A new method for the model-independent assessment of thickness in three-dimensional images
TL;DR: A general thickness definition for arbitrary structures is proposed allowing us to calculate the mean structure thickness and the thickness distribution of 3‐D objects in a direct way and independently of an assumed structure model.
Abstract: Three-dimensional (3-D) structural parameters derived from lower-dimensional measurements using indirect morphometric methods may be strongly biased if the measured objects deviate from the assumed structure model. With the introduction of 3-D microscopic measuring techniques it is possible to obtain a complete depiction of complex spatial structures. As a consequence, new 3-D methods have recently been developed for the estimation of morphometric parameters such as volume, surface area and connectivity by direct processing of the 3-D images. Structure thickness is an important morphometric parameter which is usually defined for specific structure models only. In this paper we propose a general thickness definition for arbitrary structures allowing us to calculate the mean structure thickness and the thickness distribution of 3-D objects in a direct way and independently of an assumed structure model. Additionally, an efficient implementation for the practical usage of the method is described using distance transformation. The new method is applied to trabecular bone structures measured with a 3-D micro-computed tomography system.
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TL;DR: Standard nomenclature, outlined in this article, should be followed for reporting of results of µCT‐derived bone morphometry and density measurements.
Abstract: Use of high-resolution micro-computed tomography (microCT) imaging to assess trabecular and cortical bone morphology has grown immensely. There are several commercially available microCT systems, each with different approaches to image acquisition, evaluation, and reporting of outcomes. This lack of consistency makes it difficult to interpret reported results and to compare findings across different studies. This article addresses this critical need for standardized terminology and consistent reporting of parameters related to image acquisition and analysis, and key outcome assessments, particularly with respect to ex vivo analysis of rodent specimens. Thus the guidelines herein provide recommendations regarding (1) standardized terminology and units, (2) information to be included in describing the methods for a given experiment, and (3) a minimal set of outcome variables that should be reported. Whereas the specific research objective will determine the experimental design, these guidelines are intended to ensure accurate and consistent reporting of microCT-derived bone morphometry and density measurements. In particular, the methods section for papers that present microCT-based outcomes must include details of the following scan aspects: (1) image acquisition, including the scanning medium, X-ray tube potential, and voxel size, as well as clear descriptions of the size and location of the volume of interest and the method used to delineate trabecular and cortical bone regions, and (2) image processing, including the algorithms used for image filtration and the approach used for image segmentation. Morphometric analyses should be based on 3D algorithms that do not rely on assumptions about the underlying structure whenever possible. When reporting microCT results, the minimal set of variables that should be used to describe trabecular bone morphometry includes bone volume fraction and trabecular number, thickness, and separation. The minimal set of variables that should be used to describe cortical bone morphometry includes total cross-sectional area, cortical bone area, cortical bone area fraction, and cortical thickness. Other variables also may be appropriate depending on the research question and technical quality of the scan. Standard nomenclature, outlined in this article, should be followed for reporting of results.
3,298 citations
Cites methods from "A new method for the model-independ..."
...Th, mm), where it is recommended that cortical thickness be computed using distance-transform methods.((14)) If image resolution is sufficient (ie, pores can be resolved), one also may report cortical porosity (Ct....
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...N) all should be based on 3D calculations, namely, a spherefitting method, where for thickness measurement the spheres are fitted to the object and for separation the spheres are fitted to the background((14)) (Fig....
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TL;DR: This work implemented standard bone measurements in a novel ImageJ plugin, BoneJ, with which it analysed trabecular bone, whole bones and osteocyte lacunae and found that available software solutions were expensive, inflexible or methodologically opaque.
1,723 citations
Cites methods from "A new method for the model-independ..."
...Modelindependent methods were preferred over techniques that make assumptions of underlying geometry [10]....
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...architecture of the public domain image processing program ImageJ [9] and implemented standard bone measurements [10-15] as an ImageJ plugin, BoneJ [16], to make full use of our computer hardware....
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TL;DR: Based on the direct 3D analysis of human bone biopsies, it appears that samples with a lower bone mass are primarily characterized by a smaller plate‐to‐rod ratio, and to a lesser extent by thinner trabecular elements.
