A simple computer vision pipeline reveals the effects of isolation on social interaction dynamics in Drosophila.

Isolation profoundly influences social behavior in all animals. In humans, isolation has serious effects on health. Drosophila melanogaster is a powerful model to study small-scale, temporally-transient social behavior. However, longer-term analysis of large groups of flies is hampered by the lack of effective and reliable tools. We built a new imaging arena and improved the existing tracking algorithm to reliably follow a large number of flies simultaneously. Next, based on the automatic classification of touch and graph-based social network analysis, we designed an algorithm to quantify changes in the social network in response to prior social isolation. We observed that isolation significantly and swiftly enhanced individual and local social network parameters depicting near-neighbor relationships. We explored the genome-wide molecular correlates of these behavioral changes and found that whereas behavior changed throughout the six days of isolation, gene expression alterations occurred largely on day one. These changes occurred mostly in metabolic genes, and we verified the metabolic changes by showing an increase of lipid content in isolated flies. In summary, we describe a highly reliable tracking and analysis pipeline for large groups of flies that we use to unravel the behavioral, molecular and physiological impact of isolation on social network dynamics in Drosophila.

Diffusion kurtosis imaging allows the early detection and longitudinal follow-up of amyloid-ß-induced pathology.

BACKGROUND: Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the most common cause of dementia in the elderly population. In this study, we used the APP/PS1 transgenic mouse model to explore the feasibility of using diffusion kurtosis imaging (DKI) as a tool for the early detection of microstructural changes in the brain due to amyloid-ß (Aß) plaque deposition. METHODS: We longitudinally acquired DKI data of wild-type (WT) and APP/PS1 mice at 2, 4, 6 and 8 months of age, after which these mice were sacrificed for histological examination. Three additional cohorts of mice were also included at 2, 4 and 6 months of age to allow voxel-based co-registration between diffusion tensor and diffusion kurtosis  metrics and immunohistochemistry. RESULTS: Changes were observed in diffusion tensor (DT) and diffusion kurtosis (DK) metrics in many of the 23 regions of interest that were analysed. Mean and axial kurtosis were greatly increased owing to Aß-induced pathological changes in the motor cortex of APP/PS1 mice at 4, 6 and 8 months of age. Additionally, fractional anisotropy (FA) was decreased in APP/PS1 mice at these respective ages. Linear discriminant analysis of the motor cortex data indicated that combining diffusion tensor and diffusion kurtosis metrics permits improved separation of WT from APP/PS1 mice compared with either diffusion tensor or diffusion kurtosis metrics alone. We observed that mean kurtosis and FA are the critical metrics for a correct genotype classification. Furthermore, using a newly developed platform to co-register the in vivo diffusion-weighted magnetic resonance imaging with multiple 3D histological stacks, we found high correlations between DK metrics and anti-Aß (clone 4G8) antibody, glial fibrillary acidic protein, ionised calcium-binding adapter molecule 1 and myelin basic protein immunohistochemistry. Finally, we observed reduced FA in the septal nuclei of APP/PS1 mice at all ages investigated. The latter was at least partially also observed by voxel-based statistical parametric mapping, which showed significantly reduced FA in the septal nuclei, as well as in the corpus callosum, of 8-month-old APP/PS1 mice compared with WT mice. CONCLUSIONS: Our results indicate that DKI metrics hold tremendous potential for the early detection and longitudinal follow-up of Aß-induced pathology.

Machine learning study of several classifiers trained with texture analysis features to differentiate benign from malignant soft-tissue tumors in T1-MRI images.

PURPOSE: To study, from a machine learning perspective, the performance of several machine learning classifiers that use texture analysis features extracted from soft-tissue tumors in nonenhanced T1-MRI images to discriminate between malignant and benign tumors. MATERIALS AND METHODS: Texture analysis features were extracted from the tumor regions from T1-MRI images of clinically proven cases of 49 malignant and 86 benign soft-tissue tumors. Three conventional machine learning classifiers were trained and tested. The best classifier was compared to the radiologists by means of the McNemar's statistical test. RESULTS: The SVM classifier performs better than the neural network and the C4.5 decision tree based on the analysis of their receiver operating curves (ROC) and cost curves. The classification accuracy of the SVM, which was 93% (91% specificity; 94% sensitivity), was better than the radiologist classification accuracy of 90% (92% specificity; 81% sensitivity). CONCLUSION: Machine learning classifiers trained with texture analysis features are potentially valuable for detecting malignant tumors in T1-MRI images. Analysis of the learning curves of the classifiers showed that a training data size smaller than 100 T1-MRI images is sufficient to train a machine learning classifier that performs as well as expert radiologists.

