Surface landmark quantification of embryonic mouse craniofacial morphogenesis
© Percival et al.; licensee BioMed Central Ltd. 2014
Received: 13 March 2014
Accepted: 1 July 2014
Published: 24 July 2014
Morphometric quantification of subtle craniofacial variation in studies of experimentally modified embryonic mice has proved valuable in determining the effects of developmental perturbations on craniofacial morphogenesis. The direct comparison of landmark coordinate data from embryos of many different mouse strains and mouse models can advance our understanding of the bases for craniofacial variation. We propose a standard set of craniofacial surface landmarks, for use with embryonic day (E) 10.5-12.5 mice, to serve as the foundation for this type of data compilation and analysis. We quantify the intra- and inter-observer landmark placement variation associated with each landmark and determine how the results of a simple ontogenetic analysis might be influenced by selection of landmark set.
Intraobserver landmark placement error for experienced landmarkers generally remains below 0.1 mm, with some landmarks exhibiting higher values at E11.5 and E12.5. Interobserver error tends to increase with embryonic age and those landmarks defined on wide inflections of curves or facial processes exhibit the highest error. Landmarks with highest intra- or inter-observer are identified and we determine that their removal from the dataset does not significantly change the vectors of craniofacial shape change associated with an ontogenetic regression.
Our quantification of landmark placement error demonstrates that it is preferable for a single observer to identify all landmark coordinates within a single study and that significant training and experience are necessary before a landmarker can produce data for use in larger meta-analyses. However, we are confident that this standard landmark set, once landmarks with higher error are removed, can serve as a foundation for a comparative dataset of facial morphogenesis across various mouse populations to help identify the developmental bases for phenotypic variation in the craniofacial complex.
KeywordsMorphometrics Landmark error Facial prominences Craniofacial morphogenesis Mouse embryo 3D imaging Micro-CT
Morphometric quantification of variation in complex phenotypes is increasingly important to developmental studies of morphogenesis [1–3]. Integrating morphometric methods into studies of experimentally modified embryonic development has proved valuable in determining the simultaneous effects of a given perturbation on morphogenesis across the developing head (eg. [4–9]). Similarly, these methods allow quantification of subtle changes in phenotype that is necessary when examining the simultaneous effects of multiple factors on development of a given trait, as is increasingly common in systems-biology informed approaches .
Landmark based morphometric methods have commonly been used to quantify the size and shape of individual craniofacial bones, a skeletal region, or the whole skull (eg. [6, 10–15]). While skeletal landmarks have been used to quantify craniofacial morphogenesis during the late embryonic period, there is also a need to quantify the effects of epithelial-mesenchymal interactions that control initial growth and fusion of facial prominences before ossification begins and which have a significant influence on subsequent craniofacial morphology [16–19]. Given a lack of skeletal features and difficulties distinguishing soft tissue layers using computed tomography and other 3D imaging modalities during the earliest period of facial morphogenesis, the external ectodermal surface of the embryo provides the best features upon which to place landmarks for the measurement of craniofacial form .
Head surface landmarks based on either 2D photographs or 3D surfaces have previously served as a basis for quantifying the effect of developmental perturbations in embryonic chicks [7, 20–22] and mice [5, 6, 23–25]. With increasing demand for quantification of craniofacial morphogenesis during the earlier embryonic period , the direct comparison of morphometric data between studies of different species, mouse strains, disease models, and ages becomes an enticing possibility. Just as large collections of publically-available and well-annotated genomic data facilitate new directions in hypothesis-driven research, a phenomic collection of directly comparable morphometric data has the potential to advance our understanding of the bases for typical and dysmorphic craniofacial variation [26, 27].
Biological definitions of all landmarks and landmark subset categories
Abbreviated biological definition
The dorsal midline point between the growing forebrain and midbrain lobes.
The dorso-rostral midline extent of the growing forebrain.
The midline dorsal most extent of the face.
Midline most rostral extent of the medial nasal processes.
The ventral midline point on the primary palate, in the region that develops into the vermillion of the lip.
The border between the medial nasal process and the forebrain, in line with the center of the body of the medial nasal process.
Most dorsal extent of the rostral portion of the lateral nasal process, marking the original rostrolateral intersection of the lateral nasal process and the forbrain.
The dorso-caudal most point of the lateral nasal process.
The caudal most point of the intersection between the lateral nasal process and the maxillary process, representing the caudal end of the future nasolacrimal duct.
The caudo lateral projection of the dorsal edge of the maxillary process.
Point at the nasal aperture representing the intersection of the lateral nasal process and the maxillary process.
