Free form deformation and symmetry constraint‐based multimodal brain image registration using generative adversarial nets

Multi‐modal brain image registration has been widely applied to functional localisation,neurosurgery and computational anatomy.The existing registration methods based on the dense deformation fields involve too many parameters,which is not conducive to the exploration of correct spatial correspondence between the float and reference images.Meanwhile,the unidirectional registration may involve the deformation folding,which will result in the change of topology during registration.To address these issues,this work has presented an unsupervised image registration method using the free form deformation(FFD)and the symmetry constraint‐based generative adversarial networks(FSGAN).The FSGAN utilises the principle component analysis network‐based structural representations of the reference and float images as the inputs and uses the generator to learn the FFD model parameters,thereby producing two deformation fields.Meanwhile,the FSGAN uses two discriminators to decide whether the bilateral registration have been realised simultaneously.Besides,the symmetry constraint is utilised to construct the loss function,thereby avoiding the deformation folding.Experiments on BrainWeb,high grade gliomas,IXI and LPBA40 show that compared with state‐of‐the‐art methods,the FSGAN provides superior performance in terms of visual comparisons and such quantitative indexes as dice value,target registration error and computational efficiency.

An Improved Jellyfish Algorithm for Multilevel Thresholding of Magnetic Resonance Brain Image Segmentations

Image segmentation is vital when analyzing medical images,especially magnetic resonance(MR)images of the brain.Recently,several image segmentation techniques based on multilevel thresholding have been proposed for medical image segmentation;however,the algorithms become trapped in local minima and have low convergence speeds,particularly as the number of threshold levels increases.Consequently,in this paper,we develop a new multilevel thresholding image segmentation technique based on the jellyfish search algorithm(JSA)(an optimizer).We modify the JSA to prevent descents into local minima,and we accelerate convergence toward optimal solutions.The improvement is achieved by applying two novel strategies:Rankingbased updating and an adaptive method.Ranking-based updating is used to replace undesirable solutions with other solutions generated by a novel updating scheme that improves the qualities of the removed solutions.We develop a new adaptive strategy to exploit the ability of the JSA to find a best-so-far solution;we allow a small amount of exploration to avoid descents into local minima.The two strategies are integrated with the JSA to produce an improved JSA(IJSA)that optimally thresholds brain MR images.To compare the performances of the IJSA and JSA,seven brain MR images were segmented at threshold levels of 3,4,5,6,7,8,10,15,20,25,and 30.IJSA was compared with several other recent image segmentation algorithms,including the improved and standard marine predator algorithms,the modified salp and standard salp swarm algorithms,the equilibrium optimizer,and the standard JSA in terms of fitness,the Structured Similarity Index Metric(SSIM),the peak signal-to-noise ratio(PSNR),the standard deviation(SD),and the Features Similarity Index Metric(FSIM).The experimental outcomes and the Wilcoxon rank-sum test demonstrate the superiority of the proposed algorithm in terms of the FSIM,the PSNR,the objective values,and the SD;in terms of the SSIM,IJSA was competitive with the others.

An Automated Brain Image Analysis System for Brain Cancer using Shearlets

In this paper,an Automated Brain Image Analysis(ABIA)system that classifies the Magnetic Resonance Imaging(MRI)of human brain is presented.The classification of MRI images into normal or low grade or high grade plays a vital role for the early diagnosis.The Non-Subsampled Shearlet Transform(NSST)that captures more visual information than conventional wavelet transforms is employed for feature extraction.As the feature space of NSST is very high,a statistical t-test is applied to select the dominant directional sub-bands at each level of NSST decomposition based on sub-band energies.A combination of features that includes Gray Level Co-occurrence Matrix(GLCM)based features,Histograms of Positive Shearlet Coefficients(HPSC),and Histograms of Negative Shearlet Coefficients(HNSC)are estimated.The combined feature set is utilized in the classification phase where a hybrid approach is designed with three classifiers;k-Nearest Neighbor(kNN),Naive Bayes(NB)and Support Vector Machine(SVM)classifiers.The output of individual trained classifiers for a testing input is hybridized to take a final decision.The quantitative results of ABIA system on Repository of Molecular Brain Neoplasia Data(REMBRANDT)database show the overall improved performance in comparison with a single classifier model with accuracy of 99% for normal/abnormal classification and 98% for low and high risk classification.

