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Landmark precision and reliability and accuracy of linear distances estimated by using 3D computed micro-tomography and the open-source TINA Manual Landmarking Tool software.

Simon MN, Marroig G - Front. Zool. (2015)

Bottom Line: Landmark precision and linear distances calculated from 3D images were compared to the same landmarks and distances obtained with a 3D digitizer in the same skulls.We also compared landmarks and linear distances in 3D images of the same individuals scanned with distinct filters, since we detected variation in bone thickness or density among the individuals used.Scanning with distinct filters does not introduce a high level of error and is recommended when individuals differ in bone density.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, 05508-090 São Paulo-SP, Brazil.

ABSTRACT

Introduction: The wider availability of non-destructive and high-resolution methods, such as micro-computed tomography (micro-CT), has prompted its use in anatomical and morphometric studies. Yet, because of the actual scanning procedure and the processing of CT data by software that renders 3D surfaces or volumes, systematic errors might be introduced in placing landmarks as well as in estimating linear distances. Here we assess landmark precision and measurement reliability and accuracy of using micro-CT images of toad skulls and the TINA Manual Landmarking Tool software to place 20 landmarks and extract 24 linear distances. Landmark precision and linear distances calculated from 3D images were compared to the same landmarks and distances obtained with a 3D digitizer in the same skulls. We also compared landmarks and linear distances in 3D images of the same individuals scanned with distinct filters, since we detected variation in bone thickness or density among the individuals used.

Results: We show that landmark precision is higher for micro-CT than for the 3D digitizer. Distance reliability was very high within-methods, but decreased in 20 % when 3D digitizer and micro-CT data were joined together. Still, we did not find any systematic bias in estimating linear distances with the micro-CT data and the between-methods errors were similar for all distances (around 0.25 mm). Absolute errors correspond to about 6.5 % of the distance's means for micro-CT resolutions and 3D digitizer comparisons, and to 3 % for the filter type analysis.

Conclusions: We conclude that using micro-CT data for morphometric analysis results in acceptable landmark precision and similar estimates of most linear distances compared to 3D digitizer, although some distances are more prone to discrepancies between-methods. Yet, caution in relation to the scale of the measurements needs to be taken, since the proportional between-method error is higher for smaller distances. Scanning with distinct filters does not introduce a high level of error and is recommended when individuals differ in bone density.

No MeSH data available.


Related in: MedlinePlus

Landmarks and linear distances used in the toad skulls. Numbered landmarks in both sides of the skull are shown as red dots in dorsal (a) and ventral (b) views, and only landmarks of the right side of the skull are shown in the lateral (c) view (descriptions in Table 1). Landmarks were placed in bone sutures or bone processes either with TINA-Landmark software in 3D images or with a 3D digitizer in the real skulls. Linear distances are shown as white lines and represent individual bone dimensions, as shown in Table 2
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Fig2: Landmarks and linear distances used in the toad skulls. Numbered landmarks in both sides of the skull are shown as red dots in dorsal (a) and ventral (b) views, and only landmarks of the right side of the skull are shown in the lateral (c) view (descriptions in Table 1). Landmarks were placed in bone sutures or bone processes either with TINA-Landmark software in 3D images or with a 3D digitizer in the real skulls. Linear distances are shown as white lines and represent individual bone dimensions, as shown in Table 2

Mentions: Although there is no specific theory relating the potential effects on landmarks and on distances when using distinct resolutions, filters and reconstruction algorithms, some expectations based on landmark position and bone thickness can be made. Some of the landmarks that we selected in the toad skulls (Table 1 and Fig. 2) were more difficult to visualize in the 3D images than in the real skulls because of their position (landmarks 4, 10, 11, 17 and 20) or because they were placed at thinner bones (landmarks 6, 7, 8 and 13). Thus, we expect more variation in the positioning of these landmarks among methods, and as a consequence, less reliability and accuracy of the linear distances extracted from them (Table 2 and Fig. 2). We report that placing landmarks in 3D images obtained by micro-CT scanning is more precise than placing the same landmarks with the 3D digitizer. Yet, average differences in linear distances among methods are acceptable and represent a low error proportion in relation to the distances lengths. Scanning with distinct resolutions and distinct filters do not introduce high errors.Table 1


Landmark precision and reliability and accuracy of linear distances estimated by using 3D computed micro-tomography and the open-source TINA Manual Landmarking Tool software.