The most rostro-ventral intersection between the medial nasal process and the maxillary process. Between E10.5 and E11.5, it shows the growth of the medial nasal process as a contributor to the labial margin.
The rostro-caudal most extension of the lateral nasal prominence, illustrating the rostral growth of the lateral nasal process between E10.5 and E12.5.
Point representing the middle of the medial side of the nasal aperture as a lateral extent of the medial nasal process.
The dorsal most point of the nasal aperture representing the rostro-dorsal extreme of the border between the medial and lateral nasal processes.
The corner of the developing mouth, found at the most caudo-lateral point on the rostral border of the maxillary and mandibular processes.
The lateral extent of the center of the maxillary process as it exists in E10.5 and E11.5.
The intersection of the buldge of the trigeminal ganglion and the pontine flexure of the developing brain.
The medial, rostral, dorsal corner of the developing mandibular process.
The ventral caudal most point on the bulge of the growing forebrain, as noted from the lateral perspective.
The most caudal midline point on back of the head, just ventral to the midbrain.
Landmark homology is widely recognized as a critical feature of sparse landmark based morphometrics, although the definition of homology may shift depending on research question and sample [29, 30]. Previous landmark based studies of mouse embryos between E10.5 and E12.5 are typically related to questions of growth and development of facial prominences and the structures derived from them [5, 6, 23–25]. Therefore, our landmark set, influenced greatly by this previous work, is composed of points at the borders between or at the extreme edges of prominences and/or other craniofacial features. Realizing that the specific cells found at the edges of a facial prominence may shift as it grows outward (discussed in ), we define homology based on the extent of the cellular populations whose proliferation and differentiation serve to modify the form of a given prominence and its derivative craniofacial features.
For example, point 9/26 is placed in a position that is near the ventral/rostral corner of the eye of E10.5 specimens (Figure 1). Based on this geometric relationship with the eye, this landmark might also be placed at the corner of the eye on E12.5 specimens. However, because our main questions are about the growth and relationship between the facial prominences, it is more important that landmark 9/26 continue to represent the caudal end of the border between the lateral nasal and maxillary processes at the developing lacrimal duct. It has been shown that the valley between the second and third whisker rows, counting from the dorsal aspect of the nose, represents the border between tissues derived from these cell populations [31, 32]. Therefore, the E12.5 version of this point was defined at the posterior extreme of this valley between the whisker rows, found halfway up the anterior border of the eye (Figure 1). Similarly, we chose age specific locations for each landmark, as defined within the practical definitions, to represent homologous biological features, as defined within the biological definitions.
Overall, the median and variance of interobserver error is lower for E10.5 and E11.5 data than for E12.5 data. Landmarks that were identified as having relatively high intraobserver error across ages, including 2, 13/30, 17/34, 18/35, 21/38 are among the landmarks with higher mean interobserver error at E10.5 and E11.5. However, the landmark that displays the most interobserver error at E10.5 and E11.5 is 7/24, which showed relatively low intraobserver error. At E12.5, landmark 17/34, 18/35 and 21/38 display he highest median interobserver error, although 18/35 seems to be much more problematic on the right side than the left.
Results of two-way ANOVA for association between relevant factors and landmark coordinate variation
Intra- and inter-observer error
Bookstein  defined a commonly used landmark classification system based on the features used to determine landmark location. Type 1 landmarks are defined as the location of a discrete anatomical structure, independent of other anatomical features. Several of the landmarks in our set (Figure 2) are Type 1, including 8/25 that is found at the intersection of the eye, forebrain, and lateral nasal prominence. Type 2 landmarks are extreme points along curves or grooves and represent the majority of landmarks defined on the surfaces of embryos for this and previously defined sets (eg. [6, 25]). Type 3 landmarks, those defined with respect to relatively distant anatomical structures, do not necessarily share biological meaning and homology across specimens. They are considered mathematically deficient, because their locations are partially dependent on the locations of other anatomical structures [28, 33]. However, because Type 1 and Type 2 landmarks cannot comprehensively represent the shape of the early facial prominences , we defined a few landmarks on the extreme of craniofacial bulges in order to improve our coverage of the anatomical features of interest. Because the face develops quickly between E10.5 and E12.5 (Figure 1), biologically homologous landmarks may switch between landmark types across this period of development. For example, landmark 17/34 is the extreme lateral edge of the maxillary prominence at E10.5 and E11.5 (type 3), but is defined based on location between whisker rows at E12.5 (type 2). Even if a landmark does not change type, the error associated with its identification may change across this developmental period.
