An optimized approach for extensive segmentation and classification of brain MRI

With the significant contribution in medical image processing for an effective diagnosis of critical health condition in human, there has been evolution of various methods and techniques in abnormality detection and classification process. An insight to the existing approaches highlights that potential amount of work is being carried out in detection and segmentation process but less effective modelling towards classification problems. This manuscript discusses about a simple and robust modelling of a technique that offers comprehensive segmentation process as well as classification process using Artificial Neural Network. Different from any existing approach, the study offers more granularities towards foreground/background indexing with its comprehensive segmentation process while introducing a unique morphological operation along with graph-believe network for ensuring approximately 99% of accuracy of proposed system in contrast to existing learning scheme

Learning task-optimal image registration with applications in localizing structure and function in the cerebral cortex

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2010.Cataloged from PDF version of thesis.Includes bibliographical references (p. 127-141).In medical image analysis, registration is necessary to establish spatial correspondences across two or more images. Registration is rarely the end-goal, but instead, the results of image registration are used in other tasks, such as voxel-based morphometry, functional group analysis, image segmentation and tracking. In this thesis, we argue that the quality of image registration should be evaluated in the context of the application. Consequently, we develop a framework for learning registration cost functions optimized for specific tasks. We demonstrate that by taking into account the application, we not only achieve better registration, but also potentially resolve certain ambiguities and ill-posed nature of image registration. We first develop a generative model for joint registration and segmentation of images. By jointly modeling registration and the application of image segmentation, we demonstrate improvements in parcellation of the cerebral cortex into different structural units. In this thesis, we work with spherical representations of the human cerebral cortex. Consequently, we develop a fast algorithm for registering spherical images. Application to the cortex shows that our algorithm achieves state-of-the-art accuracy, while being an order of magnitude faster than competing diffeomorphic, landmark-free algorithms. Finally, we consider the problem of automatically determining the "free" parameters of registration cost functions.(cont.) Registration is usually formulated as an optimization problem with multiple tunable parameters that are manually set. By introducing a second layer of optimization over and above the usual registration, this thesis provides the first effective approach to optimizing thousands of registration parameters to improve alignment of a new image as measured by an application-specific performance measure. Much previous work has been devoted to developing generic registration algorithms, which are then specialized to particular imaging modalities (e.g., MR), particular imaging targets (e.g., cardiac) and particular post- registration analyses (e.g., segmentation). Our framework provides a principled method for adapting generic algorithms to specific applications. For example, we estimate the optimal weights or cortical folding template of the generic weighted Sum of Squared Differences dissimilarity measure for localizing underlying cytoarchitecture and functional regions of the cerebral cortex. The generality of the framework suggests potential applications to other problems in science and engineering formulated as optimization problems.by B.T. Thomas Yeo.Ph.D

The neural circuit basis of learning

The astounding capacity for learning ranks among the nervous system’s most impressive features. This thesis comprises studies employing varied approaches to improve understanding, at the level of neural circuits, of the brain’s capacity for learning. The first part of the thesis contains investigations of hippocampal circuitry – both theoretical work and experimental work in the mouse Mus musculus – as a model system for declarative memory. To begin, Chapter 2 presents a theory of hippocampal memory storage and retrieval that reflects nonlinear dendritic processing within hippocampal pyramidal neurons. As a prelude to the experimental work that comprises the remainder of this part, Chapter 3 describes an open source software platform that we have developed for analysis of data acquired with in vivo Ca2+ imaging, the main experimental technique used throughout the remainder of this part of the thesis. As a first application of this technique, Chapter 4 characterizes the content of signaling at synapses between GABAergic neurons of the medial septum and interneurons in stratum oriens of hippocampal area CA1. Chapter 5 then combines these techniques with optogenetic, pharmacogenetic, and pharmacological manipulations to uncover inhibitory circuit mechanisms underlying fear learning. The second part of this thesis focuses on the cerebellum-like electrosensory lobe in the weakly electric mormyrid fish Gnathonemus petersii, as a model system for non-declarative memory. In Chapter 6, we study how short-duration EOD motor commands are recoded into a complex temporal basis in the granule cell layer, which can be used to cancel Purkinje-like cell firing to the longer duration and temporally varying EOD-driven sensory responses. In Chapter 7, we consider not only the temporal aspects of the granule cell code, but also the encoding of body position provided from proprioceptive and efference copy sources. Together these studies clarify how the cerebellum-like circuitry of the electrosensory lobe combines information of different forms and then uses this combined information to predict the complex dependence of sensory responses on body position and timing relative to electric organ discharge

