Activity dynamics lead to diverse structural plasticity at single dendritic spines

Synapses are the sites at which learning is proposed to occur through changes in the strength of neuronal connections. Utilizing 2-photon mediated glutamate uncaging and imaging, the size of a dendritic spine and the amount of current which that synapse conducts has been shown to be linearly correlated and thus allows for structural changes in spine volumes to serve as a proxy for measuring plasticity. In order to e ciently and accurately quantify such structural dynamics, we developed a Matlab-based toolbox, named SpineS, which automatically analyses dendritic spine volume changes more rapidly, and with greater precision, based on a learned library of representative images. Regularly spaced stimulations, such as the high- and low-frequency patterns traditionally used to induce plasticity in the hippocampus, are not the most common forms of activity which occur in the brain.(...)TÜBiTAK_Grant Nº 113E60

AR-PCA-HMM approach for sensorimotor task classification in EEG-based brain-computer interfaces

We propose an approach based on Hidden Markov models (HMMs) combined with principal component analysis (PCA) for classification of four-class single trial motor imagery EEG data for brain computer interfacing (BCI) purposes. We extract autoregressive (AR) parameters from EEG data and use PCA to decrease the number of features for better training of HMMs. We present experimental results demonstrating the improvements provided by our approach over an existing HMM-based EEG single trial classification approach as well as over state-of-the-art classification methods

Saklı Markov modelleri ve boyut indirgemeye dayalı bir beyin-bilgisayar arayüzü algoritması (A brain-computer interface algorithm based on hidden Markov models and dimensionality reduction)

Beyin-bilgisayar arayüzleri (BBA) bağlamında zihinde hareket canlandırma sürecinde toplanan EEG verilerinin sınıflandırılması problemini ele alıyoruz. Saklı Markov Modelleri (HMM) üzerine kurulu bir yaklaşım öneriyoruz. Yaklaşımımız özbağlanımlı parametrelere dayalı öznitelikleri temel bileşen analizi (PCA) tabanlı boyut indirgeme ile birlikte kullanması bakımından mevcut HMM yöntemlerinden farklıdır. Yaklaşımımızın etkinliğini genel kullanıma açık bir veri kümesi ve kendi laboratuvarımızda topladığımız veriler üzerinde, iki ve dört sınıflı problemlerdeki deneysel sonuçlar ile gösteriyoruz. -- (We consider the problem of motor imagery EEG data classification within the context of brain-computer interfaces. We propose an approach based on Hidden Markov models (HMMs). Our approach is different from existing HMM-based techniques in that it uses features based on autoregressive parameters together with dimensionality reduction based on principal component analysis (PCA). We demonstrate the effectiveness of our approach through experimental results for two and four-class problems based on a public dataset, as well as data collected in our laboratory.

Combining nonparametric spatial context priors with nonparametric shape priors for dendritic spine segmentation in 2-photon microscopy images

Data driven segmentation is an important initial step of shape prior-based segmentation methods since it is assumed that the data term brings a curve to a plausible level so that shape and data terms can then work together to produce better segmentations. When purely data driven segmentation produces poor results, the final segmentation is generally affected adversely. One challenge faced by many existing data terms is due to the fact that they consider only pixel intensities to decide whether to assign a pixel to the foreground or to the background region. When the distributions of the foreground and background pixel intensities have significant overlap, such data terms become ineffective, as they produce uncertain results for many pixels in a test image. In such cases, using prior information about the spatial context of the object to be segmented together with the data term can bring a curve to a plausible stage, which would then serve as a good initial point to launch shape-based segmentation. In this paper, we propose a new segmentation approach that combines nonparametric context priors with a learned-intensity-based data term and nonparametric shape priors. We perform experiments for dendritic spine segmentation in both 2D and 3D 2-photon microscopy images. The experimental results demonstrate that using spatial context priors leads to significant improvements.Comment: IEEE International Symposium on Biomedical Imagin

Factors that affect classification performance in EEG based brain-computer interfaces

In this paper, some of the factors that affect classification performance of EEG based Brain-Computer Interfaces (BCI) is studied. Study is specified on P300 speller system which is also an EEG based BCI system. P300 is a physiological signal that represents a response of brain to a given stimulus which occurs right 300ms after the stimulus onset. When this signal occurs, it changes the continuous EEG some micro volts. Since this is not a very distinguished change, some other physiological signals (movement of muscles and heart, blinking or other neural activities) may distort this signal. In order to understand if there is really a P300 component in the signal, consecutive P300 epochs are averaged over trials. In this study, we have been tried two different multi channel data handling methods with two different frequency windows. Resulted data have been classified using Support Vector Machines (SVM). It has been shown that proposed method has a better classification performance

