Tania S. Douglas

Motion Artifact Removal for Functional Near Infrared Spectroscopy: A Comparison of Methods

Near infrared spectroscopy (NIRS) is rapidly gaining popularity for functional brain imaging. It is well suited to studies of patients or children; however, in these populations particularly, motion artifacts can present a problem. Here, we propose the use of imaging channels with negligible distance between light source and detector to detect subject motion, without the need for an additional motion sensor. Datasets containing deliberate motion artifacts were obtained from three subjects. Motion artifacts could be detected in the signal from the co-located channels with a minimum sensitivity of 0.75 and specificity of 0.98. Five techniques for removing motion artifact from the functional signals were compared, namely two-input recursive least squares (RLS) adaptive filtering, wavelet-based filtering, independent component analysis (ICA), and two-channel and multiple-channel regression. In most datasets, the median change in SNR across all channels was the greatest using ICA or multiple-channel regression. RLS adaptive filtering produced the smallest increase in SNR. Where sharp spikes were present, wavelet filtering produced the largest SNR increase. ICA and multiple-channel regression are promising ways to reduce motion artifact in functional NIRS without requiring time-consuming manual techniques.

Classification of Mycobacterium tuberculosis in Images of ZN-Stained Sputum Smears

Screening for tuberculosis (TB) in low- and middle-income countries is centered on the microscope. We present methods for the automated identification of Mycobacterium tuberculosis in images of Ziehl-Neelsen (ZN) stained sputum smears obtained using a bright-field microscope. We segment candidate bacillus objects using a combination of two-class pixel classifiers. The algorithm produces results that agree well with manual segmentations, as judged by the Hausdorff distance and the modified Williams index. The extraction of geometric-transformation-invariant features and optimization of the feature set by feature subset selection and Fisher transformation follow. Finally, different two-class object classifiers are compared. The sensitivity and specificity of all tested classifiers is above 95% for the identification of bacillus objects represented by Fisher-transformed features. Our results may be used to reduce technician involvement in screening for TB, and would be particularly useful in laboratories in countries with a high burden of TB, where, typically, ZN rather than auramine staining of sputum smears is the method of choice.

A stereo-photogrammetric method to measure the facial dysmorphology of children in the diagnosis of fetal alcohol syndrome

In diagnosing a child with fetal alcohol syndrome (FAS), anthropometric measurements of the face are conventionally performed by highly trained dysmorphologists using a hand-held ruler. This renders the screening of large populations of children for the facial features characteristic of FAS very time-consuming and costly. This study proposes a new, cost-effective, and non-intrusive method to measure in three dimensions the facial dysmorphology of children using stereo-photogrammetry. The face of each child is photographed in a control frame simultaneously by a pair of high-resolution digital cameras mounted 1.04 m from the child and 0.26 m apart. Software has been developed to calibrate the images and to compute the three-dimensional object-space coordinates of any point on the face from a measurement of the point on each of the images. The palpebral fissure lengths, inner canthal-, and interpupillary distances of 44 subjects were measured in this manner independently by two investigators and compared with measurements obtained by clinical specialists in the conventional manner. There was found to be no statistically significant difference between palpebral fissure lengths determined using the two techniques (paired Students t-test p-values are 0.29 and 0.18, respectively). It has also been demonstrated that facial measurements can be performed with greater consistency from a pair of stereo photographs than direct measurements from live subjects.

Automated focusing in bright-field microscopy for tuberculosis detection

Automated microscopy to detect Mycobacterium tuberculosis in sputum smear slides would enable laboratories in countries with a high tuberculosis burden to cope efficiently with large numbers of smears. Focusing is a core component of automated microscopy, and successful autofocusing depends on selection of an appropriate focus algorithm for a specific task. We examined autofocusing algorithms for bright‐field microscopy of Ziehl–Neelsen stained sputum smears. Six focus measures, defined in the spatial domain, were examined with respect to accuracy, execution time, range, full width at half maximum of the peak and the presence of local maxima. Curve fitting around an estimate of the focal plane was found to produce good results and is therefore an acceptable strategy to reduce the number of images captured for focusing and the processing time. Vollaths F4 measure performed best for full z‐stacks, with a mean difference of 0.27 μm between manually and automatically determined focal positions, whereas it is jointly ranked best with the Brenner gradient for curve fitting.

Morphometric analysis of facial landmark data to characterize the facial phenotype associated with fetal alcohol syndrome

Procrustes analysis and principal component analysis were applied to stereo‐photogrammetrically obtained landmarks to compare the facial features associated with fetal alcohol syndrome (FAS) in subjects with FAS and normal controls. Two studies were performed; both compared facial landmark data of FAS and normal subjects, but they differed in the number of landmarks chosen. The first study compared landmarks representing palpebral fissure length, upper lip thinness and philtrum smoothness and revealed no significant difference in shape. The second study added to the landmarks used in the first those affected by mid‐face hypoplasia, and revealed significant differences in shape between the two groups, broadly confirming the FAS gestalt reported in the literature. Some disagreement in the characteristic FAS facial shape between our results and those reported in the literature may be due to ethnic variation.

