Largest contour segmentation: a tool for the localization of spots in confocal images

An accurate determination of the 3-D positions of multiple spots in images obtained by confocal microscopy is essential for the investigation of the spatial distribution of specific components or processes in biological specimens. The position of the centroid, as an estimator for the position of a spot, can be calculated on the basis of all voxels that belong to the domain of the spot. For this calculation a domain that defines which voxels belong to the spot must be delimited. To create a boundary for a domain we developed a 3-D image segmentation procedure: the largest contour segmentation (LCS). This procedure is based on an iterative region-growing procedure around each local maximum of intensity. By means of this procedure the position of each spot was determined accurately and automatically. Qualities of the procedure were evaluated by means of simulated test-images as well as 3-D images of real biological specimens.     

A novel method for the three-dimensional (3-D) analysis of orthodontic tooth movement-calculation of rotation about and translation along the finite helical axis.

The purpose of this study was to establish a novel method for evaluating orthodontic tooth movement in three-dimensional (3-D) space. The present system consisted of the following procedures at a given treatment period: (1) 3-D tooth positions were measured with a 3-D surface-scanning system using a slit laser beam; (2) the 3-D shape data were registered automatically at the maxillary first molars, and the coordinate systems were normalized; (3) the rotation matrix and translation vector were calculated from the automatic registration of the two position data for a given tooth; (4) the finite helical axes of teeth were calculated as the locus of zero rotational displacement; and (5) tooth movement was presented as rotation about and translation along the finite helical axis. To test this system, a male patient (age 22 yr 2 months) with Angle Class III malocclusion and moderate crowding of the anterior teeth, who had been treated using a standard multi-bracket appliance, was used as a model case in this study. Impressions for a dental cast model were taken at five phases; immediately before and after application of the appliance, and 10 days, 1 month and 2 months after beginning treatment. The results demonstrated that the present analytical method can more simply describe the movement of a given tooth by rotation about and translation along the finite helical axis, and provides quantitative visual 3-D information on complicated tooth movement during orthodontic treatment.     

Electron microscope analysis of tissue components identified and located by computer-assisted 3-D reconstructions: ultrastructural segmentation of the developing human proximal tubule

A method is described for ultrastructural analysis of renal tubules after precise identification of tubule segments by computerized 3-D reconstruction at the light microscope level. Semithin serial sections were cut of entire nephrons and 3-D coordinate information was obtained by digitization of tubule cross sections in the semithin sections. With the aid of the computer the tubule axis was traced from one section to the other. Precise lengths and positions of the tubules in three dimensions were calculated and stereoscopic images generated. The method was used to analyze the 3-D structure of developing human nephrons, and the ultrastructural development of the proximal tubule. Ultrastructural segmentation of the proximal tubule was demonstrated in the human fetal nephron in developmental stage IV.     

In vivo determination of the Achilles tendon moment arm in three-dimensions

Two-dimensional methods have been applied to determine the Achilles tendon moment arm in previous studies, although the talocrural joint rotates in three-dimension. The purpose of this study was to develop a method for determining the Achilles tendon moment arm in three-dimensions (3DMA). A series of sagittal ankle images were obtained at ankle positions of -20°, -10° (dorsiflexed position), 0° (neutral position), +10°, +20°, and +30° (plantarflexed position). The talocrural joint axis was determined as the finite helical axis of the ankle joint over 20° of displacement, and the 3DMA was determined as the shortest distance from the talocrural joint axis to the line of action of the Achilles tendon force. The corresponding 2DMA was determined with the center of rotation method using the images captured on the sagittal plane passing through the mid-point of the medio-lateral width of the tibia. The 3DMA ranged from 35 to 41 mm across various ankle positions and was, on average, 11 mm smaller than 2DMA. The difference between the two measures was attributable primarily to the deviations of the talocrural joint axis from the anatomical medio-lateral direction. The deviations on the coronal plane (21.4±20.7°) and on the transverse planes (14.8±22.6°) accounted for the errors of 1.3 mm and 3.0 mm, respectively. In addition, selecting either a medially or laterally misaligned sagittal-plane image for determining the 2DMA gave rise to error by 3.5 mm. The remaining difference was accounted for by the random measurement error.     

A mathematical model of the primary visual cortex and hypercolumn

A mathematical model of the primary visual cortex is presented. Basically, the model comprises two features. Firstly, in analogy with the principle of the computerized tomography (CT), it assumes that simple cells in each hypercolumn are not merely detecting line segments in images as features, but rather that they are as a whole representing the local image with a certain representation. Secondly, it assumes that each hypercolumn is performing spatial frequency analyses of local images using that representation, and that the resultant spectra are represented by complex cells. The model is analyzed using numerical simulations and its advantages are discussed from the viewpoint of visual information processing. It is shown that 1) the proposed processing is tolerant to shifts in position of input images, and that 2) spatial frequency filtering operations can be easily performed in the model.     

