scholarly journals Robust Diffeomorphic Mapping via Geodesically Controlled Active Shapes

2013 ◽  
Vol 2013 ◽  
pp. 1-19 ◽  
Author(s):  
Daniel J. Tward ◽  
Jun Ma ◽  
Michael I. Miller ◽  
Laurent Younes
Keyword(s):  
Numerical Optimization ◽  
Gradient Descent ◽  
Principal Component ◽  
Surface Matching ◽  
Imaging Data ◽  
Matching Algorithm ◽  
Training Samples ◽  
Diffeomorphic Metric Mapping ◽  
Surface Representations ◽  
Landmark Matching

This paper presents recent advances in the use of diffeomorphic active shapes which incorporate the conservation laws of large deformation diffeomorphic metric mapping. The equations of evolution satisfying the conservation law are geodesics under the diffeomorphism metric and therefore termed geodesically controlled diffeomorphic active shapes (GDAS). Our principal application in this paper is on robust diffeomorphic mapping methods based on parameterized surface representations of subcortical template structures. Our parametrization of the GDAS evolution is via the initial momentum representation in the tangent space of the template surface. The dimension of this representation is constrained using principal component analysis generated from training samples. In this work, we seek to use template surfaces to generate segmentations of the hippocampus with three data attachment terms: surface matching, landmark matching, and inside-outside modeling from grayscale T1 MR imaging data. This is formulated as an energy minimization problem, where energy describes shape variability and data attachment accuracy, and we derive a variational solution. A gradient descent strategy is employed in the numerical optimization. For the landmark matching case, we demonstrate the robustness of this algorithm as applied to the workflow of a large neuroanatomical study by comparing to an existing diffeomorphic landmark matching algorithm.

scholarly journals Time lapse synchrotron IR chemical imaging for observing the acclimation of a single algal cell to CO2 treatment

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ghazal Azarfar ◽  
Ebrahim Aboualizadeh ◽  
Simona Ratti ◽  
Camilla Olivieri ◽  
Alessandra Norici ◽  
...  
Keyword(s):  
Algal Cell ◽  
Principal Component ◽  
External Perturbation ◽  
Time Lapse ◽  
Chemical Imaging ◽  
Hyperspectral Data ◽  
Aqueous Environment ◽  
Ir Absorption ◽  
Imaging Data ◽  
Mid Infrared

AbstractAlgae are the main primary producers in aquatic environments and therefore of fundamental importance for the global ecosystem. Mid-infrared (IR) microspectroscopy is a non-invasive tool that allows in principle studying chemical composition on a single-cell level. For a long time, however, mid-infrared (IR) imaging of living algal cells in an aqueous environment has been a challenge due to the strong IR absorption of water. In this study, we employed multi-beam synchrotron radiation to measure time-resolved IR hyperspectral images of individual Thalassiosira weissflogii cells in water in the course of acclimation to an abrupt change of CO2 availability (from 390 to 5000 ppm and vice versa) over 75 min. We used a previously developed algorithm to correct sinusoidal interference fringes from IR hyperspectral imaging data. After preprocessing and fringe correction of the hyperspectral data, principal component analysis (PCA) was performed to assess the spatial distribution of organic pools within the algal cells. Through the analysis of 200,000 spectra, we were able to identify compositional modifications associated with CO2 treatment. PCA revealed changes in the carbohydrate pool (1200–950 cm$$^{-1}$$ - 1 ), lipids (1740, 2852, 2922 cm$$^{-1}$$ - 1 ), and nucleic acid (1160 and 1201 cm$$^{-1}$$ - 1 ) as the major response of exposure to elevated CO2 concentrations. Our results show a local metabolism response to this external perturbation.

scholarly journals Transporting Deformations of Face Emotions in the Shape Spaces: A Comparison of Different Approaches

