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.

Monique Nouailhetas Simon,Gabriel Marroig

doi:10.1186/s12983-015-0101-5

Abstract

IntroductionThe 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.ResultsWe 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.ConclusionsWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12983-015-0101-5) contains supplementary material, which is available to authorized users.

Highlights

The wider availability of non-destructive and high-resolution methods, such as micro-computed tomography, has prompted its use in anatomical and morphometric studies
We show that landmark precision is higher for micro-CT than for the 3D digitizer
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, some distances are more prone to discrepancies between-methods

Summary

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. We evaluated the precision of placing the same landmarks in the same individuals of a toad species with two distinct methods: (1) the real skulls and a 3D digitizer to place the landmarks, and (2) 3D images of these skulls, obtained by micro-CT scans at two distinct resolutions, and software to place the landmarks (TINA Manual Landmarking Tool ([7]; hereafter called TINALandmark). TINA-Landmark is recently developed open-source software created to enhance the precision of landmark positioning in 3D images by using volume rendering instead of surface rendering and by showing the cross-section images connected to the 3D volume [7]).We chose to compare the landmarks obtained from the 3D images with the ones obtained by the 3D digitizer because, for the latter, the landmarks are taken in the actual skulls, with no processing of data, not the case for the construction of 3D images. In zoological studies, several authors measure the specimens with 3D digitizers (e.g. [11,12,13,14], just to cite a few), being a widely accepted technique in the morphometry field

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Conclusion