Feeding Motor Patterns in Anurans: Insights from Biomechanical Modeling

During feeding in anurans, the mouth opens while the tongue,which is attached to the mandible at the front of the mouth,rotates forward. Due to the relative simplicity of its anatomyand the complexity of its motion, tongue protraction in frogspresents an ideal system for exploring the neural control ofmultijoint movements. In this study, we used a forward dynamic,rigid body model with four segments and two muscles to investigateopen loop control of tongue protraction in the Australian white-lippedtree frog, Litoria caerulea. Model parameters include the massdistribution, initial position and initial angular velocityof each segment and the anatomy and physiology of each muscle.Model variables include the level of muscle activation at eachtime step and impulsive torques to open and close the mouth.The model gives X,Y coordinates of each segment and joint anglesat each time step as output. The model was tested using scaled,normalized EMG signals and impulsive joint torques to predictthe paths of the lower jaw tip and tongue tip. Predicted pathswere compared to experimentally observed paths using Pearsonproduct-moment correlation coefficients. Simulations demonstratethat the genioglossus muscles likely play a minor role, if any,in determining the trajectory of the tongue in most anurans.Most of the force for tongue protraction comes from angularmomentum transferred to the tongue by the opening jaws. In anurans,tongue protraction is dynamically stable and will occur as longas the musculoskeletal elements are in the correct initial position.     

Feasibility of using orthogonal fluoroscopic images to measure in vivo joint kinematics

Accurately determining in vivo knee kinematics is still a challenge in biomedical engineering. This paper presents an imaging technique using two orthogonal images to measure 6 degree-of-freedom (DOF) knee kinematics during weight-bearing flexion. Using this technique, orthogonal images of the knee were captured using a 3-D fluoroscope at different flexion angles during weight-bearing flexion. The two orthogonal images uniquely characterized the knee position at the specific flexion angle. A virtual fluoroscope was then created in solid modeling software and was used to reproduce the relative positions of the orthogonal images and X-ray sources of the 3-D fluoroscope during the actual imaging procedure. Two virtual cameras in the software were used to represent the X-ray sources. The 3-D computer model of the knee was then introduced into the virtual fluoroscope and was projected onto the orthogonal images by the two virtual cameras. By matching the projections of the knee model to the orthogonal images of the knee obtained during weight-bearing flexion, the knee kinematics in 6 DOF were determined. Using regularly shaped objects with known positions and orientations, this technique was shown to have an accuracy of 0.1 mm and 0.1 deg in determining the positions and orientations of the objects, respectively.     

Method for determining the spatial position of the shoulder with ultrasound-based motion analyzer.

Several methods have been developed recently for the analysis of the spatial motion of the scapula and the arm, whereby the spatial position of shoulder bones is determined in static conditions by interrupting motion. The authors have developed a 3D motion analysis method recording scapular motion in progress with appropriate accuracy in the course of arm movements of various degrees. The objective of this study is to explore the applicability of the method developed, as well as to compare it with and verify it by other methods developed earlier. The position and displacements of shoulder bones were determined on 30 shoulders of 15 healthy people. The newly developed measurement method is based on the mechanical basic principle stating that the position and motion of a rigid body -- in this case, the bones (segments) forming the shoulder joint -- can be calculated at any moment from the spatial coordinates of three points of a segment and any changes thereof in the course of motion. Ultrasound-based triplets providing the three points (fundamental points) by a segment as required for measurement were fixed on the sternum (modeling the trunk), the clavicle, the acromion (modeling the scapula), the upper arm, and the lower arm. The position of the sixteen anatomical points involved in the study were determined by an ultrasound-based pointer in the local coordinate system specified by the fundamental points before starting measurements. The ZEBRIS ultrasound-based motion analysis system was used for measuring the spatial coordinates of triplets in the course of continuous motion. The spatial coordinates of the designated anatomical points can be calculated by the method of triangulation. The method was calibrated by a ZEBRIS mapping (3DCAD) software commercially available, and the measurement error rate of the method was determined by statistical calculations. On the basis of calibration and error calculations it could be established that the accuracy and the reproducibility of the method were appropriate, in accordance with the limit values to be found in the literature.     