2021 ◽  
Author(s):  
Paolo Piras ◽  
Valerio Varano ◽  
Maxime Louis ◽  
Antonio Profico ◽  
Stanley Durrleman ◽  
...  
Keyword(s):  
Computer Vision ◽  
Shape Change ◽  
Surface Matching ◽  
Human Face ◽  
Matching Algorithm ◽  
Mathematical Procedure ◽  
Shape Spaces ◽  
Diffeomorphic Deformation ◽  
Common Application ◽  
Scientific Fields

AbstractStudying the changes of shape is a common concern in many scientific fields. We address here two problems: (1) quantifying the deformation between two given shapes and (2) transporting this deformation to morph a third shape. These operations can be done with or without point correspondence, depending on the availability of a surface matching algorithm, and on the type of mathematical procedure adopted. In computer vision, the re-targeting of emotions mapped on faces is a common application. We contrast here four different methods used for transporting the deformation toward a target once it was estimated upon the matching of two shapes. These methods come from very different fields such as computational anatomy, computer vision and biology. We used the large diffeomorphic deformation metric mapping and thin plate spline, in order to estimate deformations in a deformational trajectory of a human face experiencing different emotions. Then we use naive transport (NT), linear shift (LS), direct transport (DT) and fanning scheme (FS) to transport the estimated deformations toward four alien faces constituted by 240 homologous points and identifying a triangulation structure of 416 triangles. We used both local and global criteria for evaluating the performance of the 4 methods, e.g., the maintenance of the original deformation. We found DT, LS and FS very effective in recovering the original deformation while NT fails under several aspects in transporting the shape change. As the best method may differ depending on the application, we recommend carefully testing different methods in order to choose the best one for any specific application.

scholarly journals Fast Nonsupervised 3D Registration of PET and MR Images of the Brain

1994 ◽  
Vol 14 (5) ◽  
pp. 749-762 ◽  
Author(s):  
Jean-François Mangin ◽  
Vincent Frouin ◽  
Isabelle Bloch ◽  
Bernard Bendriem ◽  
Jaime Lopez-Krahe
Keyword(s):  
Three Dimensional ◽  
Magnetic Resonance Images ◽  
Surface Matching ◽  
3D Registration ◽  
Matching Algorithm ◽  
Distance Map ◽  
Brain Surface ◽  
Discrete Surfaces ◽  
Positron Emission ◽  
The Brain

We propose a fully nonsupervised methodology dedicated to the fast registration of positron emission tomography (PET) and magnetic resonance images of the brain. First, discrete representations of the surfaces of interest (head or brain surface) are automatically extracted from both images. Then, a shape-independent surface-matching algorithm gives a rigid body transformation, which allows the transfer of information between both modalities. A three-dimensional (3D) extension of the chamfer-matching principle makes up the core of this surface-matching algorithm. The optimal transformation is inferred from the minimization of a quadratic generalized distance between discrete surfaces, taking into account between-modality differences in the localization of the segmented surfaces. The minimization process is efficiently performed via the precomputation of a 3D distance map. Validation studies using a dedicated brain-shaped phantom have shown that the maximum registration error was of the order of the PET pixel size (2 mm) for the wide variety of tested configurations. The software is routinely used today in a clinical context by the physicians of the Service Hospitalier Frédéric Joliot (>150 registrations performed). The entire registration process requires ∼5 min on a conventional workstation.

scholarly journals Centered Kernel Alignment Enhancing Neural Network Pretraining for MRI-Based Dementia Diagnosis

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
David Cárdenas-Peña ◽  
Diego Collazos-Huertas ◽  
German Castellanos-Dominguez
Keyword(s):  
Neural Network ◽  
Characteristic Curve ◽  
Principal Component ◽  
Imaging Data ◽  
Resonance Imaging ◽  
Dementia Diagnosis ◽  
Target Matrix ◽  
Computer Aided ◽  
Artificial Neural Network Ann ◽  
Aided Diagnosis

