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A multi-resolution approach to non-rigid registration of microscopy images

A multi-resolution approach to non-rigid registration of mic...

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IEEE International Symposium on Biomedical Imaging

作者： Kevin S. Lorenz Paul Salama Kenneth W. Dunn Edward J. Delp Video and Image Processing Laboratory School of Electrical and Computer Engineering Purdue University West Lafayette IN USA Department of Electrical and Computer Engineering Indiana University-Purdue University Indianapolis IN USA Division of Nephrology School of Medicine Indiana University Indianapolis IN USA

images collected by intravital microscopy suffer from motion artifacts which necessitates the use of image registration techniques to reconstruct three-dimensional or time series data. In this paper, we describe a multi-resolution/multi-level approach to non-rigid image registration using B-splines with a coarse-to-fine strategy. A control lattice with a coarse grid spacing is used first to account for slowly changing deformations. Next, a control lattice with a finer grid spacing is used to account for more localized and quickly changing deformations. We demonstrate this method on a sequence of images acquired from the lung of a living rat.

关键词： Microscopy image registration Measurement Educational institutions Splines (mathematics) Biomedical imaging Lattices

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High-speed SSVEP-based BCI: Study of various frequency pairs and inter-sources distances

High-speed SSVEP-based BCI: Study of various frequency pairs...

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IEEE EMBS International Conference on Information Technology Applications in Biomedicine (ITAB)

作者： Seyed Navid Resalat Valiallah Saba Fardin Afdideh Ali Heidarnejad Control and Intelligent Processing Center of Excellence School of Electrical and Computer Engineering College of Engineering University of Tehran Tehran Iran AJA University of Medical Sciences Iran Biomedical Signal and Image Processing Laboratory (BiSIPL) School of Electrical Engineering College of Engineering Sharif University of Technology Tehran Iran

Brain computer Interface provides a new communication channel for people who have severe brain injuries. Among different types of BCIs, SSVEP-based one has been focused in recent years. In this type of BCI, selection of twinkling frequency of external visual stimulant and the distance between stimulants (in case of more than one stimulant) is so important. In this work, a SSVEP-based BCI with two external stimulants was designed. In order to determine the best twinkling frequency of stimulants and the best distance between them, the classification accuracy for seven different twinkling frequency pairs and five different stimulants distances was calculated. Two methods for feature extraction step were proposed and the Max classifier was used for classification in order to speed up the computational burden of classification step. Features were extracted from four different segment lengths (sweeps). The results showed that nearly in all sweeps and all inter-sources distances the frequency pair of 10-15 Hz has the highest classification accuracy among other frequency pairs, which is 92% in the inter-sources distance of 24 cm and sweep length of 3 seconds. In addition, the results demonstrated that the method 2 feature extraction technique outperforms the method 1. In addition, for determining the best sweep length, Information Transfer Rate (ITR) was computed and the results indicated that the sweep length of 0.5 second has the highest ITR, so would be practical in real-time applications of BCI.

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Interpolation of Orientation Distribution Functions (ODFs) in Q-ball Imaging

Interpolation of Orientation Distribution Functions (ODFs) i...

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Iranian Conference of Biomedical engineering

作者： Maryam Afzali Emad Fatemizadeh Hamid Soltanian-Zadeh Department of Electrical Engineering Biomedical Signal and Image Processing Laboratory(BiSIPL) Sharif University of Technology Tehran Iran Control and Intelligent Processing Center of Excellence(CIPCE) School of Electrical and Computer Engineering University of Tehran Tehran Iran & Image Analysis Laboratory Radiology Department Henry Ford Health System Detroit Michigan USA