Prospective Control in Catching: The Persistent Angle-of-Approach Effect in Lateral Interception

In lateral interception tasks balls converging onto the same interception location via different trajectories give rise to systematic differences in the kinematics of hand movement. While it is generally accepted that this angle-of-approach effect reflects the prospective (on-line) control of movement, controversy exists with respect to the information used to guide the hand to the future interception location. Based on the pattern of errors observed in a task requiring visual extrapolation of line segments to their intersection with a second line, angle-of-approach effects in lateral interception have been argued to result from perceptual biases in the detection of information about the ball''s future passing distance along the axis of hand movement. Here we demonstrate that this account does not hold under experimental scrutiny: The angle-of-approach effect still emerged when participants intercepted balls moving along trajectories characterized by a zero perceptual bias with respect to the ball''s future arrival position (Experiment 4). Designing and validating such bias-controlled trajectories were done using the line-intersection extrapolation task (Experiments 2 and 3). The experimental set-up used in the present series of experiments was first validated for the lateral interception and the line-intersection extrapolation tasks: In Experiment 1 we used rectilinear ball trajectories to replicate the angle-of-approach effect in lateral interception of virtual balls. Using line segments extracted from these rectilinear ball trajectories, in Experiment 2 we replicated the reported pattern of errors in the estimated locus of intersection with the axis of hand movement. We used these errors to develop a set of bias-free trajectories. Experiment 3 confirmed that the perceptual biases had been corrected for successfully. We discuss the implications on the information-based regulation of hand movement of our finding that the angle-of-approach effect in lateral interception cannot not explained by perceptual biases in information about the ball''s future passing distance.     

Model-based inverse estimation for active contraction stresses of tongue muscles using 3D surface shape in speech production

This paper presents a novel inverse estimation approach for the active contraction stresses of tongue muscles during speech. The proposed method is based on variational data assimilation using a mechanical tongue model and 3D tongue surface shapes for speech production. The mechanical tongue model considers nonlinear hyperelasticity, finite deformation, actual geometry from computed tomography (CT) images, and anisotropic active contraction by muscle fibers, the orientations of which are ideally determined using anatomical drawings. The tongue deformation is obtained by solving a stationary force-equilibrium equation using a finite element method. An inverse problem is established to find the combination of muscle contraction stresses that minimizes the Euclidean distance of the tongue surfaces between the mechanical analysis and CT results of speech production, where a signed-distance function represents the tongue surface. Our approach is validated through an ideal numerical example and extended to the real-world case of two Japanese vowels, /ʉ/ and /ɯ/. The results capture the target shape completely and provide an excellent estimation of the active contraction stresses in the ideal case, and exhibit similar tendencies as in previous observations and simulations for the actual vowel cases. The present approach can reveal the relative relationship among the muscle contraction stresses in similar utterances with different tongue shapes, and enables the investigation of the coordination of tongue muscles during speech using only the deformed tongue shape obtained from medical images. This will enhance our understanding of speech motor control.     

Ring Artifacts Reduction in CBCT: Pixels Detection and Patch Based Correction

The ring artifacts introduced by the defective pixels with non-linear responses in the high-resolution detector, have a great impact on subsequent processing and quantitative analysis of the reconstructed images. In this paper, a multistep method is proposed to suppress the ring artifacts of micro CT images, which firstly locates the positions of the defective pixels in the sinogram, and then corrects the corresponding value in the projections. Since the defective pixels always appear as vertical stripes in the sinogram, a horizontal curve is derived by summing the pixel values along vertical direction, thus the abrupt segments related to the defective stripes are enhanced notably, and a proportion coefficient based on the second derivative of the curve is taken as the indicator for the position and the severity of the defective pixels. Then, the detected defective pixels in the sinogram are transferred and relocated in the projections, an improved 3D block matching filtering (BM3D) algorithm is applied to restore the defective pixels in corresponding projection images. In the end, the tomographic images are reconstructed from the corrected projections. In the experiment, a small piece of the motherwort’s rhizome and a part of a mouse’s lung are imaged by micro-CT, and the result shows that, compared with the other four state-of-art methods, the proposed method has a great reduction on the ring artifacts of the reconstructed images, and makes less impact in spatial resolution and contrast in the same time.     

The finite displacements vector's method: an application to the scoliotic spine

This paper presents a vectorial method to directly obtain the components of the screw displacement between two positions of a body in a three-dimensional space (position of the helical axis of motion, rotation around this axis and translation along it). This method can be applied either to the case of a bone, moving with respect to the reference frame, or to the case of the relative motion of a joint; it gives exact formulae even if the displacements are finite; it generalizes the results (already published) obtained for finite displacements in the plane. The involved computation is easy, and the use of this method deals with only a small magnification of experimental errors. The technique of a screw displacement is applied to the vertebral segments of a scoliolic spine. The necessary data is taken from a couple of in-vivo X-rays. The goals of this study are: first, to describe the shape of the spine at each step of its evolution and second, to quantify the evolution in time of any segment of the spine between two states.     

