+malocclusions+and+associated+risks+in+development+of+cleft+lip+and+palate.">Craniofacial analysis may indicate co-occurrence of skeletal malocclusions and associated risks in development of cleft lip and palate.</a> Journal of Developmental Biology. 8 (1), 2 (2020).</li><li>Whitman, M. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=TUBB3+Arg262His+causes+a+recognizable+syndrome+including+CFEOM3,+facial+palsy,+joint+contractures,+and+early-onset+peripheral+neuropathy.">TUBB3 Arg262His causes a recognizable syndrome including CFEOM3, facial palsy, joint contractures, and early-onset peripheral neuropathy.</a> Human Genetics. 140 (12), 1709-1731 (2021).</li><li>Kidwai, F. 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The authors declare no conflicts of interest.

Medicine and dentistry have already entered the 3D imaging era. In the disciplines of craniofacial and dental imaging, CBCT scans are increasingly being used, due to the low radiation and decreased cost of the updated systems in comparison to traditional CT machines, easy personnel usage calibration, relatively quick and easy acquisition with minimal patient cooperation, as well as the ability to generate multiple other diagnostic images and analyses from one single scan. Therefore, it is essential for clinicians and researchers to know how to read, diagnose, and analyze these 3D images, as well as learn how to study craniofacial growth and development in 3D.
To assist clinicians and researchers in this field, we present a step-by-step protocol and video demonstration for the conduction of 3D cephalometric analysis with the use of human CBCT scans. These landmarks have been previously defined and validated in a previous publication, where their accuracy and repeatability were confirmed4. The detailed refinement instructions for each landmark also assist users in the correct annotation of each landmark. The landmark annotation process is further simplified with the use of preset views of the scan that correspond to the area that each landmark should be positioned. This function saves significant time and effort for the user. Nevertheless, there is a learning curve involved, and practice is required by users to achieve accurate landmark annotation.
The validated 3D landmark configuration used in this protocol provides sufficient coverage of the skeletal tissue of the face, maxilla, mandible, and cranial base. In this way, the true morphology of the craniofacial structures is more accurately represented for evaluation of the dimensions, configuration, and orientation of the craniofacial complex and its component structures. Soft tissue landmarks are not included in this protocol, but users can add landmarks of choice to the provided configuration, as described in the protocol. In addition, for practical reasons, this protocol could not include specific instructions for other 3D analysis software, but can be adapted accordingly by each user.
Apart from the diagnostic value of the generated standard cephalometric measurements, mainly for clinicians, the freedom offered with the use of this analysis to compute angles and linear distances between any 3D landmarks will allow the establishment of new cephalometric analyses that will provide more detailed and complete assessments. Nevertheless, our future direction includes establishing new respective normative values, in the same way that 2D normative values were created in the past.
Moreover, the applications of landmarked based GMA in the craniofacial clinical and research field are developing at a fast pace. Researchers in evolutionary and developmental biology and anthropology for have been using this analysis for more than a decade, but new clinical applications have also been recently presented in the fields of orthodontics, dentofacial orthopedics, and craniofacial surgery. GMA can be also used as part of a quantitative phenotyping in the case of congenital diseases with craniofacial manifestations, as well as for the detection of subtle morphological differences attributed to gene mutations13,14,15,16. In addition, the integration of different quantitative approaches by linking morphometric data with functional analysis as well as genetic data can provide new knowledge regarding craniofacial development in healthy, as well as disease, groups.
Because of recent advances in computation and visualization, the conduction of this type of analysis is now feasible on personal computers, with several software packages already available, including Checkpoint, Geomorph (a package of R statistical software), Amira-Avizo, and SlicerMorph. These programs can assist researchers in the medical fields that may be unfamiliar with multivariate statistical analyses to conduct GMA with the availability of built-in automated functions.

