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用于三维偏振光成像中神经纤维分布模式的自监督表征学习

Self-supervised representation learning for nerve fiber distribution patterns in 3D-PLI.

作者信息

Oberstrass Alexander, Muenzing Sascha E A, Niu Meiqi, Palomero-Gallagher Nicola, Schiffer Christian, Axer Markus, Amunts Katrin, Dickscheid Timo

机构信息

Institute of Neuroscience and Medicine (INM- 1), Research Centre Jülich, Jülich, Germany.

Helmholtz AI, Research Centre Jülich, Jülich, Germany.

出版信息

Imaging Neurosci (Camb). 2024 Nov 7;2. doi: 10.1162/imag_a_00351. eCollection 2024.


DOI:10.1162/imag_a_00351
PMID:40800494
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12290659/
Abstract

A comprehensive understanding of the organizational principles in the human brain requires, among other factors, well-quantifiable descriptors of nerve fiber architecture. Three-dimensional polarized light imaging (3D-PLI) is a microscopic imaging technique that enables insights into the fine-grained organization of myelinated nerve fibers with high resolution. Descriptors characterizing the fiber architecture observed in 3D-PLI would enable downstream analysis tasks such as multimodal correlation studies, clustering, and mapping. However, best practices for observer-independent characterization of fiber architecture in 3D-PLI are not yet available. To this end, we propose the application of a fully data-driven approach to characterize nerve fiber architecture in 3D-PLI images using self-supervised representation learning. We introduce a(CL-3D) objective that utilizes the spatial neighborhood of texture examples across histological brain sections of a 3D reconstructed volume to sample positive pairs for contrastive learning. We combine this sampling strategy with specifically designed image augmentations to gain robustness to typical variations in 3D-PLI parameter maps. The approach is demonstrated for the 3D reconstructed occipital lobe of a vervet monkey brain. We show that extracted features are highly sensitive to different configurations of nerve fibers, yet robust to variations between consecutive brain sections arising from histological processing. We demonstrate their practical applicability for retrieving clusters of homogeneous fiber architecture, performing classification with minimal annotations and query-based retrieval of characteristic components of fiber architecture such as U-fibers.

摘要

全面理解人类大脑中的组织原则,除其他因素外,还需要对神经纤维结构进行可量化的描述。三维偏振光成像(3D-PLI)是一种显微成像技术,能够高分辨率洞察有髓神经纤维的精细组织结构。表征在3D-PLI中观察到的纤维结构的描述符将有助于进行下游分析任务,如多模态相关性研究、聚类和映射。然而,目前尚无用于在3D-PLI中对纤维结构进行独立于观察者的表征的最佳实践方法。为此,我们提出应用一种完全数据驱动的方法,使用自监督表示学习来表征3D-PLI图像中的神经纤维结构。我们引入了一个(CL-3D)目标,该目标利用3D重建体积的组织学脑切片中纹理示例的空间邻域来采样正样本对进行对比学习。我们将这种采样策略与专门设计的图像增强相结合,以增强对3D-PLI参数图中典型变化的鲁棒性。该方法在一只黑长尾猴大脑的3D重建枕叶上得到了验证。我们表明,提取的特征对神经纤维的不同配置高度敏感,但对组织学处理导致的连续脑切片之间的变化具有鲁棒性。我们展示了它们在检索同质纤维结构簇、使用最少注释进行分类以及基于查询检索纤维结构的特征组件(如U形纤维)方面的实际适用性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/17e515891a35/imag_a_00351_fig14.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/2cb29eaaf112/imag_a_00351_fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/2a46a0261334/imag_a_00351_fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/b048894ed6bd/imag_a_00351_fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/b9ba70a15242/imag_a_00351_fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/d65fd224af3e/imag_a_00351_fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/1d9c2e77d581/imag_a_00351_fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/ca92936163db/imag_a_00351_fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/ce67e979ee07/imag_a_00351_fig8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/b680d50a7f19/imag_a_00351_fig9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/87a037623bc5/imag_a_00351_fig10.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/415ed7015a73/imag_a_00351_fig11.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/bf495d427922/imag_a_00351_fig12.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/92f166c47b40/imag_a_00351_fig13.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/17e515891a35/imag_a_00351_fig14.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/2cb29eaaf112/imag_a_00351_fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/2a46a0261334/imag_a_00351_fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/b048894ed6bd/imag_a_00351_fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/b9ba70a15242/imag_a_00351_fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/d65fd224af3e/imag_a_00351_fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/1d9c2e77d581/imag_a_00351_fig6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/ca92936163db/imag_a_00351_fig7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/ce67e979ee07/imag_a_00351_fig8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/b680d50a7f19/imag_a_00351_fig9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/87a037623bc5/imag_a_00351_fig10.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/415ed7015a73/imag_a_00351_fig11.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/bf495d427922/imag_a_00351_fig12.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/92f166c47b40/imag_a_00351_fig13.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eff3/12290659/17e515891a35/imag_a_00351_fig14.jpg

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An open resource combining multi-contrast MRI and microscopy in the macaque brain.

Nat Commun. 2023-7-19

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Science. 2022-11-4

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Nat Biomed Eng. 2022-12

[4]
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Med Image Anal. 2022-7

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Sci Rep. 2022-3-14

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