Simon MN, Marroig G - Front. Zool. (2015)

Landmarks and linear distances used in the toad skulls. Numbered landmarks in both sides of the skull are shown as red dots in dorsal (a) and ventral (b) views, and only landmarks of the right side of the skull are shown in the lateral (c) view (descriptions in Table 1). Landmarks were placed in bone sutures or bone processes either with TINA-Landmark software in 3D images or with a 3D digitizer in the real skulls. Linear distances are shown as white lines and represent individual bone dimensions, as shown in Table 2
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4481120&req=5

Fig2: Landmarks and linear distances used in the toad skulls. Numbered landmarks in both sides of the skull are shown as red dots in dorsal (a) and ventral (b) views, and only landmarks of the right side of the skull are shown in the lateral (c) view (descriptions in Table 1). Landmarks were placed in bone sutures or bone processes either with TINA-Landmark software in 3D images or with a 3D digitizer in the real skulls. Linear distances are shown as white lines and represent individual bone dimensions, as shown in Table 2
Mentions: Although there is no specific theory relating the potential effects on landmarks and on distances when using distinct resolutions, filters and reconstruction algorithms, some expectations based on landmark position and bone thickness can be made. Some of the landmarks that we selected in the toad skulls (Table 1 and Fig. 2) were more difficult to visualize in the 3D images than in the real skulls because of their position (landmarks 4, 10, 11, 17 and 20) or because they were placed at thinner bones (landmarks 6, 7, 8 and 13). Thus, we expect more variation in the positioning of these landmarks among methods, and as a consequence, less reliability and accuracy of the linear distances extracted from them (Table 2 and Fig. 2). We report that placing landmarks in 3D images obtained by micro-CT scanning is more precise than placing the same landmarks with the 3D digitizer. Yet, average differences in linear distances among methods are acceptable and represent a low error proportion in relation to the distances lengths. Scanning with distinct resolutions and distinct filters do not introduce high errors.Table 1

Bottom Line: Landmark precision and linear distances calculated from 3D images were compared to the same landmarks and distances obtained with a 3D digitizer in the same skulls.We also compared landmarks and linear distances in 3D images of the same individuals scanned with distinct filters, since we detected variation in bone thickness or density among the individuals used.Scanning with distinct filters does not introduce a high level of error and is recommended when individuals differ in bone density.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, 05508-090 São Paulo-SP, Brazil.

ABSTRACT

Introduction: The wider availability of non-destructive and high-resolution methods, such as micro-computed tomography (micro-CT), has prompted its use in anatomical and morphometric studies. Yet, because of the actual scanning procedure and the processing of CT data by software that renders 3D surfaces or volumes, systematic errors might be introduced in placing landmarks as well as in estimating linear distances. Here we assess landmark precision and measurement reliability and accuracy of using micro-CT images of toad skulls and the TINA Manual Landmarking Tool software to place 20 landmarks and extract 24 linear distances. Landmark precision and linear distances calculated from 3D images were compared to the same landmarks and distances obtained with a 3D digitizer in the same skulls. We also compared landmarks and linear distances in 3D images of the same individuals scanned with distinct filters, since we detected variation in bone thickness or density among the individuals used.

Results: We show that landmark precision is higher for micro-CT than for the 3D digitizer. Distance reliability was very high within-methods, but decreased in 20 % when 3D digitizer and micro-CT data were joined together. Still, we did not find any systematic bias in estimating linear distances with the micro-CT data and the between-methods errors were similar for all distances (around 0.25 mm). Absolute errors correspond to about 6.5 % of the distance's means for micro-CT resolutions and 3D digitizer comparisons, and to 3 % for the filter type analysis.

Conclusions: We conclude that using micro-CT data for morphometric analysis results in acceptable landmark precision and similar estimates of most linear distances compared to 3D digitizer, although some distances are more prone to discrepancies between-methods. Yet, caution in relation to the scale of the measurements needs to be taken, since the proportional between-method error is higher for smaller distances. Scanning with distinct filters does not introduce a high level of error and is recommended when individuals differ in bone density.

No MeSH data available.


Related in: MedlinePlus