scholarly journals Flexible annotation atlas of the mouse brain: combining and dividing brain structures of the Allen Brain Atlas while maintaining anatomical hierarchy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Norio Takata ◽  
Nobuhiko Sato ◽  
Yuji Komaki ◽  
Hideyuki Okano ◽  
Kenji F. Tanaka
Keyword(s):  
Mouse Brain ◽  
Brain Structures ◽  
Brain Atlas ◽  
Resting State Functional Connectivity ◽  
Brain Science ◽  
Step Procedure ◽  
Public Resources ◽  
Large Brain ◽  
Magnetic Resonance Imaging Mri ◽  
And Function

AbstractA brain atlas is necessary for analyzing structure and function in neuroimaging research. Although various annotation volumes (AVs) for the mouse brain have been proposed, it is common in magnetic resonance imaging (MRI) of the mouse brain that regions-of-interest (ROIs) for brain structures (nodes) are created arbitrarily according to each researcher’s necessity, leading to inconsistent ROIs among studies. One reason for such a situation is the fact that earlier AVs were fixed, i.e. combination and division of nodes were not implemented. This report presents a pipeline for constructing a flexible annotation atlas (FAA) of the mouse brain by leveraging public resources of the Allen Institute for Brain Science on brain structure, gene expression, and axonal projection. A mere two-step procedure with user-specified, text-based information and Python codes constructs FAA with nodes which can be combined or divided objectively while maintaining anatomical hierarchy of brain structures. Four FAAs with total node count of 4, 101, 866, and 1381 were demonstrated. Unique characteristics of FAA realized analysis of resting-state functional connectivity (FC) across the anatomical hierarchy and among cortical layers, which were thin but large brain structures. FAA can improve the consistency of whole brain ROI definition among laboratories by fulfilling various requests from researchers with its flexibility and reproducibility.

scholarly journals Flexible annotation atlas of the mouse brain: combining and dividing brain structures of the Allen Brain Atlas while maintaining anatomical hierarchy

2020 ◽  
Author(s):  
Norio Takata ◽  
Nobuhiko Sato ◽  
Yuji Komaki ◽  
Hideyuki Okano ◽  
Kenji F. Tanaka
Keyword(s):  
Functional Connectivity ◽  
Mouse Brain ◽  
Resting State ◽  
Brain Structures ◽  
Resting State Fmri ◽  
Brain Atlas ◽  
List Type ◽  
Resting State Functional Connectivity ◽  
Whole Brain ◽  
Link Type

AbstractA brain atlas is necessary for analyzing structure and function in neuroimaging research. Although various annotation volumes (AVs) for the mouse brain have been proposed, it is common in magnetic resonance imaging (MRI) of the mouse brain that regions-of-interest (ROIs) for brain structures (nodes) are created arbitrarily according to each researcher’s necessity, leading to inconsistent ROIs among studies. One reason for such a situation is the fact that earlier AVs were fixed, i.e. combination and division of nodes were not implemented. This report presents a pipeline for constructing a flexible annotation atlas (FAA) of the mouse brain by leveraging public resources of the Allen Institute for Brain Science on brain structure, gene expression, and axonal projection. A mere two-step procedure with user-specified, text-based information and Python codes constructs FAA with nodes which can be combined or divided objectively while maintaining anatomical hierarchy of brain structures. Four FAAs with total node count of 4, 101, 866, and 1,381 were demonstrated. Unique characteristics of FAA realized analysis of resting-state functional connectivity (FC) across the anatomical hierarchy and among cortical layers, which were thin but large brain structures. FAA can improve the consistency of whole brain ROI definition among laboratories by fulfilling various requests from researchers with its flexibility and reproducibility.Highlights–A flexible annotation atlas (FAA) for the mouse brain is proposed.–FAA is expected to improve whole brain ROI-definition consistency among laboratories.–The ROI can be combined or divided objectively while maintaining anatomical hierarchy.–FAA realizes functional connectivity analysis across the anatomical hierarchy.–Codes for FAA reconstruction is available at https://github.com/ntakata/flexible-annotation-atlas–Datasets for resting-state fMRI in awake mice are available at https://openneuro.org/datasets/ds002551

scholarly journals Supervised Learning With Perceptual Similarity for Multimodal Gene Expression Registration of a Mouse Brain Atlas

2021 ◽  
Vol 15 ◽  
Author(s):  
Jan Krepl ◽  
Francesco Casalegno ◽  
Emilie Delattre ◽  
Csaba Erö ◽  
Huanxiang Lu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Supervised Learning ◽  
Mouse Brain ◽  
Brain Structures ◽  
Brain Atlas ◽  
Perceptual Similarity ◽  
Gene Expressions ◽  
Individual Gene ◽  
Staining Techniques ◽  
Quality Maps

