A Toolkit for Analysis and Visualization of Preclinical Rodent Neuroimaging Experiments

用于临床前啮齿动物神经影像实验分析和可视化的工具包

基本信息

批准号：
10584587
负责人：
Allan James MacKenzie-Graham
金额：
$ 61.25万
依托单位：
UNIVERSITY OF CALIFORNIA LOS ANGELES
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-04-01 至 2027-03-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10584587
关键词：
Address Aging Anatomy Animal Disease Models Animals Area Atlases Automobile Driving Axon Brain Brain Diseases Brain imaging Cell Count Classification Collection Communities Compensation Computer software Computing Methodologies Confocal Microscopy Data Data Analyses Data Set Dedications Dendritic Spines Development Diffusion Diffusion Magnetic Resonance Imaging Documentation Drug or chemical Tissue Distribution Ensure Evaluation Experimental Autoimmune Encephalomyelitis Feedback Functional Magnetic Resonance Imaging Generations Goals Head Human Image Image Analysis Imagery Imaging Device Informatics Investigation Label Licensing Magnetic Resonance Imaging Manuals Maps Measures Methods Microscopy Modality Modeling Multimodal Imaging Multiple Sclerosis Mus Nerve Degeneration Neuroanatomy Neurons Neurosciences Optics Performance Play Process Public Health Reporting Reproducibility Research Research Personnel Resort Resources Rodent Rodent Model Role Scanning Shapes Software Tools Statistical Data Interpretation Structural Models Structure Techniques Testing Tissue Sample Tissues Training Visualization Visualization software Work animal imaging automated segmentation brain tissue community engagement computerized data processing data integration data visualization deep learning experience experimental study graphical user interface human data image processing imaging modality imaging study improved insight interoperability learning strategy microscopic imaging mouse model multidimensional data multimodality nervous system disorder neuroimaging novel open source open source tool optical imaging pre-clinical preclinical study recruit software development statistics tool tractography web site

项目摘要

Project Summary Rodent models remain an important in preclinical studies of brain disease and disorders, as well as basic neuroscience investigations. Rodent imaging data, acquired through techniques including MRI and microscopy, play a critical role in many of these studies. While a great deal of effort has gone into the development of software tools for analyzing MRI of the brain, much of this work has been focused largely on human data, and investigators studying animal models of disease must often resort to adapting these tools for their research. In this project, we will address this need by developing a dedicated suite of open source software tools for processing, analyzing, and visualizing neuroimaging data acquired from rodent brains. These tools will operate on structural diffusion, and functional MRI, as well as optical microscopy of optically cleared serially sectioned tissue samples. These tools will build upon our decades of experience developing software for analyzing human and mouse imaging data, our experience in developing multimodal atlases of the mouse brain, and our active efforts in community engagement and dissemination while applying these resources in neuroscientific studies. Where suitable, we will make use of deep learning methods to produce powerful segmentation and registration networks trained on manually annotated and delineated data. We will also develop easy-to-use interfaces that will facilitate data processing and provide advanced visualization capabilities of datasets with sizes on the order of one terapixel. The project has five specific aims. Aim 1 will develop MRI processing tools, which will include intrasubject co- registration of MRI modalities, extraction of brain tissue from whole head scans, tissue classification, and processing of diffusion and functional MRI data. Aim 2 will develop tools for processing microscopy of cleared and sectioned tissue, with the major goal of aligning these data to a reference atlas generated from either optical microscopy or MRI. These tools will perform cell counting in automatically segmented regions; axon following; dendritic arborization; and dendritic spine counting. In Aim 3, we will develop a statistical analysis toolbox, which will perform statistical inference for neuroimaging measures from microscopy and MRI data analyzed using methods from Aims 1 and 2. In Aim 4, we will integrate the components from Aims 1-3 into an informatics platform that will provide command line tools for easy scripting, interoperability with related imaging tools, and a graphical interface for visualizing data across different scales. In Aim 5, we will perform evaluation of our software tools using two studies: imaging an experimental autoimmune encephalomyelitis (EAE) mouse model of multiple sclerosis; and imaging a mouse model of normative aging. We will also work with a network of small animal imaging experts external to the project, who will use and evaluate the software. These driving projects will serve as testbeds to ensure the practical utility of the software in a research setting, providing direction for the development of our research platform. We will distribute the software freely under an open source license, and provide user support through our website.

项目摘要啮齿动物模型在脑病和疾病的临床前研究中仍然是重要的神经科学调查。啮齿动物成像数据，通过包括MRI和显微镜在内的技术获取，在许多研究中起关键作用。虽然软件开发的努力已大大努力分析大脑MRI的工具，这项工作的大部分都集中在人类数据上，研究人员研究动物模型的疾病模型通常必须诉诸于这些工具进行研究。在这个项目中，我们将通过开发专门的开源软件工具来解决这一需求，以处理，分析，分析，并可视化从啮齿动物大脑中获得的神经影像学数据。这些工具将在结构扩散上运作，和功能性MRI以及光学清除的连续截面组织样品的光学显微镜。这些工具将基于我们数十年来开发用于分析人类和鼠标成像的软件的经验数据，我们在开发鼠标大脑多模式地图集方面的经验以及我们在社区中的积极努力在神经科学研究中应用这些资源时，参与和传播。在合适的地方，我们将利用深度学习方法来产生强大的细分和注册网络。手动注释和描述数据。我们还将开发易于使用的接口，以促进数据处理并提供具有一个尺寸的数据集的高级可视化功能，该数据集的大小按一个Terapixel的顺序。该项目具有五个特定的目标。 AIM 1将开发MRI处理工具，其中包括对象内共同 MRI方式的注册，从整个头部扫描中提取脑组织，组织分类和处理扩散和功能性MRI数据。 AIM 2将开发用于处理清除的显微镜的工具和截面组织，其主要目标是将这些数据与由两种光学产生的参考地图集对齐显微镜或MRI。这些工具将在自动分割区域中执行细胞计数；轴突跟随；树突状树博；和树突状的脊柱计数。在AIM 3中，我们将开发一个统计分析工具箱，该工具箱将对使用显微镜和使用MRI数据进行神经影像措施进行统计推断目标1和2。在AIM 4中，我们将将AIMS 1-3的组件集成到信息平台中这将提供命令行工具，可轻松脚本，与相关成像工具的互操作性以及图形用于可视化数据的接口。在AIM 5中，我们将对我们的软件工具进行评估使用两项研究：成像多重的实验性自身免疫性脑脊髓炎（EAE）小鼠模型硬化;并成像规范衰老的小鼠模型。我们还将与小动物网络合作对项目外部的成像专家，他们将使用和评估软件。这些驾驶项目将服务作为测试台以确保软件在研究环境中的实际实用性，为开发我们的研究平台。我们将根据开源许可自由分发软件，并通过我们的网站提供用户支持。