A watershed and active contours based method for dendritic spine segmentation in 2-photon microscopy images (2-Foton mikroskopi görüntülerindeki dendritik dikenlerin bölütlenmesi için watershed ve etkin çevritlere dayalı bir yöntem)

Analysing morphological and volumetric properties of dendritic spines from 2-photon microscopy images has been of interest to neuroscientists in recent years. Developing robust and reliable tools for automatic analysis depends on the segmentation quality. In this paper, we propose a new segmentation algorithm for dendritic spine segmentation based on watershed and active contour methods. First, our proposed method coarsely segments the dendritic spine area using the watershed algorithm. Then, these results are further refined using a region-based active contour approach. We compare our results and the results of existing methods in the literature to manual delineations of a domain expert. Experimental results demonstrate that our proposed method produces more accurate results than the existing algorithms proposed for dendritic spine segmentation

Automatic dendritic spine detection using multiscale dot enhancement filters and sift features

Statistical characterization of morphological changes of dendritic spines is becoming of crucial interest in the field of neurobiology. Automatic detection and segmentation of dendritic spines promises significant reductions on the time spent by the scientists and reduces the subjectivity concerns. In this paper, we present two approaches for automated detection of dendritic spines in 2-photon laser scanning microscopy (2pLSM) images. The first method combines the idea of dot enhancement filters with information from the dendritic skeleton. The second method learns an SVM classifier by utilizing some pre-labeled SIFT feature descriptors and uses the classifier to detect dendritic spines in new images. For the segmentation of detected spines, we employ a watershed-variational segmentation algorithm. We evaluate the proposed approaches by comparing with manual segmentations of domain experts and the results of a noncommercial software, NeuronIQ. Our methods produce promising detection rate with high segmentation accuracy thus can serve as a useful tool for spine analysis

A joint classification and segmentation approach for dendritic spine segmentation in 2-photon microscopy images

Shape priors have been successfully used in challenging biomedical imaging problems. However when the shape distribution involves multiple shape classes, leading to a multimodal shape density, effective use of shape priors in segmentation becomes more challenging. In such scenarios, knowing the class of the shape can aid the segmentation process, which is of course unknown a priori. In this paper, we propose a joint classification and segmentation approach for dendritic spine segmentation which infers the class of the spine during segmentation and adapts the remaining segmentation process accordingly. We evaluate our proposed approach on 2-photon microscopy images containing dendritic spines and compare its performance quantitatively to an existing approach based on nonparametric shape priors. Both visual and quantitative results demonstrate the effectiveness of our approach in dendritic spine segmentation

On comparison of manifold learning techniques for dendritic spine classification

Dendritic spines are one of the key functional components of neurons. Their morphological changes are correlated with neuronal activity. Neuroscientists study spine shape variations to understand their relation with neuronal activity. Currently this analysis performed manually, the availability of reliable automated tools would assist neuroscientists and accelerate this research. Previously, morphological features based spine analysis has been performed and reported in the literature. In this paper, we explore the idea of using and comparing manifold learning techniques for classifying spine shapes. We start with automatically segmented data and construct our feature vector by stacking and concatenating the columns of images. Further, we apply unsupervised manifold learning algorithms and compare their performance in the context of dendritic spine classification. We achieved 85.95% accuracy on a dataset of 242 automatically segmented mushroom and stubby spines. We also observed that ISOMAP implicitly computes prominent features suitable for classification purposes

Dendritic spine shape classification from two-photon microscopy images (Dendritik diken şekillerinin iki foton mikroskopi görüntüleri kullanılarak sınıflandırılması)

Functional properties of a neuron are coupled with its morphology, particularly the morphology of dendritic spines. Spine volume has been used as the primary morphological parameter in order the characterize the structure and function coupling. However, this reductionist approach neglects the rich shape repertoire of dendritic spines. First step to incorporate spine shape information into functional coupling is classifying main spine shapes that were proposed in the literature. Due to the lack of reliable and fully automatic tools to analyze the morphology of the spines, such analysis is often performed manually, which is a laborious and time intensive task and prone to subjectivity. In this paper we present an automated approach to extract features using basic image processing techniques, and classify spines into mushroom or stubby by applying machine learning algorithms. Out of 50 manually segmented mushroom and stubby spines, Support Vector Machine was able to classify 98% of the spines correctly