The acquisition of high quality maps of gene expression in the rodent brain is of fundamental importance to the neuroscience community. The generation of such datasets relies on registering individual gene expression images to a reference volume, a task encumbered by the diversity of staining techniques employed, and by deformations and artifacts in the soft tissue. Recently, deep learning models have garnered particular interest as a viable alternative to traditional intensity-based algorithms for image registration. In this work, we propose a supervised learning model for general multimodal 2D registration tasks, trained with a perceptual similarity loss on a dataset labeled by a human expert and augmented by synthetic local deformations. We demonstrate the results of our approach on the Allen Mouse Brain Atlas (AMBA), comprising whole brain Nissl and gene expression stains. We show that our framework and design of the loss function result in accurate and smooth predictions. Our model is able to generalize to unseen gene expressions and coronal sections, outperforming traditional intensity-based approaches in aligning complex brain structures.

scholarly journals Enhanced and Unified Anatomical Labeling for a Common Mouse Brain Atlas

2019 ◽  
Author(s):  
Uree Chon ◽  
Daniel J. Vanselow ◽  
Keith C. Cheng ◽  
Yongsoo Kim
Keyword(s):  
Mouse Brain ◽  
Dorsal Striatum ◽  
Spatial Context ◽  
Brain Atlas ◽  
Web Interface ◽  
Cell Type ◽  
Brain Science ◽  
Research Findings ◽  
Cell Type Specific ◽  
The Common

AbstractAnatomical atlases in standard coordinates are necessary for the interpretation and integration of research findings in a common spatial context. However, the two most-used mouse brain atlases, the Franklin and Paxinos (FP) and the common coordinate framework (CCF) from the Allen Institute for Brain Science, have accumulated inconsistencies in anatomical delineations and nomenclature, creating confusion among neuroscientists. To overcome these issues, we adopted the FP labels into the CCF to merge two labels in the single atlas framework. We used cell type specific transgenic mice and an MRI atlas to adjust and further segment our labels. Moreover, new segmentations were added to the dorsal striatum using cortico-striatal connectivity data. Lastly, we have digitized our anatomical labels based on the Allen ontology, created a web-interface for visualization, and provided tools for comprehensive comparisons between the Allen and FP labels. Our open-source labels signify a key step towards a unified mouse brain atlas.

scholarly journals Enhanced and unified anatomical labeling for a common mouse brain atlas

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Uree Chon ◽  
Daniel J. Vanselow ◽  
Keith C. Cheng ◽  
Yongsoo Kim
Keyword(s):  
Mouse Brain ◽  
Dorsal Striatum ◽  
Spatial Context ◽  
Brain Atlas ◽  
Web Interface ◽  
Cell Type ◽  
Brain Science ◽  
Research Findings ◽  
Cell Type Specific ◽  
The Common

Abstract Anatomical atlases in standard coordinates are necessary for the interpretation and integration of research findings in a common spatial context. However, the two most-used mouse brain atlases, the Franklin-Paxinos (FP) and the common coordinate framework (CCF) from the Allen Institute for Brain Science, have accumulated inconsistencies in anatomical delineations and nomenclature, creating confusion among neuroscientists. To overcome these issues, we adopt here the FP labels into the CCF to merge the labels in the single atlas framework. We use cell type-specific transgenic mice and an MRI atlas to adjust and further segment our labels. Moreover, detailed segmentations are added to the dorsal striatum using cortico-striatal connectivity data. Lastly, we digitize our anatomical labels based on the Allen ontology, create a web-interface for visualization, and provide tools for comprehensive comparisons between the CCF and FP labels. Our open-source labels signify a key step towards a unified mouse brain atlas.

scholarly journals Automated high-throughput registration for localizing 3D mouse brain gene expression using ITK

2005 ◽  
Author(s):  
Lydia Ng ◽  
Michael Hawrylycz ◽  
David Haynor
Keyword(s):  
Gene Expression ◽  
Mouse Brain ◽  
High Throughput ◽  
Image Data ◽  
Brain Structures ◽  
Brain Atlas ◽  
The Public ◽  
Brain Gene Expression ◽  
Genome Wide ◽  
Registration Scheme

The Allen Brain Atlas (ABA) project aims to create a cellular-resolution, genome-wide map of gene expression in the adult mouse brain. The resulting in situ hybridization (ISH) image data will be available free-of-charge to the public. Additionally, we are developing an informatics pipeline to support searching of the data by anatomic region and expression level and/or pattern. This paper describes a robust, high-throughput registration scheme to automatically annotate hierarchical brain structures in the ISH imagery.