Modified Visual Geometric Group Architecture for MRI Brain Image Classification

The advancement of automated medical diagnosis in biomedical engineering has become an important area of research.Image classification is one of the diagnostic approaches that do not require segmentation which can draw quicker inferences.The proposed non-invasive diagnostic support system in this study is considered as an image classification system where the given brain image is classified as normal or abnormal.The ability of deep learning allows a single model for feature extraction as well as classification whereas the rational models require separate models.One of the best models for image localization and classification is the Visual Geometric Group(VGG)model.In this study,an efficient modified VGG architecture for brain image classification is developed using transfer learning.The pooling layer is modified to enhance the classification capability of VGG architecture.Results show that the modified VGG architecture outperforms the conventional VGG architecture with a 5%improvement in classification accuracy using 16 layers on MRI images of the REpository of Molecular BRAin Neoplasia DaTa(REMBRANDT)database.

Classification of Medical Brain Images

Since brain tumors endanger people’s living quality and even their lives, the accuracy of classification becomes more important. Conventional classifying techniques are used to deal with those datasets with characters and numbers. It is difficult, however, to apply them to datasets that include brain images and medical history (alphanumeric data), especially to guarantee the accuracy. For these datasets, this paper combines the knowledge of medical field and improves the traditional decision tree. The new classification algorithm with the direction of the medical knowledge not only adds the interaction with the doctors, but also enhances the quality of classification. The algorithm has been used on real brain CT images and a precious rule has been gained from the experiments. This paper shows that the algorithm works well for real CT data.

De-Noising Brain MRI Images by Mixing Concatenation and Residual Learning(MCR)

Brain magnetic resonance images(MRI)are used to diagnose the different diseases of the brain,such as swelling and tumor detection.The quality of the brain MR images is degraded by different noises,usually salt&pepper and Gaussian noises,which are added to the MR images during the acquisition process.In the presence of these noises,medical experts are facing problems in diagnosing diseases from noisy brain MR images.Therefore,we have proposed a de-noising method by mixing concatenation,and residual deep learning techniques called the MCR de-noising method.Our proposed MCR method is to eliminate salt&pepper and gaussian noises as much as possible from the brain MRI images.The MCR method has been trained and tested on the noise quantity levels 2%to 20%for both salt&pepper and gaussian noise.The experiments have been done on publically available brain MRI image datasets,which can easily be accessible in the experiments and result section.The Structure Similarity Index Measure(SSIM)and Peak Signal-to-Noise Ratio(PSNR)calculate the similarity score between the denoised images by the proposed MCR method and the original clean images.Also,the Mean Squared Error(MSE)measures the error or difference between generated denoised and the original images.The proposed MCR denoising method has a 0.9763 SSIM score,84.3182 PSNR,and 0.0004 MSE for salt&pepper noise;similarly,0.7402 SSIM score,72.7601 PSNR,and 0.0041 MSE for Gaussian noise at the highest level of 20%noise.In the end,we have compared the MCR method with the state-of-the-art de-noising filters such as median and wiener de-noising filters.

An Improved Soft Subspace Clustering Algorithm for Brain MR Image Segmentation

In recent years,the soft subspace clustering algorithm has shown good results for high-dimensional data,which can assign different weights to each cluster class and use weights to measure the contribution of each dimension in various features.The enhanced soft subspace clustering algorithm combines interclass separation and intraclass tightness information,which has strong results for image segmentation,but the clustering algorithm is vulnerable to noisy data and dependence on the initialized clustering center.However,the clustering algorithmis susceptible to the influence of noisydata and reliance on initializedclustering centers andfalls into a local optimum;the clustering effect is poor for brain MR images with unclear boundaries and noise effects.To address these problems,a soft subspace clustering algorithm for brain MR images based on genetic algorithm optimization is proposed,which combines the generalized noise technique,relaxes the equational weight constraint in the objective function as the boundary constraint,and uses a genetic algorithm as a method to optimize the initialized clustering center.The genetic algorithm finds the best clustering center and reduces the algorithm’s dependence on the initial clustering center.The experiment verifies the robustness of the algorithm,as well as the noise immunity in various ways and shows good results on the common dataset and the brain MR images provided by the Changshu First People’s Hospital with specific high accuracy for clinical medicine.

