Computational and mathematical methods in brain atlasing

Nowinski, Wiesław L.

doi:10.1177/1971400917740362

Cited by 8 publications

(6 citation statements)

References 104 publications

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“…Human brain atlases have been tremendously developed in terms of content, functionality, and applications [8]. There are numerous methods and tools for the construction of brain atlases, and they have extensively been discussed and reviewed earlier [13,58]. Several atlases have been built for the human whole brain from neuroimaging, such as Digital Anatomist [14], atlas for education, segmentation, and surgical planning [15], VOXEL-MAN [16], and The Human Brain, Head and Neck in 2953 Pieces (the 2953 atlas) [17].…”

Section: Discussionmentioning

confidence: 99%

Toward Morphologic Atlasing of the Human Whole Brain at the Nanoscale

Nowinski

2023

BDCC

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Although no dataset at the nanoscale for the entire human brain has yet been acquired and neither a nanoscale human whole brain atlas has been constructed, tremendous progress in neuroimaging and high-performance computing makes them feasible in the non-distant future. To construct the human whole brain nanoscale atlas, there are several challenges, and here, we address two, i.e., the morphology modeling of the brain at the nanoscale and designing of a nanoscale brain atlas. A new nanoscale neuronal format is introduced to describe data necessary and sufficient to model the entire human brain at the nanoscale, enabling calculations of the synaptome and connectome. The design of the nanoscale brain atlas covers design principles, content, architecture, navigation, functionality, and user interface. Three novel design principles are introduced supporting navigation, exploration, and calculations, namely, a gross neuroanatomy-guided navigation of micro/nanoscale neuroanatomy; a movable and zoomable sampling volume of interest for navigation and exploration; and a nanoscale data processing in a parallel-pipeline mode exploiting parallelism resulting from the decomposition of gross neuroanatomy parcellated into structures and regions as well as nano neuroanatomy decomposed into neurons and synapses, enabling the distributed construction and continual enhancement of the nanoscale atlas. Numerous applications of this atlas can be contemplated ranging from proofreading and continual multi-site extension to exploration, morphometric and network-related analyses, and knowledge discovery. To my best knowledge, this is the first proposed neuronal morphology nanoscale model and the first attempt to design a human whole brain atlas at the nanoscale.

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Section: Discussionmentioning

confidence: 99%

Toward Morphologic Atlasing of the Human Whole Brain at the Nanoscale

Nowinski

2023

BDCC

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“…Atlas-to-scan mapping (or spatial registration) methods, producing an individualized atlas, have been reviewed in (Nowinski 2017b ), and any known methods can be employed in the stroke applications discussed below. In our stroke prototypes developed we used our own atlas-to-scan mapping methods because they are very fast (of a few seconds), automatic with no parameter setting, conceptually simple (also for the clinicians to understand the underlying processing), and easier to us to modify, extend and integrate them into stroke applications.…”

Section: Methods Materials and Applicationsmentioning

confidence: 99%

Human Brain Atlases in Stroke Management

Nowinski

2020

Neuroinform

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Stroke is a leading cause of death and a major cause of permanent disability. Its management is demanding because of variety of protocols, imaging modalities, pulse sequences, hemodynamic maps, criteria for treatment, and time constraints to promptly evaluate and treat. To cope with some of these issues, we propose novel, patented solutions in stroke management by employing multiple brain atlases for diagnosis, treatment, and prediction. Numerous and diverse CT and MRI scans are used: ARIC cohort, ischemic and hemorrhagic stroke CT cases, MRI cases with multiple pulse sequences, and 128 stroke CT patients, each with 170 variables and one year follow-up. The method employs brain atlases of anatomy, blood supply territories, and probabilistic stroke atlas. It rapidly maps an atlas to scan and provides atlas-assisted scan processing. Atlas-to-scan mapping is application-dependent and handles three types of regions of interest (ROIs): atlas-defined ROIs, atlas-quantified ROIs, and ROIs creating an atlas. An ROI is defined by atlas-guided anatomy or scan-derived pathology. The atlas defines ROI or quantifies it. A brain atlas potential has been illustrated in four atlas-assisted applications for stroke occurrence prediction and screening, rapid and automatic stroke diagnosis in emergency room, quantitative decision support in thrombolysis in ischemic stroke, and stroke outcome prediction and treatment assessment. The use of brain atlases in stroke has many potential advantages, including rapid processing, automated and robust handling, wide range of applications, and quantitative assessment. Further work is needed to enhance the developed prototypes, clinically validate proposed solutions, and introduce them to clinical practice.

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“…The design, development, and validation of a human brain atlas is a painstaking and time-consuming process that requires high attention to detail. The design principles of a holistic and reference brain atlas are formulated in [105], computational methods employed in brain atlas development are addressed in [106], visualization and interac-tion are discussed in [107], and a user-centric and application-balanced architecture cum implementation of a reference human brain atlas is proposed in [13].…”

Section: Creation Of Human Brain Maps and Atlasesmentioning

confidence: 99%

Advances in Neuroanatomy through Brain Atlasing

Nowinski¹

2023

Anatomia

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Human brain atlases are tools to gather, present, use, and discover knowledge about the human brain. The developments in brain atlases parallel the advances in neuroanatomy. The brain atlas evolution has been from hand-drawn cortical maps to print atlases to digital platforms which, thanks to tremendous advancements in acquisition techniques and computing, has enabled progress in neuroanatomy from gross (macro) to meso-, micro-, and nano-neuroanatomy. Advances in neuroanatomy have been feasible because of introducing new modalities, from the initial cadaveric dissections, morphology, light microscopy imaging and neuroelectrophysiology to non-invasive in vivo imaging, connectivity, electron microscopy imaging, genomics, proteomics, transcriptomics, and epigenomics. Presently, large and long-term brain projects along with big data drive the development in micro- and nano-neuroanatomy. The goal of this work is to address the relationship between neuroanatomy and human brain atlases and, particularly, the impact of these atlases on the understanding, presentation, and advancement of neuroanatomy. To better illustrate this relationship, a brief outline on the evolution of the human brain atlas concept, creation of brain atlases, atlas-based applications, and future brain-related developments is also presented. In conclusion, human brain atlases are excellent means to represent, present, disseminate, and support neuroanatomy.

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Computational and mathematical methods in brain atlasing

Cited by 8 publications

References 104 publications

Toward Morphologic Atlasing of the Human Whole Brain at the Nanoscale

Toward Morphologic Atlasing of the Human Whole Brain at the Nanoscale

Human Brain Atlases in Stroke Management

Advances in Neuroanatomy through Brain Atlasing

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