Cephalometric analysis, which examines the dental and skeletal relationships of the human skull, is the clinical application of cephalometry. In addition to anthropologists, developmental biologists, forensic experts, and craniofacial researchers who study human evolution and craniofacial development, it is utilized by oral health professionals, including dentists, orthodontists, and oral and maxillofacial surgeons, as a treatment planning tool. The earliest institutions that used cephalometric analysis in orthodontics were Hofrath in Germany and Broadbent in the USA in 19311,2,3. The primary objective of the analysis was to provide a theoretical and practical resource to evaluate the craniofacial proportions of an individual and to define the anatomical source of malocclusion1. This allowed for the growth pattern of the maxilla and mandible to be tracked, their relational positions in space to be monitored, and changes in soft tissue and teeth displacement to be observed. As a result, changes brought about by orthodontic treatment could be monitored, and skeletal and dental relationships could be characterized for a diagnosis to be made for treatment planning. Evaluation of the dentofacial complex was done by comparing a patient&#39;s cephalometric tracing with reference values that were representative of a normal population of similar age, race, and ethnicity1.
The traditional method of analysis consisted of a two-dimensional (2D) depiction of three-dimensional (3D) structures4,5. A major setback of this technique is the distortion and magnification of anatomical structures via conventional x-ray imaging on plain film or digital formats, which can lead to inaccurate cephalometric tracings and interpretations6,7. The initial introduction of 3D imaging in the form of axial computed tomography (CT) and spiral CT did not include dental or non-medical applications due to high cost and high radiation doses. However, the emergence of cone beam computed tomography (CBCT) scans mitigated these concerns, as expenses and radiation doses were significantly lower than CT1. The shift in this imaging narrative galvanized the widespread use of CBCT in orthodontics for improvement in diagnosis and treatment planning. The main advantage of 3D imaging over the conventional 2D image technique is that 3D allows the examiner to view anatomical structures without superimpositions and spatial distortions (i.e., head position of the individual). Therefore, a much more accurate positioning of the anatomical landmarks used for the conduction of cephalometric analysis is possible, especially in cases of facial asymmetry. Moreover, a much larger anatomical area can be analyzed.
One of the most recent advances in the field of cephalometry is the implementation of deep learning (DL) for automated landmark detection8,9,10,11. Although the results of these studies are promising, the levels of accuracy in the placement of the landmarks are not yet satisfactory. Moreover, most of these studies use relatively small landmark sets that are derived from previous 2D cephalometric analyses, providing insufficient coverage of the cranial base, which is an important structure for the study of craniofacial growth and development. This demonstration video showcases in detail a methodology for the conduction of manual, high-accuracy 3D cephalometric analysis with the use of a validated set of 3D skeletal tissue landmarks covering the areas of the face, cranial base, mandible, and teeth for use in clinical and research studies involving CBCT imaging4. An example of a completed 3D analysis can be seen in Figure 1.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Invivo6 Dental Software</td>
			<td>Anatomage</td>
			<td>N/A</td>
			<td>3D Imaging Software (including 3D analysis module)</td>
		</tr>
	</tbody>
</table>

three-dimensional cephalometric landmark annotation demonstration on human cone beam computed tomography scans

Craniofacial cephalometric analysis is a diagnostic tool used for the assessment of the relationship of various bones and soft tissues in the head and face. Cephalometric analysis has been traditionally conducted with the use of 2D radiographs and landmark sets and restricted to size, linear and angular measurements, and 2D relationships. The increasing use of 3D cone beam computed tomography (CBCT) scans in the dental field dictates the need for the evolution to 3D cephalometric analysis, which incorporates shape and a more realistic analysis of longitudinal development in all three planes. This study is a demonstration of 3D cephalometric analysis with the use of a validated set of skeletal tissue landmarks on human CBCT scans. Detailed instructions for the annotation of each landmark on a 3D volume are provided as part of a step-by-step protocol. The generated measurements and 3D coordinates of the landmarks can be exported and used both for clinical and research purposes. The introduction of 3D cephalometric analysis in basic and clinical craniofacial studies will lead to future advancements in the field of craniofacial growth and development.

