Air artifact suppression in phase contrast micro-CT using conditional generative adversarial networks.

IF 2.5 3区 物理与天体物理
Journal of Synchrotron Radiation Pub Date : 2025-05-01 Epub Date: 2025-03-26 DOI:10.1107/S1600577525001511
Md Motiur Rahman Sagar, Lorenzo D'Amico, Elena Longo, Irma Mahmutovic Persson, Richard Deyhle, Giuliana Tromba, Sam Bayat, Frauke Alves, Christian Dullin
{"title":"Air artifact suppression in phase contrast micro-CT using conditional generative adversarial networks.","authors":"Md Motiur Rahman Sagar, Lorenzo D'Amico, Elena Longo, Irma Mahmutovic Persson, Richard Deyhle, Giuliana Tromba, Sam Bayat, Frauke Alves, Christian Dullin","doi":"10.1107/S1600577525001511","DOIUrl":null,"url":null,"abstract":"<p><p>3D virtual histology of formalin-fixed and paraffin-embedded (FFPE) tissue by means of phase contrast micro-computed tomography (micro-CT) is an increasingly popular technique, as it allows the 3D architecture of the tissue to be addressed without the need of additional heavy ion based staining approaches. Therefore, it can be applied on archived standard FFPE tissue blocks. However, one of the major concerns of using phase contrast micro-CT in combination with FFPE tissue blocks is the trapped air within the tissue. While air inclusion within the FFPE tissue block does not strongly impact the workflow and quality of classical histology, it creates serious obstacles in 3D visualization of detailed morphology. In particular, the 3D analysis of structural features is challenging, due to a strong edge effect caused by the phase shift at the air-tissue/paraffin interface. Despite certain improvements in sample preparation to eliminate air inclusion, such as the use of negative pressure, it is not always possible to remove all trapped air, for example in soft tissues such as lung. Here, we present a novel workflow based on conditional generative adversarial networks (cGANs) to effectively replace these air artifact regions with generated tissue, which are influenced by the surrounding content. Our results show that this approach not only improves the visualization of the lung tissue but also eases the use of structural analysis on the air artifact-suppressed phase contrast micro-CT scans. In addition, we demonstrate the transferability of the generative model to FFPE specimens of porcine lung tissue.</p>","PeriodicalId":48729,"journal":{"name":"Journal of Synchrotron Radiation","volume":" ","pages":"678-689"},"PeriodicalIF":2.5000,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12067328/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Synchrotron Radiation","FirstCategoryId":"101","ListUrlMain":"https://doi.org/10.1107/S1600577525001511","RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/3/26 0:00:00","PubModel":"Epub","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0

Abstract

3D virtual histology of formalin-fixed and paraffin-embedded (FFPE) tissue by means of phase contrast micro-computed tomography (micro-CT) is an increasingly popular technique, as it allows the 3D architecture of the tissue to be addressed without the need of additional heavy ion based staining approaches. Therefore, it can be applied on archived standard FFPE tissue blocks. However, one of the major concerns of using phase contrast micro-CT in combination with FFPE tissue blocks is the trapped air within the tissue. While air inclusion within the FFPE tissue block does not strongly impact the workflow and quality of classical histology, it creates serious obstacles in 3D visualization of detailed morphology. In particular, the 3D analysis of structural features is challenging, due to a strong edge effect caused by the phase shift at the air-tissue/paraffin interface. Despite certain improvements in sample preparation to eliminate air inclusion, such as the use of negative pressure, it is not always possible to remove all trapped air, for example in soft tissues such as lung. Here, we present a novel workflow based on conditional generative adversarial networks (cGANs) to effectively replace these air artifact regions with generated tissue, which are influenced by the surrounding content. Our results show that this approach not only improves the visualization of the lung tissue but also eases the use of structural analysis on the air artifact-suppressed phase contrast micro-CT scans. In addition, we demonstrate the transferability of the generative model to FFPE specimens of porcine lung tissue.

基于条件生成对抗网络的相衬微ct空气伪影抑制。
通过相衬显微计算机断层扫描(micro-CT)对福尔马林固定和石蜡包埋(FFPE)组织进行三维虚拟组织学检查是一项日益流行的技术,因为它允许在不需要额外的重离子染色方法的情况下处理组织的三维结构。因此,它可以应用于存档的标准FFPE组织块。然而,将相衬显微ct与FFPE组织块结合使用的主要问题之一是组织内被困的空气。虽然FFPE组织块内的空气夹杂物不会严重影响经典组织学的工作流程和质量,但它会对详细形态学的3D可视化造成严重障碍。特别是,由于空气组织/石蜡界面的相移引起的强烈边缘效应,结构特征的三维分析具有挑战性。尽管在样品制备方面有一定的改进以消除空气夹杂,例如使用负压,但并不总是可能去除所有捕获的空气,例如在软组织(如肺)中。在这里,我们提出了一种基于条件生成对抗网络(cgan)的新工作流程,以有效地用受周围内容影响的生成组织替换这些空气伪影区域。我们的研究结果表明,这种方法不仅提高了肺组织的可视化,而且简化了在空气伪影抑制相衬微ct扫描上结构分析的使用。此外,我们证明了生成模型在猪肺组织FFPE标本上的可移植性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Journal of Synchrotron Radiation
Journal of Synchrotron Radiation INSTRUMENTS & INSTRUMENTATIONOPTICS&-OPTICS
CiteScore
5.60
自引率
12.00%
发文量
289
审稿时长
1 months
期刊介绍: Synchrotron radiation research is rapidly expanding with many new sources of radiation being created globally. Synchrotron radiation plays a leading role in pure science and in emerging technologies. The Journal of Synchrotron Radiation provides comprehensive coverage of the entire field of synchrotron radiation and free-electron laser research including instrumentation, theory, computing and scientific applications in areas such as biology, nanoscience and materials science. Rapid publication ensures an up-to-date information resource for scientists and engineers in the field.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术官方微信