Comparing isotropic and anisotropic smoothing for voxel-based DTI analyses: A simulation study.

Voxel-based analysis (VBA) methods are increasingly being used to compare diffusion tensor image (DTI) properties across different populations of subjects. Although VBA has many advantages, its results are highly dependent on several parameter settings, such as those from the coregistration technique applied to align the data, the smoothing kernel, the statistics, and the post-hoc analyses. In particular, to increase the signal-to-noise ratio and to mitigate the adverse effect of residual image misalignments, DTI data are often smoothed before VBA with an isotropic Gaussian kernel with a full width half maximum up to 16 x 16 x 16 mm(3). However, using isotropic smoothing kernels can significantly partial volume or voxel averaging artifacts, adversely affecting the true diffusion properties of the underlying fiber tissue. In this work, we compared VBA results between the isotropic and an anisotropic Gaussian filtering method using a simulated framework. Our results clearly demonstrate an increased sensitivity and specificity of detecting a predefined simulated pathology when the anisotropic smoothing kernel was used.

On the construction of a ground truth framework for evaluating voxel-based diffusion tensor MRI analysis methods.

Although many studies are starting to use voxel-based analysis (VBA) methods to compare diffusion tensor images between healthy and diseased subjects, it has been demonstrated that VBA results depend heavily on parameter settings and implementation strategies, such as the applied coregistration technique, smoothing kernel width, statistical analysis, etc. In order to investigate the effect of different parameter settings and implementations on the accuracy and precision of the VBA results quantitatively, ground truth knowledge regarding the underlying microstructural alterations is required. To address the lack of such a gold standard, simulated diffusion tensor data sets are developed, which can model an array of anomalies in the diffusion properties of a predefined location. These data sets can be employed to evaluate the numerous parameters that characterize the pipeline of a VBA algorithm and to compare the accuracy, precision, and reproducibility of different post-processing approaches quantitatively. We are convinced that the use of these simulated data sets can improve the understanding of how different diffusion tensor image post-processing techniques affect the outcome of VBA. In turn, this may possibly lead to a more standardized and reliable evaluation of diffusion tensor data sets of large study groups with a wide range of white matter altering pathologies. The simulated DTI data sets will be made available online (http://www.dti.ua.ac.be).

On the construction of an inter-subject diffusion tensor magnetic resonance atlas of the healthy human brain.

Voxel based morphometry (VBM) has been increasingly applied to detect diffusion tensor (DT) image abnormalities in patients for different pathologies. An important requisite for a robust VBM analysis is the availability of a high-dimensional non-rigid coregistration technique that is able to align both the spatial and the orientational DT information. Consequently, there is a need for an inter-subject DTI atlas as a group specific reference frame that also contains this orientational DT information. In this work, a population based DTI atlas has been developed that incorporates such orientational DT information with high accuracy and precision. The proposed methodology for constructing such an atlas is compared with a subject based DTI atlas, in which a single subject is selected as the reference image. Our results demonstrate that the population based atlas framework is more accurate with respect to the underlying diffusion information.

Nonrigid coregistration of diffusion tensor images using a viscous fluid model and mutual information.

In this paper, a nonrigid coregistration algorithm based on a viscous fluid model is proposed that has been optimized for diffusion tensor images (DTI), in which image correspondence is measured by the mutual information criterion. Several coregistration strategies are introduced and evaluated both on simulated data and on brain intersubject DTI data. Two tensor reorientation methods have been incorporated and quantitatively evaluated. Simulation as well as experimental results show that the proposed viscous fluid model can provide a high coregistration accuracy, although the tensor reorientation was observed to be highly sensitive to the local deformation field. Nevertheless, this coregistration method has demonstrated to significantly improve spatial alignment compared to affine image matching.

Wavelet denoising of multicomponent images using gaussian scale mixture models and a noise-free image as priors.

In this paper, a Bayesian wavelet-based denoising procedure for multicomponent images is proposed. A denoising procedure is constructed that (1) fully accounts for the multicomponent image covariances, (2) makes use of Gaussian scale mixtures as prior models that approximate the marginal distributions of the wavelet coefficients well, and (3) makes use of a noise-free image as extra prior information. It is shown that such prior information is available with specific multicomponent image data of, e.g., remote sensing and biomedical imaging. Experiments are conducted in these two domains, in both simulated and real noisy conditions.