Multi Class Brain Cancer Prediction System Empowered with BRISK Descriptor

Magnetic Resonance Imaging(MRI)is one of the important resources for identifying abnormalities in the human brain.This work proposes an effective Multi-Class Classification(MCC)system using Binary Robust Invariant Scalable Keypoints(BRISK)as texture descriptors for effective classification.Atfirst,the potential Region Of Interests(ROIs)are detected using features from the acceler-ated segment test algorithm.Then,non-maxima suppression is employed in scale space based on the information in the ROIs.The discriminating power of BRISK is examined using three machine learning classifiers such as k-Nearest Neighbour(kNN),Support Vector Machine(SVM)and Random Forest(RF).An MCC sys-tem is developed which classifies the MRI images into normal,glioma,meningio-ma and pituitary.A total of 3264 MRI brain images are employed in this study to evaluate the proposed MCC system.Results show that the average accuracy of the proposed MCC-RF based system is 99.62%with a sensitivity of 99.16%and spe-cificity of 99.75%.The average accuracy of the MCC-kNN system is 93.65%and 97.59%by the MCC-SVM based system.

Image Segmentation of Brain MR Images Using Otsu’s Based Hybrid WCMFO Algorithm

In this study,a novel hybrid Water Cycle Moth-Flame Optimization(WCMFO)algorithm is proposed for multilevel thresholding brain image segmentation in Magnetic Resonance(MR)image slices.WCMFO constitutes a hybrid between the two techniques,comprising the water cycle and moth-flame optimization algorithms.The optimal thresholds are obtained by maximizing the between class variance(Otsu’s function)of the image.To test the performance of threshold searching process,the proposed algorithm has been evaluated on standard benchmark of ten axial T2-weighted brain MR images for image segmentation.The experimental outcomes infer that it produces better optimal threshold values at a greater and quicker convergence rate.In contrast to other state-of-the-art methods,namely Adaptive Wind Driven Optimization(AWDO),Adaptive Bacterial Foraging(ABF)and Particle Swarm Optimization(PSO),the proposed algorithm has been found to be better at producing the best objective function,Peak Signal-to-Noise Ratio(PSNR),Standard Deviation(STD)and lower computational time values.Further,it was observed thatthe segmented image gives greater detail when the threshold level increases.Moreover,the statistical test result confirms that the best and mean values are almost zero and the average difference between best and mean value 1.86 is obtained through the 30 executions of the proposed algorithm.Thus,these images will lead to better segments of gray,white and cerebrospinal fluid that enable better clinical choices and diagnoses using a proposed algorithm.

Early Tumor Diagnosis in Brain MR Images via Deep Convolutional Neural Network Model

Machine learning based image analysis for predicting and diagnosing certain diseases has been entirely trustworthy and even as efficient as a domain expert’s inspection.However,the style of non-transparency functioning by a trained machine learning system poses a more significant impediment for seamless knowledge trajectory,clinical mapping,and delusion tracing.In this proposed study,a deep learning based framework that employs deep convolution neural network(Deep-CNN),by utilizing both clinical presentations and conventional magnetic resonance imaging(MRI)investigations,for diagnosing tumors is explored.This research aims to develop a model that can be used for abnormality detection over MRI data quite efficiently with high accuracy.This research is based on deep learning and Deep-CNN was deployed to examine the MR brain image for tracing the tumor.The system runs on Tensor flow and uses a feature extraction module in DeepCNN to elicit the factors of that part of the image from where underlying issues are identified and subsequently succeeded in prediction of the disease in the MR image.The results of this study showed that our model did not have any adverse effect on classification,achieved higher accuracy than the peers in recent years,and attained good detection outcomes including case of abnormality.In the future work,further improvement can be made by designing models that can drastically reduce the parameter space without affecting classification accuracy.