Our landmark set was compiled with the goals of 1) creating an explicit homologous association between each landmark and a biological feature across E10.5-E12.5 and 2) serving as the basis for ontogenetic analyses that include datasets produced by multiple observers. Therefore, we have attempted to choose landmarks that represent relevant biological features well and which can be repeatably placed between trials and by multiple observers. However, we acknowledge that a given landmark may not necessarily be more biologically relevant or repeatable than other nearby locations, particularly if the landmark is defined along a curve or curved surface (i.e. type 2 and 3 landmarks). We have endeavored to transparently report our biological interpretations of landmarks and the repeatability of landmark placement in order to allow other researchers to judge the usefulness of this landmark set for their own studies.
None of the landmarks identified as having high intra- or inter-observer error in this study are Type 1 landmarks. Instead, they tend to be Type 2 landmarks along curves with wide inflection (eg 2, 7/24, 18/35) or Type 3 landmarks on the extreme extents of bulges (eg. 17/34). After reviewing the landmarks identified as having high error (the subset of trouble landmarks) we are confident that we can clarify the definitions of 10/27 and 13/30 in order to reduce landmark placement error, based on noted systematic differences in placement between landmarkers. However, we suggest that 2, 7/24, 17/34, 18/35, and 21/38 be removed from our standardized landmark set for E10.5-E12.5 mice. This does not mean that these landmarks are necessarily inappropriate for a specific embryonic age or as an additional landmark for studies that include only one observer. For instance, landmark 7/24 displays high interobserver error and relatively low intraobserver error for the experienced observers, suggesting that observers developed their own stable (although different) interpretations of the landmark. Similarly, the median intraobserver error across the three experienced landmarkers increases for landmark 21/38 from E10.5 to E12.5 as the forebrain expands, suggesting that the landmark may be appropriate for use at E10.5 but not at E12.5.
After removing trouble landmarks from our landmark set, and assuming minimal modification of craniofacial shape during preparation and imaging of specimens , median intraobserver error of our experienced landmarkers is below 0.1 mm. In the case of E10.5 specimens, it tends to be below 0.05 mm. Therefore, the application of this landmark set by an experienced landmarker should allow the capture of differences in facial shape between groups of specimens that are significantly larger than 0.1 mm. For comparative purposes, the width of the ridge lateral to the nasal aperture is 0.13 mm at E10.5, while the width of the nasal aperture measured from the rostro-ventral extent of the lateral and medial ridges is 0.14 mm at E12.5. The significantly higher intraobserver error noted for the first time landmarker highlights the need for landmark training and experience in order to reduce error to acceptable levels.
One of the major reasons to design this standard set of landmarks was to allow landmarks taken by multiple observers to be combined in comparative analyses. Unfortunately, the interobserver error noted for many landmarks indicates significant differences in the interpretation of landmark definitions even though we provided precise biological and practical landmark definitions, examples of landmarks identified on a 3D craniofacial surface for each age, illustrations of standard head orientation, and face to face discussion. Measures of interobserver error can illustrate the need for further clarification of certain landmark definitions or the removal of a landmark from analysis entirely. Alternatively, assuming that there is high interobserver and low intraobserver error, it may be possible to remove typical differences in interobserver landmark placement via regression of landmark coordinate values on observer identity. While completely removing interobserver landmark error may not be possible, comparative error studies like this are highly recommended in order to identify and address problematic landmarks as a way to reduce the level of landmark placement error included within subsequent analyses.
The variation in landmark placement, measured as the distance between an observer’s landmark coordinates and mean landmark coordinates, is strongly associated with the factors of landmark and observer identity at E10.5, E11.5, and E12.5, according to our two-way ANOVA analysis. Specimen identity is associated with landmark variation at E10.5 and E11.5, although with reduced significance at E11.5 (Table 2). The significant effect of observer identity on landmark coordinate variation indicates that significant differences in landmark placement exist between observers for at least some of the landmarks. The significant effect of landmark identity suggests that this interobserver variation in landmark placement is higher for some landmarks than others. Although significant at all three embryonic days, the sum of squares values for both observer and landmark increase from E10.5 through E12.5, which matches the observation that mean inter- and intra-observer error values tend to increase from E10.5 to E12.5 (Figures 3 and 4). The significant effect of specimen identity in the earlier ages does not suggest that interobserver error is higher for younger specimens. It merely suggests that the level of interobserver error varies between specimens at the younger ages. This difference in landmark placement error may be associated with larger relative differences in morphology between specimens at slightly different stages of development within the younger age categories. It may also be due to relatively more significant fixation based changes in morphology within some younger specimens.