scholarly journals FUNCTIONAL BRAIN CORRELATES OF RISK FOR MAJOR DEPRESSION IN CHILDREN AND YOUNG ADULTS

2020 ◽  
Vol 4 (11) ◽  
pp. 25-35
Author(s):  
N. Senthilkumar ◽  
R. Thangarajan
Keyword(s):  
Functional Neuroimaging ◽  
Statistical Parametric Mapping ◽  
Brain Structures ◽  
Medical Problem ◽  
Control Group ◽  
Brain Correlates ◽  
Magnetic Resonance Imaging Mri ◽  
Fmri Analysis ◽  
And Function ◽  
The Brain

The brain is arguably the most important organ in the human body. It controls and coordinates actions and reactions, allows us to think and feel, and enables us to have memories and feelings. Three brain structures namely the hippocampus, amygdala and prefrontal cortex help the brain determine what is stressful and how to respond. Depression in teenagers is a very serious medical problem that leads to long-lasting feelings of sadness along with a loss of interest in once enjoyed activities. Neuroimaging is the use of various techniques to either directly or indirectly image the structure and function of the nervous system. Magnetic resonance imaging (MRI) are two in types, viz., structural and functional imaging. Functional neuroimaging has greatly helped in understanding the cognitive functions of the brain and its impact on mental health and human behaviour. This paper describes the different types of neuroimaging techniques and its needed software configurations with statistical parametric mapping. This paper also elaborates the basic operations and MATLAB activities and it compare the at-risk and control group depression imaging fMRI analysis techniques with its snapshots.

scholarly journals Homologous laminar organization of the mouse and human subiculum

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Michael S. Bienkowski ◽  
Farshid Sepehrband ◽  
Nyoman D. Kurniawan ◽  
Jim Stanis ◽  
Laura Korobkova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hippocampal Formation ◽  
Expression Patterns ◽  
Pyramidal Cells ◽  
Brain Structures ◽  
Longitudinal Axis ◽  
Brain Atlas ◽  
Fiber Density ◽  
Laminar Organization ◽  
Hybridization Data

AbstractThe subiculum is the major output component of the hippocampal formation and one of the major brain structures most affected by Alzheimer’s disease. Our previous work revealed a hidden laminar architecture within the mouse subiculum. However, the rotation of the hippocampal longitudinal axis across species makes it unclear how the laminar organization is represented in human subiculum. Using in situ hybridization data from the Allen Human Brain Atlas, we demonstrate that the human subiculum also contains complementary laminar gene expression patterns similar to the mouse. In addition, we provide evidence that the molecular domain boundaries in human subiculum correspond to microstructural differences observed in high resolution MRI and fiber density imaging. Finally, we show both similarities and differences in the gene expression profile of subiculum pyramidal cells within homologous lamina. Overall, we present a new 3D model of the anatomical organization of human subiculum and its evolution from the mouse.

scholarly journals Structural and functional brain asymmetries in the early phases of life: a scoping review

2021 ◽  
Author(s):  
Patrizia Bisiacchi ◽  
Elisa Cainelli
Keyword(s):  
Scoping Review ◽  
Right Hemisphere ◽  
Final Analysis ◽  
Brain Structures ◽  
Large Variability ◽  
Speech Stimuli ◽  
Morphological Asymmetry ◽  
Cerebral Asymmetries ◽  
The Right ◽  
And Function

AbstractAsymmetry characterizes the brain in both structure and function. Anatomical asymmetries explain only a fraction of functional variability in lateralization, with structural and functional asymmetries developing at different periods of life and in different ways. In this work, we perform a scoping review of the cerebral asymmetries in the first brain development phases. We included all English-written studies providing direct evidence of hemispheric asymmetries in full-term neonates, foetuses, and premature infants, both at term post-conception and before. The final analysis included 57 studies. The reviewed literature shows large variability in the used techniques and methodological procedures. Most structural studies investigated the temporal lobe, showing a temporal planum more pronounced on the left than on the right (although not all data agree), a morphological asymmetry already present from the 29th week of gestation. Other brain structures have been poorly investigated, and the results are even more discordant. Unlike data on structural asymmetries, functional data agree with each other, identifying a leftward dominance for speech stimuli and an overall dominance of the right hemisphere in all other functional conditions. This generalized dominance of the right hemisphere for all conditions (except linguistic stimuli) is in line with theories stating that the right hemisphere develops earlier and that its development is less subject to external influences because it sustains functions necessary to survive.