Dementia is a growing problem that affects elderly people worldwide. More accurate evaluation of dementia diagnosis can help during the medical examination. Several methods for computer-aided dementia diagnosis have been proposed using resonance imaging scans to discriminate between patients with Alzheimer’s disease (AD) or mild cognitive impairment (MCI) and healthy controls (NC). Nonetheless, the computer-aided diagnosis is especially challenging because of the heterogeneous and intermediate nature of MCI. We address the automated dementia diagnosis by introducing a novel supervised pretraining approach that takes advantage of the artificial neural network (ANN) for complex classification tasks. The proposal initializes an ANN based on linear projections to achieve more discriminating spaces. Such projections are estimated by maximizing the centered kernel alignment criterion that assesses the affinity between the resonance imaging data kernel matrix and the label target matrix. As a result, the performed linear embedding allows accounting for features that contribute the most to the MCI class discrimination. We compare the supervised pretraining approach to two unsupervised initialization methods (autoencoders and Principal Component Analysis) and against the best four performing classification methods of the 2014CADDementiachallenge. As a result, our proposal outperforms all the baselines (7% of classification accuracy and area under the receiver-operating-characteristic curve) at the time it reduces the class biasing.

scholarly journals LAND COVER CLASSIFICATION ALOS AVNIR DATA USING IKONOS AS REFERENCE

2012 ◽  
Vol 9 (1) ◽  
Author(s):  
Bambang Trisakti ◽  
Dini Oktaviana Ambarwati
Keyword(s):  
Land Cover ◽  
Near Infrared ◽  
Good Accuracy ◽  
Confusion Matrix ◽  
Principal Component ◽  
Land Cover Classification ◽  
Accuracy Evaluation ◽  
Post Processing ◽  
Classification Result ◽  
Training Samples

Abstract.  Advanced Land Observation Satellite (ALOS) is a Japanese satellite equipped with 3  sensors  i.e.,  PRISM,  AVNIR,  and  PALSAR.  The  Advanced  Visible  and  Near  Infrared Radiometer (AVNIR) provides multi spectral sensors ranging from Visible to Near Infrared to observe  land  and  coastal  zones.  It  has  10  meter  spatial  resolution,  which  can  be  used  to map  land  cover  with  a  scale  of 1:25000.  The  purpose  of  this  research  was  to  determineclassification  for  land  cover  mapping  using  ALOS  AVNIR  data.  Training  samples  were collected  for  11  land  cover  classes  from  Bromo  volcano  by  visually  referring  to  very  high resolution  data  of  IKONOS  panchromatic  data.  The  training  samples  were  divided  into samples  for  classification  input  and  samples  for  accuracy  evaluation.  Principal  component analysis (PCA) was conducted for AVNIR data, and the generated PCA bands were classified using Maximum Likehood  Enhanced Neighbor method. The classification result was filtered and  re-classed  into  8  classes.  Misclassifications  were  evaluated  and  corrected  in  the  post processing  stage.  The  accuracy  of  classifications  results,  before  and  after  post  processing, were  evaluated  using  confusion  matrix  method.  The  result  showed  that  Maximum Likelihood  Enhanced  Neighbor  classifier  with  post  processing  can  produce  land  cover classification  result  of  AVNIR  data  with  good  accuracy  (total  accuracy  94%  and  kappa statistic 0.92).  ALOS AVNIR has been proven as a potential satellite data to map land cover in the study area with good accuracy.

scholarly journals Preserved representations and decodability of diverse cognitive functions across the cortex, cerebellum, and subcortex

2021 ◽  
Author(s):  
Tomoya Nakai ◽  
Shinji Nishimoto
Keyword(s):  
Cognitive Functions ◽  
Principal Component ◽  
Cognitive Tasks ◽  
Sufficient Information ◽  
The Novel ◽  
Imaging Data ◽  
Functional Representations ◽  
Model Training ◽  
Task Representations ◽  
The Brain