ISBN: (纸本)9781467331289

Diffusion tensor magnetic resonance imaging (DTMRI) is a non-invasive method for investigating the brain white matter structure. It can be used to evaluate fiber bundles in the brain but in the regions with crossing fibers, it fails. To resolve this problem, high angular resolution diffusion imaging (HARDI) with a large number of diffusion encoding directions is used and for reconstruction, the Q-ball method is applied. In this method, orientation distribution function (ODF) of fibers can be calculated. Mathematical models play a crucial role in the field of ODF. For instance, in registering Q-ball images for applications like group analysis or atlas construction, one needs to interpolate ODFs. To this end, principal diffusion directions (PDDs) of each ODF are needed. In this paper, PDDs are defined as vectors that connect the corresponding local maxima of ODF values. Then, ODFs are interpolated using PDDs. The proposed method is evaluated and compared with previous protocols. Experimental results show that the proposed interpolation algorithm preserves the principal direction of fiber tracts without producing any deviations in the tracts. It is shown that changes in the entropy of the interpolated ODFs are almost linear and the bloating effect (blurring of the principal directions) can be removed.

关键词： High angular resolution diffusion imaging (HARDI) Q-ball imaging Orientation distribution function (ODF) Interpolation Principal diffusion direction (PDD)

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Feature-Based Approach to Fuse fMRI and DTI in Epilepsy Using Joint Independent Component Analysis

Feature-Based Approach to Fuse fMRI and DTI in Epilepsy Usin...

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Iranian Conference of Biomedical engineering

作者： Amir Hosein Riazi Hamid Soltanian-Zadeh Gholam-Ali Hossein-Zadeh Control and Intelligent Processing Center of Excellence (CIPCE) School of Electrical and Computer Engineering University College of Engineering University of Tehran Tehran Iran Control and Intelligent Processing Center of Excellence (CIPCE) School of Electrical and Computer Engineering University College of Engineering University of Tehran Tehran Iran & Image Analysis Laboratory Henry Ford Health System Detroit Michigan

ISBN: (纸本)9781467331289

Functional magnetic resonance imaging (fMRI) and structural MRI (sMRI) provide complementary information. Signal processing and statistical models may be used to fuse neuroimaging data across different imaging modalities. In this paper, we present a data driven method for fusing resting state fMRI and diffusion tensor imaging (DTI) data at feature level. The features are amplitude of low frequency fluctuations (ALFF) and fractional anisotropy (FA) extracted from fMRI and DTI datasets of epilepsy and healthy controls, respectively. We discuss main issues associated with group independent component analysis (ICA) as a fusion method. We address our proposed approach for combining two modalities across subjects and back reconstruction of independent components for each group and each subject. Our results indicate that connectivity of regions in default mode network depends on integrity of white matter that connects the two hemispheres (corpus callosum). The proposed signal processing and statistical methods facilitate evaluation of brain connectivity using different modalities. Separate analysis of data modalities does not reveal results of joint analysis.

关键词： FMRI DTI Joint ICA Group Analysis

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Voxel-based treatment prediction of glioblastoma multiform tumor using diffusion tensor imaging

Voxel-based treatment prediction of glioblastoma multiform t...

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IEEE-EMBS International Conference on Biomedical and Health Informatics, BHI 2012. In Conj. with the 8th Int. Symp.on Medical Devices and Biosensors and the 7th Int. Symp. on Biomedical and Health engineering

作者： Sabahi, Hadi Soltanian-Zadeh, Hamid Scarpace, Lisa Mikkelsen, Tom Control and Intelligent Processing Center of Excellence School of Electrical and Computer Engineering University of Tehran Tehran 14395-515 Iran Image Analysis Laboratory Radiology Department Henry Ford Hospital Detroit MI 48202 United States Hermelin Brain Tumor Research Center Neurosurgery Department Henry Ford Health System Detroit MI 48202 United States