Study on threshold segmentation of multi-resolution 3D human brain CT image

In order to effectively improve the pathological diagnosis capability and feature resolution of 3D human brain CT images,a threshold segmentation method of multi-resolution 3D human brain CT image based on edge pixel grayscale feature decomposition is proposed in this paper.In this method,first,original 3D human brain image information is collected,and CT image filtering is performed to the collected information through the gradient value decomposition method,and edge contour features of the 3D human brain CT image are extracted.Then,the threshold segmentation method is adopted to segment the regional pixel feature block of the 3D human brain CT image to segment the image into block vectors with high-resolution feature points,and the 3D human brain CT image is reconstructed with the salient feature point as center.Simulation results show that the method proposed in this paper can provide accuracy up to 100%when the signal-to-noise ratio is 0,and with the increase of signal-to-noise ratio,the accuracy provided by this method is stable at 100%.Comparison results show that the threshold segmentation method of multi-resolution 3D human brain CT image based on edge pixel grayscale feature decomposition is signicantly better than traditional methods in pathological feature estimation accuracy,and it effectively improves the rapid pathological diagnosis and positioning recognition abilities to CT images.

Decoding brain responses to pixelized images in the primary visual cortex: implications for visual cortical prostheses

Visual cortical prostheses have the potential to restore partial vision. Still limited by the low-resolution visual percepts provided by visual cortical prostheses, implant wearers can currently only ＂see＂ pixelized images, and how to obtain the specific brain responses to different pixelized images in the primary visual cortex（the implant area） is still unknown. We conducted a functional magnetic resonance imaging experiment on normal human participants to investigate the brain activation patterns in response to 18 different pixelized images. There were 100 voxels in the brain activation pattern that were selected from the primary visual cortex, and voxel size was 4 mm × 4 mm × 4 mm. Multi-voxel pattern analysis was used to test if these 18 different brain activation patterns were specific. We chose a Linear Support Vector Machine（LSVM） as the classifier in this study. The results showed that the classification accuracies of different brain activation patterns were significantly above chance level, which suggests that the classifier can successfully distinguish the brain activation patterns. Our results suggest that the specific brain activation patterns to different pixelized images can be obtained in the primary visual cortex using a 4 mm × 4 mm × 4 mm voxel size and a 100-voxel pattern.

Quantitative ultrasound brain imaging with multiscale deconvolutional waveform inversion

High-resolution images of human brain are critical for monitoring the neurological conditions in a portable and safe manner.Sound speed mapping of brain tissues provides unique information for such a purpose.In addition,it is particularly important for building digital human acoustic models,which form a reference for future ultrasound research.Conventional ultrasound modalities can hardly image the human brain at high spatial resolution inside the skull due to the strong impedance contrast between hard tissue and soft tissue.We carry out numerical experiments to demonstrate that the time-domain waveform inversion technique,originating from the geophysics community,is promising to deliver quantitative images of human brains within the skull at a sub-millimeter level by using ultra-sound signals.The successful implementation of such an approach to brain imaging requires the following items:signals of sub-megahertz frequencies transmitting across the inside of skull,an accurate numerical wave equation solver simulating the wave propagation,and well-designed inversion schemes to reconstruct the physical parameters of targeted model based on the optimization theory.Here we propose an innovative modality of multiscale deconvolutional waveform inversion that improves ultrasound imaging resolution,by evaluating the similarity between synthetic data and observed data through using limited length Wiener filter.We implement the proposed approach to iteratively update the parametric models of the human brain.The quantitative imaging method paves the way for building the accurate acoustic brain model to diagnose associated diseases,in a potentially more portable,more dynamic and safer way than magnetic resonance imaging and x-ray computed tomography.

Appearance of a neural bypass between injured cingulum and brainstem cholinergic nuclei of a patient with traumatic brain injury on follow-up diffusion tensor tractography images

The human brain is known to contain a maximum of eight cholinergic nuclei： the basal forebrain region： the medial septal nucleus （Ch 1）, the vertical nucleus of the diagonal band （Ch 2）, the horizontal limb of the diago- nal band （Ch 3）, and the nucleus basalis of Meynert （Ch 4）; the brainstem： the pedunculopontine nucleus （Ch 5）, the laterodorsal tegmental nucleus （Ch 6）, and the para- bigeminal nucleus （Ch 8）; and the thalamus： the medial habenular nucleus （Ch 7） （Nieuwenhuys et al., 2008; Naidich and Duvernoy, 2009）. The cingulum is the neu- ral tract extending from the orbitofrontal cortex to the medial temporal lobe （Mufson and Pandya, 1984）. The cingulum plays an important role in memory because it is a passage of the medial cholinergic pathway, which pro- vides cholinergic innervations to the cerebral cortex after originating from Ch 1 and Ch 2 as well as Ch 4 （mainly） （Selden et al., 1998; Nieuwenhuys et al., 2008; Hong and lang, 2010）.