Abstract: The appearance of cancellous bone architecture is different for various skeletal sites and various disease states. During aging and disease, plates are perforated and connecting rods are dissolved. There is a continuous shift from one structural type to the other. So traditional histomorphometric procedures, which are based on a fixed model type, will lead to questionable results. The introduction of three-dimensional (3D) measuring techniques in bone research makes it possible to capture the actual architecture of cancellous bone without assumptions of the structure type. This requires, however, new methods that make direct use of the 3D information. Within the framework of a BIOMED I project of the European Union, we analyzed a total of 260 human bone biopsies taken from five different skeletal sites (femoral head, vertebral bodies L2 and L4, iliac crest, and calcaneus) from 52 donors. The samples were measured three-dimensionally with a microcomputed tomography scanner and subsequently evaluated with both traditional indirect histomorphometric methods and newly developed direct ones. The results show significant differences between the methods and in their relation to the bone volume fraction. Based on the direct 3D analysis of human bone biopsies, it appears that samples with a lower bone mass are primarily characterized by a smaller plate-to-rod ratio, and to a lesser extent by thinner trabecular elements.
1,326 citations
Cites background from "A new method for the model-independ..."
...Examples of such procedures are direct volume and surface determination,((11)) model independent assessment of thickness,((12)) three-dimensional connectivity estimation,((13)) and 3D structure type assessment....
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...Th* is determined by filling maximal spheres into the structure with the distance transformation.((12)) Then the average thickness of all bone voxels is calculated to give Tb....
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TL;DR: In this paper, a morphometric parameter called Structure Model Index (SMI) is introduced, which makes it possible to quantify the characteristic form of a three-dimensionalally described structure in terms of the amount of plates and rods composing the structure.
Abstract: The deterioration of cancellous bone structure due to aging and disease is characterized by a conversion from plate elements to rod elements. Consequently the terms “rod-like” and “plate-like” are frequently used for a subjective classification of cancellous bone. In this work a new morphometric parameter called Structure Model Index (SMI) is introduced, which makes it possible to quantify the characteristic form of a three-dimensionally described structure in terms of the amount of plates and rod composing the structure. The SMI is calculated by means of three-dimensional image analysis based on a differential analysis of the triangulated bone surface. For an ideal plate and rod structure the SMI value is 0 and 3, respectively, independent of the physical dimensions. For a structure with both plates and rods of equal thickness the value lies between 0 and 3, depending on the volume ratio of rods and plates. The SMI parameter is evaluated by examining bone biopsies from different skeletal sites. The bone ...
1,080 citations
TL;DR: There were significant differences between the three canal types investigated, but very few differences were found with respect to instrument types.
Abstract: Peters OA, Schonenberger K, Laib A. Effects of four Ni‐Ti preparation techniques on root canal geometry assessed by micro computed tomography. International Endodontic Journal , 34 , 221‐230, 2001. Aim The aim of this study was to compare the effects of four preparation techniques on canal volume and surface area using three-dimensionally reconstructed root canals in extracted human maxillary molars. In addition, μ CT data was used to describe morphometric parameters related to the four preparation techniques. Methodology A micro computed tomography scanner was used to analyse root canals in extracted maxillary molars. Specimens were scanned before and after canals were prepared using Ni‐Ti ‐ K-Files, Lightspeed instruments, ProFile .04 and GT rotary instruments. Differences in dentine volume removed, canal straightening, the proportion of unchanged area and canal transportation were calculated using specially developed software. Results Instrumentation of canals increased volume and surface area. Prepared canals were significantly more rounded, had greater diameters and were straighter than unprepared canals. However, all instrumentation techniques left 35% or more of the canals’ surface area unchanged. Whilst there were significant differences between the three canal types investigated, very few differences were found with respect to instrument types. Conclusions Within the limitations of the μ CT system, there were few differences between the four canal instrumentation techniques used. By contrast, a strong impact of variations of canal anatomy was demonstrated. Further studies with 3D-techniques are required to fully understand the biomechanical aspects of root canal preparation.