ISBN: (纸本)9781457721779

This paper proposes a method to predict the effect of Bevacizumab therapy on Glioblastoma Multiform (GBM) tumors. The prediction is critical for effective treatment planning. The proposed method is developed and evaluated using Diffusion Tensor Imaging (DTI) and post-contrast T1-weighted Magnetic Resonance images (pc-T1-MRI) of 14 patients with GBM tumors gathered before and after the treatment. First, the proposed method calculates diffusion anisotropy indices (DAI) of all voxels in the brain. These diffusion anisotropy indices are Fractional Anisotropy (FA), Mean Diffusivity (MD), Relative Anisotropy (RA), and Volume Ratio (VR). Then, it registers post-treatment pc-T1-MRI and pre-treatment DAI maps to pre-treatment pc-T1-MRI. Next, it uses a thresholding method to segment the tumor from pc-T1-MRI studies. Comparing Gd-enhanced voxels of the pre- and post-treatment pc-T1-MRI, the DAIs of the tumor are labeled based on their response to the treatment. The voxels of 7 patients are randomly selected to train 4 classifiers (ANN, SVM, KNN, and ANFIS) and then all voxels of the other 7 patients are used to test them. For each classifier, four performance measures (sensitivity, specificity, positive predictive value, and accuracy) are calculated. Experimental results show that the ANFIS is more accurate than the other classifiers in predicting the treatment response. © 2012 IEEE.

关键词： Tumors

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3D computational modeling of epiretinal prosthesis stimulation of the ganglion cell

3D computational modeling of epiretinal prosthesis stimulati...

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IEEE EMBS International Conference on Information Technology Applications in Biomedicine (ITAB)

作者： Shabnam Novin Hamid Abrishami Moghaddam Amir Masoud Sodagar Amin Mahnam Research Laboratory for Integrated Circuits and Systems (I CAS) Department of Electrical and Computer Engineering K.N. Toosi University of Technology Tehran Iran Research Laboratory for Machine Vision and Medical Image Processing (MVMIP) Department of Electrical and Computer Engineering K.N. Toosi University of Technology Tehran Iran Ecole Polytechnique de Montreal Montreal QUE Canada Department of Biomedical Engineering School of Engineering University of Isfahan Isfahan Iran

Here we present a modeling for electrical stimulation of retinal ganglion cell. This modeling can be used in epiretinal prosthesis to come up with proper electrical stimulation parameters. The model that we present is a novel one based on the anatomy of the cell. The excitation process of the electrically stimulated retinal cells is simulated in a two step procedure. In the first step the ganglion target cell is represented considering all of its compartments and in a second step the extracellular potential along the neural structure is calculated and finally the membrane voltage response to the applied stimulations is analyzed. A monopolar point electrode was positioned above the cell in an infinite and homogenous environment and the monophasic and biphasic pulses were used as stimulating current. The results show that the responses are in accordance with the values and diagrams of experimental results more than the previous models.

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Single camera-based full depth map estimation using color shifting property of a multiple color-filter aperture

Single camera-based full depth map estimation using color sh...

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International Conference on Acoustics, Speech, and Signal processing (ICASSP)

作者： Seungwon Lee Junghyun Lee Monson H. Hayes Aggelos K. Katsaggelos Joonki Paik Image Processing and Intelligent Systems Laboratory Graduate School of Advanced Imaging Science Multimedia and Film Chung-Ang University Seoul South Korea Department of Electrical Engineering and Computer Science Northwestern University Evanston IL USA

A multiple color-filter aperture (MCA) camera can provide depth information as well as color and intensity in the single-camera framework, where the MCA generates misalignment between color channels depending on the distance of a region-of-interest. In this paper, we present a single camera-based estimation of the full depth map using the color shifting property of the MCA. For estimating the color shifting vectors (CSVs) among red, green, and blue color channels, edges are extracted at each color channel. At the edge, we estimate CSVs using normalized cross correlation combined with color shifting mask map. A full depth map is then generated by depth interpolation using the matting Laplacian method from sparsely estimated CSVs at an edge location. Experimental results show that the proposed method can not only estimate the full depth map but also correct the misaligned color image to generate photorealistic color images using a single camera equipped with MCA.

