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用于二维组织学与磁共振图像配准的开源块面成像系统的设计与评估

Design and evaluation of an open-source block face imaging system for 2D histology to magnetic resonance image registration.

作者信息

Shao Mingzhen, Singh Amanpreet, Johnson Sara, Pessin Alissa, Merrill Robb, Page Ariana, Odéen Henrik, Joshi Sarang, Payne Allison

机构信息

Kahlert School of Computing, Scientific Computing and Imaging Institute, University of Utah, 72 S Central Campus Drive, Salt Lake City, UT, 84112, USA.

Department of Radiology and Imaging Sciences, University of Utah, 729 Arapeen Drive, Salt Lake City, UT, 84109, USA.

出版信息

MethodsX. 2024 Nov 20;13:103062. doi: 10.1016/j.mex.2024.103062. eCollection 2024 Dec.

DOI:10.1016/j.mex.2024.103062
PMID:39687592
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11647474/
Abstract

This study introduces a comprehensive hardware-software framework designed to enhance the quality of block face image capture-an essential intermediary step for registering 2D histology images to ex vivo magnetic resonance (MR) images. A customized camera mounting and lighting system is employed to maintain consistent relative positioning and lighting conditions. Departing from traditional transparent paraffin, dyed paraffin is utilized to enhance contrast for subsequent automatic segmentation. Our software facilitates fully automated data collection and organization, complemented by a real-time Quality Assurance (QA) section to assess the captured image's quality during the sectioning process. The setup is evaluated and validated using rabbit muscle and rat brain which underwent MR-guided focused ultrasound ablations. The customized hardware system establishes a robust image capturing environment. The software with a real-time QA section, enables operators to promptly rectify low-quality captures, thereby preventing data loss. The execution of our proposed framework produces robust registration results for H&E images to ex vivo MR images.•The presented hardware-software framework ensures the uniformity and resilience of the block face image capture process, contributing to a more reliable and efficient registration of 2D histology images to ex vivo MR images.

摘要

本研究介绍了一个全面的硬件 - 软件框架，旨在提高块面图像采集的质量，这是将二维组织学图像与离体磁共振（MR）图像配准的关键中间步骤。采用定制的相机安装和照明系统来保持一致的相对定位和照明条件。与传统透明石蜡不同，使用染色石蜡来增强对比度，以便后续进行自动分割。我们的软件有助于实现完全自动化的数据采集和整理，并辅以实时质量保证（QA）部分，以在切片过程中评估所捕获图像的质量。使用接受了MR引导聚焦超声消融的兔肌肉和大鼠脑对该设置进行评估和验证。定制的硬件系统建立了一个强大的图像捕获环境。带有实时QA部分的软件使操作员能够及时纠正低质量的捕获，从而防止数据丢失。我们提出的框架的执行产生了H&E图像与离体MR图像的稳健配准结果。所展示的硬件 - 软件框架确保了块面图像捕获过程的一致性和弹性，有助于将二维组织学图像更可靠、高效地与离体MR图像配准。

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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e788/11647474/184098d38866/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e788/11647474/53bc7daf9295/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e788/11647474/2904bff61cb8/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e788/11647474/266c8cf18a0e/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e788/11647474/1150bb433c46/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e788/11647474/73e6797eb7fc/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e788/11647474/32bbc33908b6/gr7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e788/11647474/de632e4cabd9/gr8.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e788/11647474/ffda6ba2112c/gr9.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e788/11647474/ff92b20ed42a/gr10.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e788/11647474/17dec0b52ca3/gr11.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e788/11647474/4289c03716b0/gr12.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e788/11647474/25e8f343c02d/gr13.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e788/11647474/3b6755ecfcb0/gr15.jpg

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