Interpreting ontogenetic analyses
Another major reason to define this set of landmarks was as a basis for ontogenetic analyses of craniofacial shape in mice between E10.5 and E12.5. Therefore, we carried out a series of linear regressions between size and shape in order to determine how the selection of landmarks might influence the results and interpretation of this type of analysis. Omitting major groups of landmarks from these regressions did not substantially modify the nature of the craniofacial shape change associated with an increase in centroid size between E10.5 and E12.5, suggesting that the specific landmarks selected should not influence interpretation of shape change across this ontogenetic period.
However, removing the non-facial or trouble landmarks from the dataset reduced the linearity between landmark coordinate regression coefficients and centroid size, as well as the total landmark coordinate variation explained by the regression on centroid size. In our regressions, centroid size is a proxy for developmental age. Between E10.5 and E12.5, the growth of the facial prominences outward is not as pronounced as the growth and definition of the various regions of the brain  (Figure 1). The lower explanatory power of the regression when non-facial landmarks were removed suggests that including these landmarks improves the usefulness of centroid size as a proxy for developmental age, because it is linked to the overall change in craniofacial size over this developmental period. The intermediate reduction in explanatory power for the regression when the trouble landmarks were removed is likely based on the fact that a high proportion of the trouble landmarks are non-facial landmarks.
We recommend that landmarks across the head be included in ontogenetic analyses in order to better estimate centroid size as a measure of developmental age, but also to provide a broader anatomical context within which to interpret morphological changes of the face or another specific region of interest. If possible, using a measure of developmental age that is independent of the landmarks under analysis, such as tail somite number, may be preferable .
Great progress has been made in the automation of craniofacial surface quantification and comparison ([35–41]), which might make issues of intra- and inter-observer landmark placement error irrelevant. However, despite significant effort, an adequate automatic method has not yet been developed that allows for the quantification of subtle craniofacial variation in young embryos. This is partially due to difficulty in producing standardized and complete ectodermal surfaces from μCT images, as well as the fact that craniofacial features change very quickly during embryonic development to the point where a great deal of variation exists within a sample of specimens from a single embryonic day. The human eye remains, unfortunately, superior to computational methods in locating homologous features on incomplete surfaces and across gradations of developmental age. The authors are involved in work to automate embryonic landmark placement, but must continue to rely on manual placement of landmark sets like this for the time being.
Standardization of landmarking protocols is a necessary first step, but not sufficient for phenotypic data to become phenomic data. It must also be shown that the landmark coordinates identified using the standard protocol are sufficiently comparable between landmark trials and between observers. We developed and tested a set of ectodermal surface landmarks for the measurement of craniofacial morphology of mice between E10.5, E11.5, and E12.5. Our package of landmark definitions, illustrations, and examples were developed in an effort to reduce variation in placement for all landmarks in our set. Measurements of intra- and inter-observer error for four observers reinforce the idea that landmark coordinates identified from one landmarker will have less variability than landmarks taken by multiple observers. Intraobserver error comparisons also highlight the need for landmarkers to be provided significant training and supervision before the incorporation of their landmark sets into larger meta-analyses including multiple observers. However, we are confident that this standard landmark set, once landmarks with higher error are removed, can serve as a basis for the comparison of landmarks individually collected by experienced landmarkers for different mouse strains and disease models. Finally, our results suggest that the nature of craniofacial shape changes identified with simple ontogenetic analyses are robust to the particular choice of landmarks that are included in those analyses. By using these landmarks within a variety of future studies, perhaps as part of larger study or age specific landmark sets, we plan to build a dataset for the comparison of facial morphogenesis across many mouse populations in order to help identify the developmental bases for phenotypic variation in the craniofacial complex.
Landmark definitions and data collection
This study was performed using a sample of 10 E10.5, 9 E11.5, and 10 E12.5 CT images heads from mice of various backgrounds that were collected for other studies. None of these mice display gross dysmorphology during the early embryonic period. Care and use of mice for this study were in compliance with relevant animal welfare guidelines approved by the University of Colorado - Denver and the University of Calgary. Fixation in 4%PFA/5% Gluteraldehyde was carried out according to protocols designed to minimize the level of desiccation and craniofacial shape change in these embryonic specimens . All μCT images chosen for this study were produced with a Scanco μ35 at the University of Calgary with 45 kV/177uA for images of 0.007 mm (E10.5 and E11.5) or 0.012 mm (E12.5) voxel size.