Eye feature extraction for diagnosing the facial phenotype associated with fetal alcohol syndrome

Victims of fetal alcohol syndrome (FAS) exhibit a unique facial phenotype that is emphasised in diagnosis. Among the characteristic facial features, several occurring in the region of the orbits can be evaluated quantitatively using distance measurements. An algorithm is described for automatic extraction and measurement of eye features from stereo photographs. The algorithm was applied to photographs of 46 six-seven-year-old children. The approach relies on peak and valley maps and integral projection functions, to locate the eyes and extract the iris, and genetic algorithms to fit cubic splines to the upper and lower eyelids. Measurements obtained automatically using this algorithm were compared with measurements obtained manually from the photographs. Mean absolute differences between automatic and manual measurements were less than 1 mm for palpebral fissure length (PFL) and interpupillary distance (IPD). Absolute differences were less than 1 mm for 80.4% of PFLs and 100% of IPDs. Inner canthal distance and outer canthal distance did not compare favourably with manual measurements.

Ultrasound imaging in lower limb prosthetics

The biomechanical interaction between the residual limb and the prosthetic socket determines the quality of fit of the socket in lower limb prosthetics. An understanding of this interaction and the development of quantitative measures to predict the quality of fit of the socket are important for optimal socket design. Finite-element modeling is used widely for biomechanical modeling of the limb/socket interaction and requires information on the internal and external geometry of the residual limb. Volumetric imaging methods such as X-ray computed tomography, magnetic resonance imaging, and ultrasound have been used to obtain residual limb shape information. Of these modalities, ultrasound has been introduced most recently and its development for visualization in prosthetics is the least mature. This paper reviews ultrasound image acquisition and processing methods as they have been applied in lower limb prosthetics.

Hierarchical information-based clustering for connectivity-based cortex parcellation

One of the most promising avenues for compiling connectivity data originates from the notion that individual brain regions maintain individual connectivity profiles; the functional repertoire of a cortical area (“the functional fingerprint”) is closely related to its anatomical connections (“the connectional fingerprint”) and, hence, a segregated cortical area may be characterized by a highly coherent connectivity pattern. Diffusion tractography can be used to identify borders between such cortical areas. Each cortical area is defined based upon a unique probabilistic tractogram and such a tractogram is representative of a group of tractograms, thereby forming the cortical area. The underlying methodology is called connectivity-based cortex parcellation and requires clustering or grouping of similar diffusion tractograms. Despite the relative success of this technique in producing anatomically sensible results, existing clustering techniques in the context of connectivity-based parcellation typically depend on several non-trivial assumptions. In this paper, we embody an unsupervised hierarchical information-based framework to clustering probabilistic tractograms that avoids many drawbacks offered by previous methods. Cortex parcellation of the inferior frontal gyrus together with the precentral gyrus demonstrates a proof of concept of the proposed method: The automatic parcellation reveals cortical subunits consistent with cytoarchitectonic maps and previous studies including connectivity-based parcellation. Further insight into the hierarchically modular architecture of cortical subunits is given by revealing coarser cortical structures that differentiate between primary as well as premotoric areas and those associated with pre-frontal areas.

Radiation dose from a linear slit scanning X-ray machine with full-body imaging capabilities

Doses for a range of examinations and views using digital X-ray equipment with full-body linear slit scanning capabilities (Statscan) have been compared with those from other published studies. Entrance doses (free-in-air) were measured using a dosimeter, and effective doses were generated using a Monte Carlo simulator. Doses delivered by the linear slit scanning system were significantly lower than those from conventional X-ray equipment. Effective doses were between 9 and 75% of the United Nations Scientific Committee Report on the Effects of Ionising Radiation doses for standard examinations. This dose reduction can be explained by the properties of linear slit scanning technology, including low scatter, beam geometry, the use of a digital detector and the use of higher than usual tube voltages.

Automated detection of tuberculosis in Ziehl-Neelsen-stained sputum smears using two one-class classifiers.

Screening for tuberculosis in high‐prevalence countries relies on sputum smear microscopy. We present a method for the automated identification of Mycobacterium tuberculosis in images of Ziehl‐Neelsen‐stained sputum smears obtained using a bright‐field microscope. We use two stages of classification. The first comprises a one‐class pixel classifier for object segmentation. Geometric transformation invariant features are extracted for implementation of the second stage, namely one‐class object classification. Different classifiers are compared; the sensitivity of all tested classifiers is above 90% for the identification of a single bacillus object using all extracted features. The mixture of Gaussians classifier performed well in both stages of classification. This method may be used as a step in the automation of tuberculosis screening, in order to reduce technician involvement in the process.