690 citations
Cites methods from "A new method for the model-independ..."
...As hardware improved, new measurement algorithms were developed in order to three-dimensionally describe objects of interest metrically ( Hildebrand & Ruegsegger 1997a, 1997b )....
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...This procedure compares two outlines such as the outer root contour and the root canal cross-section but the current study concentrated on root canal geometry and therefore used fully three-dimensional measures such as SMI and thickness ( Hildebrand & Ruegsegger 1997a, 1997b, Peters et al. 2000c)....
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References
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TL;DR: Methods for estimating the volume, surface area and length of any structure are described in this review and the principles on which stereology is based and the necessary sampling procedures are described and illustrated with examples.
Abstract: Stereology is a set of simple and efficient methods for quantitation of three-dimensional microscopic structures which is specifically tuned to provide reliable data from sections. Within the last few years, a number of new methods has been developed which are of special interest to pathologists. Methods for estimating the volume, surface area and length of any structure are described in this review. The principles on which stereology is based and the necessary sampling procedures are described and illustrated with examples. The necessary equipment, the measurements, and the calculations are invariably simple and easy.
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TL;DR: The new stereological methods for correct and efficient sampling and sizing of cells and other particles are reviewed and practical examples of applications to a wide range of histological entities are illustrated.
Abstract: The new stereological methods for correct and efficient sampling and sizing of cells and other particles are reviewed. There is a hierarchy of methods starting from the simplest where even the microscopic magnification may be unknown to the most complex where typically both section thickness and the magnification must be known. Optical sections in suitably modified microscopes can be used to improve the ease and speed with which even the most demanding of these methods are performed. The methods are illustrated by practical examples of applications to a wide range of histological entities including synapses, neurons and cancer cells, glomerular corpuscles and ovarian follicles.
2,471 citations
TL;DR: It is shown that skeletons can be produced by simple procedures and since these are based on Euclidean distances it is assumed that they are superior to skeletons based on d4−, d8−, and even octagonal metrics.
1,777 citations
"A new method for the model-independ..." refers background in this paper
...This can be achieved by expressing (1) in terms of the structure distance map (see Danielsson, 1980; Serra, 1988)....
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TL;DR: In this paper, a family of test-frames for obtaining an unbiased estimate of the numerical density of arbitrary profiles on a section is described, and the counting rule pertaining to the test-frame is simple and requires no corrections based on other estimated quantities.
Abstract: SUMMARY
A description is given of a family of test-frames for obtaining an unbiased estimate of the numerical density of arbitrary profiles on a section. The counting rule pertaining to the test-frame is simple and requires no corrections based on other estimated quantities.
1,292 citations
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TL;DR: A measure of three‐dimensional connectivity (Euler number/tissue volume) has been determined for the first time in human cancellous bone and shown to correlate with several two‐dimensional histomorphometric indices.
Abstract: We describe a new method for the direct examination of three-dimensional bone structure in vitro based on high-resolution computed tomography (CT). Unlike clinical CT, a three-dimensional reconstruction array is created directly, rather than a series of two-dimensional slices. All structural indices commonly determined from two-dimensional histologic sections can be obtained nondestructively from a large number of slices in each of three orthogonal directions. This permits a comprehensive description of structural variation within a specimen and greatly facilitates the study of structural anisotropy. A measure of three-dimensional connectivity (Euler number/tissue volume) has been determined for the first time in human cancellous bone and shown to correlate with several two-dimensional histomorphometric indices. The method has the potential for overcoming many of the limitations of current approaches to the study of bone architecture at the microscopic level.
1,059 citations
"A new method for the model-independ..." refers methods in this paper
...Examples of such techniques are confocal fluorescence microscopy (Wijnaends van Resandt et al., 1985; Wilson, 1990), micro-computed tomography (micro-CT) (Feldkamp et al., 1989; Rüegsegger et al., 1996) and micro-magnetic resonance imaging (Jara et al., 1993)....
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..., 1985; Wilson, 1990), micro-computed tomography (micro-CT) (Feldkamp et al., 1989; Rüegsegger et al., 1996) and micro-magnetic resonance imaging (Jara et al....
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