关键词： image color analysis Cameras Estimation Channel estimation image edge detection Interpolation Apertures

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Hippocampal shape analysis in the Laplace Beltrami feature space for temporal lobe epilepsy diagnosis and lateralization

Hippocampal shape analysis in the Laplace Beltrami feature s...

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IEEE International Symposium on Biomedical Imaging

作者： Rosita Shishegar Ziba Gandomkar Hamid Soltaman-Zadeh Seyed Reza Moghadasi Control and Intelligent Processing Centre of Excellence (CIPCE) School of Electrical and Computer Engineering College of Engineering University of Tehran Tehran Iran Radiology Image Analysis Laboratory Henry Ford Health System Detroit MI USA Department of Mathematics Sharif University of Technology Tehran Iran

Shape analysis plays an important role in many medical imaging studies. One of the recent shape analysis methods uses the Laplace Beltrami operator which is also used in this paper for hippocampal shape comparison. We proposed a feature vector which consists of size measures and shape descriptors based on Laplace Beltrami eigenvalues and eigenfunctions. The aforementioned feature space is utilised for automatic differentiating normal subjects from epileptic patients as well as distinguishing epileptic patients with left temporal lobe epilepsy (LTLE) from patients with right temporal lobe epilepsy (RTLE). Achieved results are diagnostic accuracy of 93% with 95% sensitivity and lateralization accuracy of 86%. The results are comparable to spherical harmonic based shape analysis results and notably improved in comparison to volumetric analysis results.

关键词： Shape Temporal lobe Epilepsy Abstracts Indexes Eigenvalues and eigenfunctions Feature extraction

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Development of a MATLAB-Based Toolbox for Brain computer Interface Applications in Virtual Reality

Development of a MATLAB-Based Toolbox for Brain Computer Int...

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Iranian Conference on electrical engineering

作者： Fardin Afdideh Mohammad Bagher Shamsollahi Seyed Navid Resalat Biomedical Signal and Image Processing Laboratory (BiSPL) School of Electrical Engineering Sharif University of Technology Control and Intelligent Processing Center of Excellence School of Electrical and Computer Engineering College of Engineering University of Tehran

ISBN: (纸本)9781467311496

Brain computer interface (BCI) is a widely used system to assist the disabled and paralyzed people by creating a new communication channel. Among the various methods used in BCI area, motor imagery (MI) is the most popular and the most common one due to its the most natural way of communication for the subject. Some software applications are used to implement BCI systems, and some toolboxes exist for EEG signal processing. In recent years virtual reality (VR) technology has entered into the BCI research area to simulate the real world situations and enhance the subject performance. In this work, a completely MATLAB-based Mi-based BCI system is proposed and implemented in order to navigate into a virtual environment. In addition, a variety of features types were employed to select the best ones in the proposed system with the use of linear discriminant analysis (LDA) classifier through some interactive graphical user interfaces (GUIs). The results show the feasibility of the proposed BCI system in the subject training with or without feedback and even navigation into a virtual home.

关键词： Brain computer Interface (BCI) MATLAB Motor imagery (MI) Virtual Reality (VR) Real-time EEG signal processing

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Voxel-based treatment prediction of glioblastoma multiform tumor using diffusion tensor imaging

Voxel-based treatment prediction of glioblastoma multiform t...

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IEEE EMBS International Conference on Information Technology Applications in Biomedicine (ITAB)

作者： Hadi Sabahi Hamid Soltanian-Zadeh Lisa Scarpace Tom Mikkelsen Control and Intelligent Processing Center of Excellence School of Electrical and Computer Engineering University of Tehran Tehran Iran Image Analysis Laboratory Radiology Department Henry Ford Hospital Detroit MI USA Hermelin Brain Tumor Research Center Neurosurgery Department Henry Ford Health System Detroit MI USA

关键词： Support vector machines Noise Magnetic resonance imaging Sensitivity Tumors Biomedical imaging Artificial neural networks

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