scholarly journals The Brain Resting-State Functional Connectivity Underlying Violence Proneness: Is It a Reliable Marker for Neurocriminology? A Systematic Review

2019 ◽  
Vol 9 (1) ◽  
pp. 11 ◽  
Author(s):  
Ángel Romero-Martínez ◽  
Macarena González ◽  
Marisol Lila ◽  
Enrique Gracia ◽  
Luis Martí-Bonmatí ◽  
...  
Keyword(s):  
Functional Connectivity ◽  
Effective Treatment ◽  
Resting State ◽  
Brain Structures ◽  
Prevention Programs ◽  
Angular Gyrus ◽  
Resting State Functional Connectivity ◽  
Treatment And Prevention ◽  
Reliable Marker ◽  
The Brain

Introduction: There is growing scientific interest in understanding the biological mechanisms affecting and/or underlying violent behaviors in order to develop effective treatment and prevention programs. In recent years, neuroscientific research has tried to demonstrate whether the intrinsic activity within the brain at rest in the absence of any external stimulation (resting-state functional connectivity; RSFC) could be employed as a reliable marker for several cognitive abilities and personality traits that are important in behavior regulation, particularly, proneness to violence. Aims: This review aims to highlight the association between the RSFC among specific brain structures and the predisposition to experiencing anger and/or responding to stressful and distressing situations with anger in several populations. Methods: The scientific literature was reviewed following the PRISMA quality criteria for reviews, using the following digital databases: PubMed, PsycINFO, Psicodoc, and Dialnet. Results: The identification of 181 abstracts and retrieval of 34 full texts led to the inclusion of 17 papers. The results described in our study offer a better understanding of the brain networks that might explain the tendency to experience anger. The majority of the studies highlighted that diminished RSFC between the prefrontal cortex and the amygdala might make people prone to reactive violence, but that it is also necessary to contemplate additional cortical (i.e. insula, gyrus [angular, supramarginal, temporal, fusiform, superior, and middle frontal], anterior and posterior cingulated cortex) and subcortical brain structures (i.e. hippocampus, cerebellum, ventral striatum, and nucleus centralis superior) in order to explain a phenomenon as complex as violence. Moreover, we also described the neural pathways that might underlie proactive violence and feelings of revenge, highlighting the RSFC between the OFC, ventral striatal, angular gyrus, mid-occipital cortex, and cerebellum. Conclusions. The results from this synthesis and critical analysis of RSFC findings in several populations offer guidelines for future research and for developing a more accurate model of proneness to violence, in order to create effective treatment and prevention programs.

scholarly journals Validating Linear Systems Analysis for Laminar fMRI: Temporal Additivity for Stimulus Duration Manipulations

2020 ◽  
Author(s):  
Jelle A. van Dijk ◽  
Alessio Fracasso ◽  
Natalia Petridou ◽  
Serge O. Dumoulin
Keyword(s):  
Systems Theory ◽  
Linear Systems ◽  
Blood Oxygenation ◽  
Ultra High Field ◽  
Feedback Information ◽  
Oxygenation Level ◽  
Early Visual Cortex ◽  
Magnetic Resonance Imaging Mri ◽  
And Function ◽  
The Relationship

AbstractAdvancements in ultra-high field (7 T and higher) magnetic resonance imaging (MRI) scanners have made it possible to investigate both the structure and function of the human brain at a sub-millimeter scale. As neuronal feedforward and feedback information arrives in different layers, sub-millimeter functional MRI has the potential to uncover information processing between cortical micro-circuits across cortical depth, i.e. laminar fMRI. For nearly all conventional fMRI analyses, the main assumption is that the relationship between local neuronal activity and the blood oxygenation level dependent (BOLD) signal adheres to the principles of linear systems theory. For laminar fMRI, however, directional blood pooling across cortical depth stemming from the anatomy of the cortical vasculature, potentially violates these linear system assumptions, thereby complicating analysis and interpretation. Here we assess whether the temporal additivity requirement of linear systems theory holds for laminar fMRI. We measured responses elicited by viewing stimuli presented for different durations and evaluated how well the responses to shorter durations predicted those elicited by longer durations. We find that BOLD response predictions are consistently good predictors for observed responses, across all cortical depths, and in all measured visual field maps (V1, V2, and V3). Our results suggest that the temporal additivity assumption for linear systems theory holds for laminar fMRI. We thus show that the temporal additivity assumption holds across cortical depth for sub-millimeter gradient-echo BOLD fMRI in early visual cortex.

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