Neural stem cell-derived exosomes promote mitochondrial biogenesis and restore abnormal protein distribution in a mouse model of Alzheimer's disease

Mitochondrial dysfunction is a hallmark of Alzheimer’s disease.We previously showed that neural stem cell-derived extracellular vesicles improved mitochondrial function in the cortex of AP P/PS1 mice.Because Alzheimer’s disease affects the entire brain,further research is needed to elucidate alterations in mitochondrial metabolism in the brain as a whole.Here,we investigated the expression of several important mitochondrial biogenesis-related cytokines in multiple brain regions after treatment with neural stem cell-derived exosomes and used a combination of whole brain clearing,immunostaining,and lightsheet imaging to clarify their spatial distribution.Additionally,to clarify whether the sirtuin 1(SIRT1)-related pathway plays a regulatory role in neural stem cell-de rived exosomes interfering with mitochondrial functional changes,we generated a novel nervous system-SIRT1 conditional knoc kout AP P/PS1mouse model.Our findings demonstrate that neural stem cell-de rived exosomes significantly increase SIRT1 levels,enhance the production of mitochondrial biogenesis-related fa ctors,and inhibit astrocyte activation,but do not suppress amyloid-βproduction.Thus,neural stem cell-derived exosomes may be a useful therapeutic strategy for Alzheimer’s disease that activates the SIRT1-PGC1αsignaling pathway and increases NRF1 and COXIV synthesis to improve mitochondrial biogenesis.In addition,we showed that the spatial distribution of mitochondrial biogenesis-related factors is disrupted in Alzheimer’s disease,and that neural stem cell-derived exosome treatment can reverse this effect,indicating that neural stem cell-derived exosomes promote mitochondrial biogenesis.

Watershed-based Image Segmentation with Region Merging and Edge Detection

The clustering technique is used to examine each pixel in the image which assigned to one of the clusters depending on the minimum distance to obtain primary classified image into different intensity regions. A watershed transformation technique is then employes. This includes: gradient of the classified image, dividing the image into markers, checking the Marker Image to see if it has zero points (watershed lines). The watershed lines are then deleted in the Marker Image created by watershed algorithm. A Region Adjacency Graph (RAG) and Region Adjacency Boundary (RAB) are created between two regions from Marker Image. Finally region merging is done according to region average intensity and two edge strengths (T1, T2). The approach of the authors is tested on remote sensing and brain MR medical images. The final segmentation result is one closed boundary per actual region in the image.

Recent progress in the applications of presynaptic dopaminergic positron emission tomography imaging in parkinsonism

Nowadays,presynaptic dopaminergic positron emission tomography,which assesses deficiencies in dopamine synthesis,storage,and transport,is widely utilized for early diagnosis and differential diagnosis of parkinsonism.This review provides a comprehensive summary of the latest developments in the application of presynaptic dopaminergic positron emission tomography imaging in disorders that manifest parkinsonism.We conducted a thorough literature search using reputable databases such as PubMed and Web of Science.Selection criteria involved identifying peer-reviewed articles published within the last 5 years,with emphasis on their relevance to clinical applications.The findings from these studies highlight that presynaptic dopaminergic positron emission tomography has demonstrated potential not only in diagnosing and differentiating various Parkinsonian conditions but also in assessing disease severity and predicting prognosis.Moreover,when employed in conjunction with other imaging modalities and advanced analytical methods,presynaptic dopaminergic positron emission tomography has been validated as a reliable in vivo biomarker.This validation extends to screening and exploring potential neuropathological mechanisms associated with dopaminergic depletion.In summary,the insights gained from interpreting these studies are crucial for enhancing the effectiveness of preclinical investigations and clinical trials,ultimately advancing toward the goals of neuroregeneration in parkinsonian disorders.

