arXiv subjects

Juan Eugenio Iglesias

Publications and source records attributed to Juan Eugenio Iglesias.

75 records · Page 5Linked to original sources

arXiv2017

Part-to-whole Registration of Histology and MRI using Shape Elements

Image registration between histology and magnetic resonance imaging (MRI) is a challenging task due to differences in structural content and contrast. Too thick and wide specimens cannot be processed all at once and must be cut into smaller pieces. This dramatically increases the complexity of the problem, since each piece should be individually and manually pre-aligned. To the best of our knowledge, no automatic method can reliably locate such piece of tissue within its respective whole in the MRI slice, and align it without any prior information. We propose here a novel automatic approach to the joint problem of multimodal registration between histology and MRI, when only a fraction of tissue is available from histology. The approach relies on the representation of images using their level lines so as to reach contrast invariance. Shape elements obtained via the extraction of bitangents are encoded in a projective-invariant manner, which permits the identification of common pieces of curves between two images. We evaluated the approach on human brain histology and compared resulting alignments against manually annotated ground truths. Considering the complexity of the brain folding patterns, preliminary results are promising and suggest the use of characteristic and meaningful shape elements for improved robustness and efficiency.

cs.CV↗

arXiv2017

Sparsity Enables Estimation of both Subcortical and Cortical Activity from MEG and EEG

Subcortical structures play a critical role in brain function. However, options for assessing electrophysiological activity in these structures are limited. Electromagnetic fields generated by neuronal activity in subcortical structures can be recorded non-invasively using magnetoencephalography (MEG) and electroencephalography (EEG). However, these subcortical signals are much weaker than those due to cortical activity. In addition, we show here that it is difficult to resolve subcortical sources, because distributed cortical activity can explain the MEG and EEG patterns due to deep sources. We then demonstrate that if the cortical activity can be assumed to be spatially sparse, both cortical and subcortical sources can be resolved with M/EEG. Building on this insight, we develop a novel hierarchical sparse inverse solution for M/EEG. We assess the performance of this algorithm on realistic simulations and auditory evoked response data and show that thalamic and brainstem sources can be correctly estimated in the presence of cortical activity. Our analysis and method suggest new opportunities and offer practical tools for characterizing electrophysiological activity in the subcortical structures of the human brain.

q-bio.QM↗

arXiv2015

Multi-Atlas Segmentation of Biomedical Images: A Survey

Multi-atlas segmentation (MAS), first introduced and popularized by the pioneering work of Rohlfing, Brandt, Menzel and Maurer Jr (2004), Klein, Mensh, Ghosh, Tourville and Hirsch (2005), and Heckemann, Hajnal, Aljabar, Rueckert and Hammers (2006), is becoming one of the most widely-used and successful image segmentation techniques in biomedical applications. By manipulating and utilizing the entire dataset of "atlases" (training images that have been previously labeled, e.g., manually by an expert), rather than some model-based average representation, MAS has the flexibility to better capture anatomical variation, thus offering superior segmentation accuracy. This benefit, however, typically comes at a high computational cost. Recent advancements in computer hardware and image processing software have been instrumental in addressing this challenge and facilitated the wide adoption of MAS. Today, MAS has come a long way and the approach includes a wide array of sophisticated algorithms that employ ideas from machine learning, probabilistic modeling, optimization, and computer vision, among other fields. This paper presents a survey of published MAS algorithms and studies that have applied these methods to various biomedical problems. In writing this survey, we have three distinct aims. Our primary goal is to document how MAS was originally conceived, later evolved, and now relates to alternative methods. Second, this paper is intended to be a detailed reference of past research activity in MAS, which now spans over a decade (2003 - 2014) and entails novel methodological developments and application-specific solutions. Finally, our goal is to also present a perspective on the future of MAS, which, we believe, will be one of the dominant approaches in biomedical image segmentation.

cs.CV↗