Analyzing Thalamocortical Tract-Tracing Experiments in a Common Reference Space.

IF 2.7 4区 医学 Q2 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Neuroinformatics Pub Date : 2024-01-01 Epub Date: 2023-10-21 DOI:10.1007/s12021-023-09644-4
Nestor Timonidis, Mario Rubio-Teves, Carmen Alonso-Martínez, Rembrandt Bakker, María García-Amado, Paul Tiesinga, Francisco Clascá
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Abstract

Current mesoscale connectivity atlases provide limited information about the organization of thalamocortical projections in the mouse brain. Labeling the projections of spatially restricted neuron populations in thalamus can provide a functionally relevant level of connectomic analysis, but these need to be integrated within the same common reference space. Here, we present a pipeline for the segmentation, registration, integration and analysis of multiple tract-tracing experiments. The key difference with other workflows is that the data is transformed to fit the reference template. As a test-case, we investigated the axonal projections and intranuclear arrangement of seven neuronal populations of the ventral posteromedial nucleus of the thalamus (VPM), which we labeled with an anterograde tracer. Their soma positions corresponded, from dorsal to ventral, to cortical representations of the whiskers, nose and mouth. They strongly targeted layer 4, with the majority exclusively targeting one cortical area and the ones in ventrolateral VPM branching to multiple somatosensory areas. We found that our experiments were more topographically precise than similar experiments from the Allen Institute and projections to the primary somatosensory area were in agreement with single-neuron morphological reconstructions from publicly available databases. This pilot study sets the basis for a shared virtual connectivity atlas that could be enriched with additional data for studying the topographical organization of different thalamic nuclei. The pipeline is accessible with only minimal programming skills via a Jupyter Notebook, and offers multiple visualization tools such as cortical flatmaps, subcortical plots and 3D renderings and can be used with custom anatomical delineations.

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在共同参考空间中分析丘脑皮质束追踪实验。
目前的中尺度连接性图谱提供了关于小鼠大脑中丘脑皮质投射组织的有限信息。标记丘脑中空间受限神经元群的投影可以提供功能相关水平的连接组分析,但这些需要整合在同一个公共参考空间内。在这里,我们提供了一个用于多通道跟踪实验的分割、配准、集成和分析的管道。与其他工作流的关键区别在于,数据经过转换以适应参考模板。作为一个测试案例,我们研究了丘脑腹侧后内侧核(VPM)的七个神经元群体的轴突投射和核内排列,我们用顺行示踪剂对其进行了标记。它们的胞体位置从背侧到腹侧与胡须、鼻子和嘴巴的皮层特征相对应。他们强烈针对第4层,大多数只针对一个皮层区域,而腹外侧VPM中的区域则分支到多个体感区域。我们发现,我们的实验在拓扑上比艾伦研究所的类似实验更精确,对主要体感区域的投影与公开数据库中的单神经元形态重建一致。这项试点研究为共享的虚拟连接图谱奠定了基础,该图谱可以丰富额外的数据,用于研究不同丘脑核的地形组织。通过Jupyter笔记本,只需最少的编程技能即可访问该管道,并提供多种可视化工具,如皮质平面图、皮质下图和3D渲染,可用于自定义解剖轮廓。
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来源期刊
Neuroinformatics
Neuroinformatics 医学-计算机:跨学科应用
CiteScore
6.00
自引率
6.70%
发文量
54
审稿时长
3 months
期刊介绍: Neuroinformatics publishes original articles and reviews with an emphasis on data structure and software tools related to analysis, modeling, integration, and sharing in all areas of neuroscience research. The editors particularly invite contributions on: (1) Theory and methodology, including discussions on ontologies, modeling approaches, database design, and meta-analyses; (2) Descriptions of developed databases and software tools, and of the methods for their distribution; (3) Relevant experimental results, such as reports accompanie by the release of massive data sets; (4) Computational simulations of models integrating and organizing complex data; and (5) Neuroengineering approaches, including hardware, robotics, and information theory studies.
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