Functional brain imaging of gastrointestinal sensation in health and disease

It has since long been known, from everyday experience as well as from animal and human studies, that psychological processes-both affective and cognitive- exert an influence on gastrointestinal sensorimotor function. More specifically, a link between psychological factors and visceral hypersensitivity has been suggested, mainly based on research in functional gastrointestinal disorder patients. However, until recently, the exact nature of this putative relationship remained unclear, mainly due to a lack of non-invasive methods to study the （neurobiological） mechanisms underlying this relationship in non-sleeping humans. As functional brain imaging, introduced in visceral sensory neuroscience some 10 years ago, does provide a method for in vivo study of brain-gut interactions, insight into the neurobiological mechanisms underlying visceral sensation in general and the influence of psychological factors more particularly, has rapidly grown. In this article, an overview of brain imaging evidence on gastrointestinal sensation will be given, with special emphasis on the brain mechanisms underlying the interaction between affective ＆ cognitive processes and visceral sensation. First, the reciprocal neural pathways between the brain and the gut （brain- gut axis） will be briefly outlined, including brain imaging evidence in healthy volunteers. Second, functional brain imaging studies assessing the influence of psychological factors on brain processing of visceral sensation in healthy humans will be discussed in more detail. Finally, brain imaging work investigating differences in brain responses to visceral distension between healthy volunteers and functional gastrointestinal disorder patients will be highlighted.

Non-invasive and low-artifact in vivo brain imaging by using a scanning acoustic-photoacoustic dual mode microscopy

Photoacoustic imaging is a potential candidate for in vivo brain imaging,whereas,its imaging performance could be degraded by inhomogeneous multi-layered media,consisted of scalp and skull.In this work,we propose a low-artifact photoacoustic microscopy(LAPAM)scheme,which combines conventional acoustic-resolution photoacoustic microscopy with scanning acoustic microscopy to suppress the reflection artifacts induced by multi-layers.Based on similar propagation characteristics of photoacoustic signals and ultrasonic echoes,the ultrasonic echoes can be employed as the filters to suppress the reflection artifacts to obtain low-artifact photoacoustic images.Phantom experiment is used to validate the effectiveness of this method.Furthermore,LAPAM is applied for in-vivo imaging mouse brain without removing the scalp and the skull.Experimental results show that the proposed method successfully achieves the low-artifact brain image,which demonstrates the practical applicability of LAPAM.This work might improve the photoacoustic imaging quality in many biomedical applications which involve tissues with complex acoustic properties,such as brain imaging through scalp and skull.

Modulatory effects of acupuncture on brain networks in mild cognitive impairment patients

Functional magnetic resonance imaging has been widely used to investigate the effects of acupuncture on neural activity. However, most functional magnetic resonance imaging studies have focused on acute changes in brain activation induced by acupuncture. Thus, the time course of the therapeutic effects of acupuncture remains unclear. In this study, 32 patients with amnestic mild cognitive impairment were randomly divided into two groups, where they received either Tiaoshen Yizhi acupuncture or sham acupoint acupuncture. The needles were either twirled at Tiaoshen Yizhi acupoints, including Sishencong（EX-HN1）, Yintang（EX-HN3）, Neiguan（PC6）, Taixi（KI3）, Fenglong（ST40）, and Taichong（LR3）, or at related sham acupoints at a depth of approximately 15 mm, an angle of ± 60°, and a rate of approximately 120 times per minute. Acupuncture was conducted for 4 consecutive weeks, five times per week, on weekdays. Resting-state functional magnetic resonance imaging indicated that connections between cognition-related regions such as the insula, dorsolateral prefrontal cortex, hippocampus, thalamus, inferior parietal lobule, and anterior cingulate cortex increased after acupuncture at Tiaoshen Yizhi acupoints. The insula, dorsolateral prefrontal cortex, and hippocampus acted as central brain hubs. Patients in the Tiaoshen Yizhi group exhibited improved cognitive performance after acupuncture. In the sham acupoint acupuncture group, connections between brain regions were dispersed, and we found no differences in cognitive function following the treatment. These results indicate that acupuncture at Tiaoshen Yizhi acupoints can regulate brain networks by increasing connectivity between cognition-related regions, thereby improving cognitive function in patients with mild cognitive impairment.