Author Spotlight: Three-Dimensional Cephalometric Landmark Annotation Demonstration on Human Cone Beam Computed Tomography Scans  

Three-Dimensional Cephalometric Landmark Annotation Demonstration on Human Cone Beam Computed Tomography Scans

The aim of this project is to provide a detailed methodology for the conduction of 3D cephalometric analysis with the use of a validated set of 3D skeletal landmarks. These landmarks cover the areas of the cranial base, face maxilla and mandible, and can be used in clinical as well as research studies. There is a learning curve for those who annotate the landmarks for the first time on the 3D volume, and a lot of practice is strongly recommended to acquire more experience and consistency before applying these landmarks on clinical and research studies.The 3D cephalometric analysis offers more accurate measures in comparison to 2D cephalometric analysis. Because of the distortion and magnification of the anatomical structures in conventional x-ray films and 2D digital formats, 2D cephalometric analysis can lead to in accurate tracings and interpretations. Moreover, the coordinates of the 3D landmarks can be exported and used for the conduction of geometric-morphometric analysis to study shape.The use of the 3D landmark data analysis can be part of an in-depth quantitative phenotypic approach in the case of craniofacial deformities. In addition, the integration of morphometric analysis with functional analysis and genetic information will provide new knowledge in the case of craniofacial development in healthy as well as disease cohorts.

The annotation of a validated 3D landmark configuration is described in detail with the use of a step-by-step protocol and video demonstration. Specific instructions are provided for the annotation of each landmark on the 3D volume, as well as the refinement of their initial positions with the help of the 2D section views that correspond to each plane of space. By following the detailed methodology provided in the protocol in combination with the video instructions, the user can learn how to conduct cephalometric analysis with the use of human CBCT scans.
Figure 1 represents frontal and three-quarter views of a full head CBCT scan of a human skull with the annotated 3D landmarks included in the current configuration. All the described landmarks are Type 1 and Type 2. Type 1 landmarks represent clearly recognizable points usually observed at the intersection of distinct anatomical structures. Type 2 landmarks represent points of maximal curvature on the contour of recognizable anatomical structures12. No Type 3 or semi-landmarks were included in this analysis.
After the completion of the annotation of the landmarks, there are two types of data that can be exported and further analyzed by the user: cephalometric measurement and 3D coordinate values. The values of key cephalometric measurements required for the diagnosis and assessment of dentoskeletal malocclusion are provided. These measurements provide a detailed assessment of the skeletal and dental relationships in all three planes of space: sagittal, vertical, and transverse. The 3D coordinate values (x, y, z) of each landmark can be exported and used for the calculation of angles and linear distances. The values of the same coordinates can be used for the conduction of multivariate geometric morphometric analysis (GMA). GMA is a method for studying shape that can capture morphologically different shape variables utilizing Cartesian landmark and/or semi-landmark coordinates. Several statistical techniques can be used to examine shape, without taking into account the size, location, or orientation of the examined structures. Geometric morphometrics is currently the most established body of morphometric theory for handling landmark-based data.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/65224/65224fig01.jpg" /> 
Figure 1: Frontal and three-quarter views of a full head CBCT scan of a human skull with the annotated 3D landmarks included in the current configuration. <a href="https://www.jove.com/files/ftp_upload/65224/65224fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Supplementary File 1: Configuration file including the landmarks used in this protocolwhich can be directly uploaded to the software for analysis. <a href="https://www.jove.com/files/ftp_upload/65224/AnalysisCFGUser.zip" target="_blank">Please click here to download this File.</a>

Watch this Scientific Journal Video about Three-Dimensional Cephalometric Landmark Annotation Demonstration on Human Cone Beam Computed Tomography Scans at JoVE.com

Presented here is a detailed protocol for the conduction of three-dimensional cephalometric analysis with the use of human cone beam computed tomography scans.

Craniofacial cephalometric analysis is a diagnostic tool used for the assessment of the relationship of various bones and soft tissues in the head and ...

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Uploading the CBCT Scan, System Set-Up, and Annotation of 3D Anatomical Landmarks