Two-dimensional versus three-dimensional morphometry of monogenoidean sclerites

A new method of three-dimensional (3-D) analysis of sclerotised structures of monogenoids was performed by processing z-series images using 3D-Doctor. Z-series were obtained from Gomori's trichrome-stained specimens of marine and freshwater monogenoids under laser scanning confocal fluorescence microscopy. Measurements obtained from 3-D images were then compared with those from 2-D images taken from both flattened and unflattened specimens. Data comparison demonstrated that 3-D morphometry allowed avoidance of over-estimation due to deformation and the reduction of errors associated with different spatial orientations. Moreover, study of 3-D images permitted observation of morphological details that are not detectable in 2-D representations.     

Rationalization of kinematic descriptors for three-dimensional hand and finger motion

Modelling joint motion in three dimensions is often based on techniques taken from classical dynamics, each analysis resulting in a set of six parameters describing the relative motion betwen two body segments. The literature on joint kinematics has been difficult to compare due to use of different anatomical landmarks, axis nomenclature, and analytical methods. It is here shown that with care in sequence definition, the three alignment-based systems (Euler, Cardan, floating axis) give identical results for angular parameters. While the equivalent screw displacement axis system can be related simply to the other methods only if the functional axis of motion is aligned with a coordinate axis, the basic matrix for relating rigid body positions before and after a motion can always be reconstructed. Therefore the changes in alignment angles may be obtained from screw displacement parameters, permitting the results of different analyses to be compared. Translation parameters are most difficult to interpret in any system. Examples of the way in which simple planar motions are characterized by the various analytical methods are given.     

An image-interpolation technique for the computation of optic flow and egomotion

 A technique for measuring the motion of a rigid, textured plane in the frontoparallel plane is developed and tested on synthetic and real image sequences. The parameters of motion – translation in two dimensions, and rotation about a previously unspecified axis perpendicular to the plane – are computed by a single-stage, non-iterative process which interpolates the position of the moving image with respect to a set of reference images. The method can be extended to measure additional parameters of motion, such as expansion or shear. Advantages of the technique are that it does not require tracking of features, measurement of local image velocities or computation of high-order spatial or temporal derivatives of the image. The technique is robust to noise, and it offers a simple, novel way of tackling the ‘aperture’ problem. An application to the computation of robot egomotion is also described. Received: 3 September 1993/Accepted in revised form: 16 April 1994     

Manual segmentation of DXA scan images results in reliable upper and lower extremity soft and rigid tissue mass estimates

Quantification of segment soft and rigid tissue masses in living people is important for a variety of clinical and biomechanical research applications including wobbling mass modeling. Although Dual-energy X-ray Absorptiometry (DXA) is widely accepted as a valid method for this purpose, the reliability of manual segmentation from DXA scans using custom regions of interest (ROIs) has not been evaluated to date. Upper and lower extremity images of 100 healthy adults who underwent a full body DXA scan in the supine position were manually segmented by 3 measurers independently using custom ROIs. Actual tissue masses (fat mass, lean mass, bone mineral content) of the arm, arm with shoulder, forearm, forearm and hand, thigh, leg, and leg and foot segments were quantified bilaterally from the ROIs. There were significant differences between-measurers, however, percentage errors were relatively small overall (<1–5.98%). Intraclass correlation coefficients (ICCs) were very high between and within-measurers, ranging from 0.990 to 0.999 and 0.990 to 1.00 for the upper and lower extremities, respectively, suggesting excellent reliability. Between and within-measurer errors were comparable in general, and differences between the tissue types were small on average (maximum of 42 and 53 g for upper and lower extremities, respectively). These results suggest that manual segmentation of DXA images using ROIs is a reliable method of estimating soft and rigid tissues in living people.     

The effect of anisotropic systematic errors in estimating helical angles

A common question in movement studies is how the results should be interpreted with respect to systematic and random errors. In this study, simulations are made in order to see how a rigid body's orientation in space (i.e. helical angle between two orientations) is affected by (1) a systematic error added to a single marker (2) a combination of this systematic error and Gaussian white noise. The orientation was estimated after adding a systematic error to one marker within the rigid body. This procedure was repeated with Gaussian noise added to each marker.

In conclusion, results show that the systematic error's effect on estimated orientation depends on number of markers in the rigid body and also on which direction the systematic error is added. The systematic error has no effect if the error is added along the radial axis (i.e. the line connecting centre of mass and the affected marker).