All landmarks in our landmark set (Table 1; Figure 2) were given a biological definition representing a biological interpretation of that landmark across all three ages of interest. A practical landmark was defined for each landmark at each age in order to guide the placement of the landmark so that its location at each age would match the biological definition. Because some of these landmarks are defined as the extremes of curved surfaces, the practical definitions may include instruction on the orientation of the surface image that a landmark should be taken from. 2D lateral images of an embryonic head from each age were produced to define a standard orientation for landmarking. Terms of anatomical direction used within the definitions are in reference to a mouse head in standard adult position and may not match the directions as defined by the embryonic body. Full landmark definitions and orientation images are available in Additional files 1, 2, 3, 4 and 5. Last, each landmark was placed on the 3D surface of a reference specimen of each embryonic age as an example to be referenced during the process of data collection. Because of the relatively large file sizes involved, these surface files and associated landmark coordinates are available upon request to the authors.
After a brief orientation and access to all landmark reference materials, four observers completed two landmark trials within MeshLab  on minimum-threshold based ectodermal surfaces produced from μCT images of each specimen. Trials 1 and 2 were completed at least one week apart in order to reduce the influence of memory on landmark placement during the second landmarking trial. The first two observers (1,2), who had experience collecting landmarks from CT images of mice, collaborated to develop the landmark set definitions, the third (3) was also an experienced mouse landmarker, and the fourth (4) was a first time landmarker (numbers as defined in Figure 3.
Landmark error analysis
Intraobserver landmark placement error was calculated for each landmarker (1-4) as Euclidian distances (mm) between the location of a landmark taken during landmark trials 1 and 2. Boxplots were used to visualize the median and variation of intralandmark error for each landmarker (Figure 3). After determining that the left and right versions of bilateral landmarks show similar levels of intraobserver error, we decide to combine these values for both sides when calculating intraobserver error for the bilateral landmarks.
Inter-observer landmark placement error was first calculated as the centroid size of the mean landmark coordinates defined by each observer for each landmark (mean of trials 1 and 2). Because of the high intraobserver error noted for the less experienced observer, our interobserver error and all further analyses focus on the data from the three more experienced observers.
The mean landmark coordinates for a given specimen were calculated as the average of the mean landmark coordinates calculated from the two trials of each observer. Variation in landmark coordinates were calculated as the Euclidian distance between the coordinates collected by a given observer on a given specimen and the mean coordinates for that specimen. A two-factor analysis of variance (ANOVA) was completed for each embryonic age to test whether specimen, landmark, or observer identity are significantly associated with this variation in landmark coordinates.
Regressions of procrustes coordinates against centroid size, a better proxy for developmental age than embryonic day, were performed in MorphoJ  to determine the strength and nature of ontogenetic change in craniofacial shape from E10.5 to E12.5. This regression was performed for the whole dataset and a dataset from which trouble landmarks with high intra- or inter-observer error were removed (Table 1; Figure 2). To further investigate how the use of different subsets of landmarks might influence the results of an ontogenetic analysis, regressions of procrustes coordinates against centroid size were also calculated for the dataset after removing nasal, maxillary/mandibular, or non-facial landmarks (Table 1; Figure 2). A summary regression score representing the regression coefficients of each specimen  was plotted against centroid size in order to visualize the strength and linearity of this association between craniofacial shape and centroid size. An estimate of the proportion of total variation for which a regression accounts, an analogue of an R-squared value, serves as an informal measure of the strength of this association.
The vectors of landmark change associated with centroid size provide a summary of the nature of the ontogenetic changes in craniofacial shape between E10.5 and E12.5. These vectors are calculated as regression coefficients of each axis of each landmark added to the mean procrustes coordinate of the landmark along each axis. A figure displaying the relative ontogenetic vectors associated with four of the landmark subsets required the use three landmarks to define parallel axes for procrustes superimposition of each subset as the basis for each regression against centroid size (these three landmarks were not found in the fifth subset of landmarks). The resulting coefficient vectors were plotted relative to the mean shape of the dataset including all landmarks for the purpose of visualization in R .
Availability of supporting data
The full landmark definitions, the original embryo orientation images, and an image illustrating the placement of the landmarks at all three embryonic days are available as Additional files 1, 2, 3, 4 and 5. Because of the size of the 3D surface meshes, these meshes and associated landmark coordinates for reference specimens at E10.5, E11.5, and E12.5 are available upon request to the authors.
Micro computed tomography
Embryonic day (followed by the number of days).
Special thanks to Tatiana Almeida and Francis Smith for their participation as landmarkers in this study. Thanks also to Denise Liberton for discussion about relevant statistical methods and R. We gratefully acknowledge funding from NIH (R01-DE19638, R01-DE021708) and NSERC (Grant #238992-12) for research funding, as well as the CIHR Training Program in Genetics, Child Development and Health and the ACHRI for support to CJP.
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