Integrative co-registration of elemental imaging and histopathology for enhanced spatial multimodal analysis of tissue sections through TRACE.

IF 2.4 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY

Bioinformatics advances Pub Date : 2025-01-07 eCollection Date: 2025-01-01 DOI:10.1093/bioadv/vbaf001

Yunrui Lu, Serin Han, Aruesha Srivastava, Neha Shaik, Matthew Chan, Alos Diallo, Naina Kumar, Nishita Paruchuri, Hrishikesh Deosthali, Vismay Ravikumar, Kevin Cornell, Elijah Stommel, Tracy Punshon, Brian Jackson, Fred Kolling, Linda Vahdat, Louis Vaickus, Jonathan Marotti, Sunita Ho, Joshua Levy

{"title":"Integrative co-registration of elemental imaging and histopathology for enhanced spatial multimodal analysis of tissue sections through TRACE.","authors":"Yunrui Lu, Serin Han, Aruesha Srivastava, Neha Shaik, Matthew Chan, Alos Diallo, Naina Kumar, Nishita Paruchuri, Hrishikesh Deosthali, Vismay Ravikumar, Kevin Cornell, Elijah Stommel, Tracy Punshon, Brian Jackson, Fred Kolling, Linda Vahdat, Louis Vaickus, Jonathan Marotti, Sunita Ho, Joshua Levy","doi":"10.1093/bioadv/vbaf001","DOIUrl":null,"url":null,"abstract":"Summary: Elemental imaging provides detailed profiling of metal bioaccumulation, offering more precision than bulk analysis by targeting specific tissue areas. However, accurately identifying comparable tissue regions from elemental maps is challenging, requiring the integration of hematoxylin and eosin (H&E) slides for effective comparison. Facilitating the streamlined co-registration of whole slide images (WSI) and elemental maps, TRACE enhances the analysis of tissue regions and elemental abundance in various pathological conditions. Through an interactive containerized web application, TRACE features real-time annotation editing, advanced statistical tools, and data export, supporting comprehensive spatial analysis. Notably, it allows for comparison of elemental abundances across annotated tissue structures and enables integration with other spatial data types through WSI co-registration.Availability and implementation: Available on the following platforms-GitHub: jlevy44/trace_app, PyPI: trace_app, Docker: joshualevy44/trace_app, Singularity: docker://joshualevy44/trace_app.","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":"5 1","pages":"vbaf001"},"PeriodicalIF":2.4000,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11742137/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics advances","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/bioadv/vbaf001","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"MATHEMATICAL & COMPUTATIONAL BIOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

Summary: Elemental imaging provides detailed profiling of metal bioaccumulation, offering more precision than bulk analysis by targeting specific tissue areas. However, accurately identifying comparable tissue regions from elemental maps is challenging, requiring the integration of hematoxylin and eosin (H&E) slides for effective comparison. Facilitating the streamlined co-registration of whole slide images (WSI) and elemental maps, TRACE enhances the analysis of tissue regions and elemental abundance in various pathological conditions. Through an interactive containerized web application, TRACE features real-time annotation editing, advanced statistical tools, and data export, supporting comprehensive spatial analysis. Notably, it allows for comparison of elemental abundances across annotated tissue structures and enables integration with other spatial data types through WSI co-registration.

Availability and implementation: Available on the following platforms-GitHub: jlevy44/trace_app, PyPI: trace_app, Docker: joshualevy44/trace_app, Singularity: docker://joshualevy44/trace_app.

查看原文本刊更多论文

结合元素成像和组织病理学，通过TRACE增强组织切片的空间多模态分析。

元素成像提供了金属生物积累的详细剖面，通过针对特定组织区域提供比批量分析更精确的分析。然而，从元素图中准确识别可比的组织区域是具有挑战性的，需要整合苏木精和伊红（H&E）载玻片进行有效的比较。促进整个幻灯片图像（WSI）和元素图的流线型共配准，TRACE增强了各种病理条件下组织区域和元素丰度的分析。通过交互式容器化web应用程序，TRACE具有实时注释编辑、高级统计工具和数据导出功能，支持全面的空间分析。值得注意的是，它允许在注释的组织结构之间比较元素丰度，并通过WSI共同注册实现与其他空间数据类型的集成。可用性和实现：可用于以下平台- github: jlevy44/trace_app， PyPI: trace_app, Docker: joshualevy44/trace_app, Singularity: Docker: //joshualevy44/trace_app。

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

Bioinformatics advances

CiteScore

1.60

自引率

0.00%

发文量