Which part of the brain contributes to our complex cognitive processes? Studies have revealed contributions of the cerebellum and subcortex to higher-order cognitive functions; however it is unclear whether such functional representations are preserved across the cortex, cerebellum, and subcortex. In this study, we used functional magnetic resonance imaging data with 103 cognitive tasks and constructed three voxel-wise encoding and decoding models independently using cortical, cerebellar, and subcortical voxels. Representational similarity analysis revealed that the structure of task representations is preserved across the three brain parts. Principal component analysis visualized distinct organizations of abstract cognitive functions in each part of the cerebellum and subcortex. More than 90% of the cognitive tasks were decodable from the cerebellum and subcortical activities, even for the novel tasks not included in model training. Furthermore, we discovered that the cerebellum and subcortex have sufficient information to reconstruct activity in the cerebral cortex.

scholarly journals PynPoint: a modular pipeline architecture for processing and analysis of high-contrast imaging data

2019 ◽  
Vol 621 ◽  
pp. A59 ◽  
Author(s):  
T. Stolker ◽  
M. J. Bonse ◽  
S. P. Quanz ◽  
A. Amara ◽  
G. Cugno ◽  
...  
Keyword(s):  
Data Reduction ◽  
Direct Detection ◽  
Principal Component ◽  
Monte Carlo Analysis ◽  
Data Sets ◽  
High Contrast ◽  
Imaging Data ◽  
Pipeline Architecture ◽  
Contrast Imaging ◽  
High Contrast Imaging

Context. The direct detection and characterization of planetary and substellar companions at small angular separations is a rapidly advancing field. Dedicated high-contrast imaging instruments deliver unprecedented sensitivity, enabling detailed insights into the atmospheres of young low-mass companions. In addition, improvements in data reduction and point spread function (PSF)-subtraction algorithms are equally relevant for maximizing the scientific yield, both from new and archival data sets. Aims. We aim at developing a generic and modular data-reduction pipeline for processing and analysis of high-contrast imaging data obtained with pupil-stabilized observations. The package should be scalable and robust for future implementations and particularly suitable for the 3–5 μm wavelength range where typically thousands of frames have to be processed and an accurate subtraction of the thermal background emission is critical. Methods. PynPoint is written in Python 2.7 and applies various image-processing techniques, as well as statistical tools for analyzing the data, building on open-source Python packages. The current version of PynPoint has evolved from an earlier version that was developed as a PSF-subtraction tool based on principal component analysis (PCA). Results. The architecture of PynPoint has been redesigned with the core functionalities decoupled from the pipeline modules. Modules have been implemented for dedicated processing and analysis steps, including background subtraction, frame registration, PSF subtraction, photometric and astrometric measurements, and estimation of detection limits. The pipeline package enables end-to-end data reduction of pupil-stabilized data and supports classical dithering and coronagraphic data sets. As an example, we processed archival VLT/NACO L′ and M′ data of β Pic b and reassessed the brightness and position of the planet with a Markov chain Monte Carlo analysis; we also provide a derivation of the photometric error budget.

Contactless Li-Ion Battery Voltage Detection by Using Walabot and Machine Learning

2019 ◽  
Author(s):  
Yanan Wang ◽  
Haoyu Niu ◽  
Tiebiao Zhao ◽  
Xiaozhong Liao ◽  
Lei Dong ◽  
...  
Keyword(s):  
Machine Learning ◽  
Gradient Descent ◽  
Learning Algorithm ◽  
Three Dimensional ◽  
Lithium Ion ◽  
Principal Component ◽  
Stochastic Gradient Descent ◽  
Li Ion Battery ◽  
Linear Discriminant ◽  
Li Ion

Abstract This paper has proposed a contactless voltage classification method for Lithium-ion batteries (LIBs). With a three-dimensional radio-frequency based sensor called Walabot, voltage data of LIBs can be collected in a contactless way. Then three machine learning algorithm, that is, principal component analysis (PCA), linear discriminant analysis (LDA), and stochastic gradient descent (SGD) classifiers, have been employed for data processing. Experiments and comparison have been conducted to verify the proposed method. The colormaps of results and prediction accuracy show that LDA may be most suitable for LIBs voltage classification.

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