New Directions for Contact Integrators

Contact integrators are a family of geometric numerical schemes which guarantee the conservation of the contact structure. In this work we review the construction of both the variational and Hamiltonian versions of these methods. We illustrate some of the advantages of geometric integration in the dissipative setting by focusing on models inspired by recent studies in celestial mechanics and cosmology.Comment: To appear as Chapter 24 in GSI 2021, Springer LNCS 1282

Psr1p interacts with SUN/sad1p and EB1/mal3p to establish the bipolar spindle

Regular Abstracts - Sunday Poster Presentations: no. 382During mitosis, interpolar microtubules from two spindle pole bodies (SPBs) interdigitate to create an antiparallel microtubule array for accommodating numerous regulatory proteins. Among these proteins, the kinesin-5 cut7p/Eg5 is the key player responsible for sliding apart antiparallel microtubules and thus helps in establishing the bipolar spindle. At the onset of mitosis, two SPBs are adjacent to one another with most microtubules running nearly parallel toward the nuclear envelope, creating an unfavorable microtubule configuration for the kinesin-5 kinesins. Therefore, how the cell organizes the antiparallel microtubule array in the first place at mitotic onset remains enigmatic. Here, we show that a novel protein psrp1p localizes to the SPB and plays a key role in organizing the antiparallel microtubule array. The absence of psr1+ leads to a transient monopolar spindle and massive chromosome loss. Further functional characterization demonstrates that psr1p is recruited to the SPB through interaction with the conserved SUN protein sad1p and that psr1p physically interacts with the conserved microtubule plus tip protein mal3p/EB1. These results suggest a model that psr1p serves as a linking protein between sad1p/SUN and mal3p/EB1 to allow microtubule plus ends to be coupled to the SPBs for organization of an antiparallel microtubule array. Thus, we conclude that psr1p is involved in organizing the antiparallel microtubule array in the first place at mitosis onset by interaction with SUN/sad1p and EB1/mal3p, thereby establishing the bipolar spindle.postprin

Removal of antagonistic spindle forces can rescue metaphase spindle length and reduce chromosome segregation defects

Regular Abstracts - Tuesday Poster Presentations: no. 1925Metaphase describes a phase of mitosis where chromosomes are attached and oriented on the bipolar spindle for subsequent segregation at anaphase. In diverse cell types, the metaphase spindle is maintained at a relatively constant length. Metaphase spindle length is proposed to be regulated by a balance of pushing and pulling forces generated by distinct sets of spindle microtubules and their interactions with motors and microtubule-associated proteins (MAPs). Spindle length appears important for chromosome segregation fidelity, as cells with shorter or longer than normal metaphase spindles, generated through deletion or inhibition of individual mitotic motors or MAPs, showed chromosome segregation defects. To test the force balance model of spindle length control and its effect on chromosome segregation, we applied fast microfluidic temperature-control with live-cell imaging to monitor the effect of switching off different combinations of antagonistic forces in the fission yeast metaphase spindle. We show that spindle midzone proteins kinesin-5 cut7p and microtubule bundler ase1p contribute to outward pushing forces, and spindle kinetochore proteins kinesin-8 klp5/6p and dam1p contribute to inward pulling forces. Removing these proteins individually led to aberrant metaphase spindle length and chromosome segregation defects. Removing these proteins in antagonistic combination rescued the defective spindle length and, in some combinations, also partially rescued chromosome segregation defects. Our results stress the importance of proper chromosome-to-microtubule attachment over spindle length regulation for proper chromosome segregation.postprin