Precise MRI-histology coregistration of paraffin-embedded tissue with blockface imaging.

Imaging neuroscience (Cambridge, Mass.) Pub Date : 2025-08-08 eCollection Date: 2025-01-01 DOI:10.1162/IMAG.a.106
Yixin Wang, William Ho, Istvan N Huszar, Phillip DiGiacomo, Hossein Moein Taghavi, Lee Tao, Matthew Choi, Nhu Nguyen, Samantha Leventis, David B Camarillo, Philipp Schlömer, Markus Axer, Wei Shao, Mirabela Rusu, Inma Cobos, Jeff Nirschl, Marios Georgiadis, Michael Zeineh
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Abstract

Magnetic resonance imaging (MRI) provides 3D spatial information on tissue, yet it lacks at the molecular level. In contrast, histology provides cellular and molecular information, but it lacks the 3D spatial context and direct in vivo translation. Coregistering the two is key for the 3D embedding of histological details, validating pathological MRI findings, and identifying quantitative imaging biomarkers of neurodegenerative diseases. However, coregistration is challenging due to non-linear distortions of the tissue from histological processing and sectioning leading to microscopic and macroscopic nonlinear 3D deformations between specimen MRI and stained histology sections. To address this, we developed a novel pipeline, named Brewster's Blockface Quantification (BBQ), integrating robust optical approaches with innovative 2D and 3D registration algorithms to achieve precise volumetric alignment of specimen MRI data with histological images. On a variety of brain tissue specimens from distinct anatomical regions and across multiple species, our methodology generated blockface volumes with minimal distortion and artifacts. Using these blockface volumes as an intermediary, we achieve a precise alignment between MRI and histology slides, yielding registration results with an overlapping Dice score of ~90% for whole tissue alignment between MRI and blockface volumes, and >95% for 2D MRI-histology registration. This correlative MRI-histology pipeline with robust 2D and 3D coregistration methods promises to enhance our understanding of neurodegenerative diseases and aid the development of MRI-based disease biomarkers.

石蜡包埋组织与块面成像的精确mri组织学共配准。
磁共振成像(MRI)提供组织的三维空间信息,但在分子水平上缺乏。相比之下,组织学提供细胞和分子信息,但缺乏三维空间背景和直接的体内翻译。这两者的共同注册是组织细节的3D嵌入,验证病理MRI结果和识别神经退行性疾病的定量成像生物标志物的关键。然而,由于组织在组织学处理和切片过程中的非线性扭曲,导致标本MRI和染色组织学切片之间的微观和宏观非线性3D变形,因此共配准是具有挑战性的。为了解决这个问题,我们开发了一种名为Brewster's Blockface Quantification (BBQ)的新型管道,将强大的光学方法与创新的2D和3D配准算法相结合,以实现标本MRI数据与组织学图像的精确体积对齐。在不同解剖区域和不同物种的各种脑组织标本上,我们的方法生成了具有最小畸变和伪影的块面体积。使用这些块面体积作为中介,我们实现了MRI和组织学切片之间的精确对齐,获得了MRI和块面体积之间整个组织对齐的重叠Dice分数为90%的配准结果,2D MRI组织学配准的重叠Dice分数为95%。这种相关的mri组织学管道具有强大的2D和3D共配方法,有望增强我们对神经退行性疾病的理解,并有助于开发基于mri的疾病生物标志物。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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