To begin, open the software invivo six, and click on browse file from this device. Select the scan to be analyzed and click open. Go to the 3D analysis module and click on the save information floppy disk icon.Then select load a configuration and browse for the configuration file. Click on the reorientation icon. In the window that opens, select the by picking landmarks option.This allows the user to orientate all the scans, in the same way. For this protocol nasion is selected as the origin landmark. Then three point definition with landmarks, right orbitally right porion left, porion, and define anterior, posterior axis, midsagittal plane with landmarks, nasion and basion are selected.Adjust the brightness and contrast, to reduce the CBCT scam image noise from the menu on the left side of the screen. Zoom in and out by holding down the control key and left clicking simultaneously and sliding across the screen. Move the image in a bodily manner by holding down the shift key and left clicking simultaneously and sliding across the screen.Enable clipping from the settings menu to create sectional views in all planes of space. To add new landmarks in the settings menu, click on landmarks, to reveal a list of available landmark options and then select the landmark of choice. To set a default view for landmarks, select tracing task.Click on edit, choose landmark. Set the view as desired, and click on use current view settings. Repeat these steps to change the default view for any additional landmark.To annotate 3D anatomical landmarks, select create tracing from the top of the menu, and click start. Start annotating the 3D landmarks by left clicking directly on the 3D volume at the location where the landmark should be placed, based on its definition. Adjust the location of the landmark using the section views on the right of the screen.In case they cannot be seen from the layout selection menu, select slice locator. To confirm the placement of a landmark, click stop and select the desired view to visualize the landmark. Then proceed to place the remaining landmarks.To change the position of the landmark using the 3D volume, stop the analysis by clicking on stop at the bottom of the tracing tasks menu. Click on the landmark point to be moved, and drag it to the new desired position. Re-annotate a landmark by double clicking on the ticked square next to the landmark and then answering yes to the follow-up question.

Definition and Specific Annotation Instructions for the 3D Cephalometric Landmarks

Start with the annotation of the preselected origin landmarks. The midpoint on the anterior border of the anterior curvature of the foramen magnum is called basion. To annotate basion for the axial section, locate the deepest end of the curvature of the section of the foramen magnum.For the sagittal section, look for the most posterior point of the midsection of the foramen magnum. For the coronal section, look for the inferior midpoint of the curvature of the foramen magnum. The most superior, posterior and external point located at the upper margin of each ear canal is called porion.To annotate porion for the axial section, look for the edge of the margin of the external auditory meatus. For the sagittal section, look for the point of intersection of the eustachian tube with the bony canal. For the coronal section, look for the midpoint on the inferior border of the superior curvature.The vertical line through the point roughly bisects the ear canal. The landmark nasion is located at the intersection of the suture between the frontal bone and the nasal bones. For the axial section, look for the midpoint at the height of curvature of the suture.For the sagittal section, look for the anterior point of the suture where the frontal and nasal bones meet. For the coronal section, look for the center of the frontal nasal suture. The vertical line through it roughly bisects the nose.Orbitale is the most an inferior point on the inferior orbital rim. To annotate this, set the frontal view or bony window as default and clip axially from inferior to superior until the curvature of the lower margin of the orbit is reached to locate the inferior most point of the lower curvature of the orbit. Use 2D views to confirm that the landmark is on the bone.Adjust the sagittal and coronal sections to reflect the anterior positioning of orbitale. Ensure that the landmark is anterior in position just to the point where the orbital rim starts to curve out. The most superior and anterior point of the superior orbital rim is called supraorbitale.To annotate it, set the frontal view as default in the 3D volume, and gradually clip axially from superior to inferior until the curvature of the upper margin of the orbit is reached to locate the most superior point of the upper border of the orbit. Adjust the sagittal and coronal sections to reflect the anterior positioning of the landmark. Ensure that the landmark is anterior in position just to the point where the orbital room starts to curve out.For the sella midpoint, look for the center of the sella turcica or hypophyseal fossa, which is a saddle shaped depression in the body of the sphenoid bone where the pituitary gland or hypothesis is positioned. Adjust the landmark to the center of the sella turcica in all planes. For the sagittal section, place the landmark in the center of the sella turcica.For the axial and coronal sections, adjust the views accordingly. Next, trace the right mandibular profile with a series of points. Then do the same for the left mandibular profile.After tracing the mandibular profile, the landmarks, condilion, gonion, and antigonion are annotated automatically. Identify the condilion as the most posterior and superior point on the condyle and the gonion as the most outward point on the angle formed by the junction of the ramus and the body of the mandible. Then identify the antigonion as the highest point of the concavity of the lower border of the ramus where it joins the body of the mandible.The frontal and three-quarter views of a full head CBCT scan of a human skull with all the annotated three D landmarks included in the current configuration are presented in this figure.

2.5K Views.  National Institute of Dental and Craniofacial Research.  Presented here is a detailed protocol for the conduction of three-dimensional cephalometric analysis with the use of human cone beam computed tomography scans.

3D Cephalometric Landmark Annotation Demonstration on Human CBCT Scans

Summary