Automated Single Cell Phenotyping of Time-of-Flight Secondary Ion Mass Spectrometry Tissue Images.

IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS
Sweta Bajaj, Spencer Tolleson, Aida Zarfeshani, Monirath Hav, Sean C Pawlowski, Danielle E Lyons, Raghav Padmanabhan, Jay G Tarolli, Máté Levente Nagy
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引用次数: 0

Abstract

Existing analytical techniques are being improved or applied in new ways to profile the tissue microenvironment (TME) to better understand the role of cells in disease research. Fully understanding the complex interactions between cells of many different types and functions is often slowed by the intense data analysis required. Multiplexed Ion Beam Imaging (MIBI) has been developed to simultaneously characterize 50+ cell types and their functions within the TME with a subcellular spatial resolution, but this results in complex data sets that are challenging to qualitatively analyze. Deep Learning (DL) techniques were used to build the MIBIsight workflow, which can process images containing thousands of cells into easily digestible reports and plots to enable researchers to easily summarize data sets in a study and make informed conclusions. Here we present the three types of DL models that have been trained with annotated MIBI images that have been pathologist validated as well as the associated workflow for the evolution of raw mass spectral data into actionable reports and plots.

飞行时间二次离子质谱组织图像的自动单细胞表型分析。
现有的分析技术正在得到改进或以新的方式应用于组织微环境(TME)的剖析,以更好地了解细胞在疾病研究中的作用。要充分了解多种不同类型和功能的细胞之间复杂的相互作用,往往需要进行大量的数据分析,因而进展缓慢。多重离子束成像(MIBI)技术的开发可同时表征TME内50多种细胞类型及其功能,并具有亚细胞空间分辨率,但这会产生复杂的数据集,对其进行定性分析具有挑战性。深度学习(DL)技术被用于构建MIBIsight工作流程,它能将包含数千个细胞的图像处理成易于消化的报告和图表,使研究人员能轻松总结研究中的数据集,并做出明智的结论。在此,我们将介绍利用经过病理学家验证的注释 MIBI 图像训练的三种 DL 模型,以及将原始质谱数据转化为可操作报告和图谱的相关工作流程。
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来源期刊
CiteScore
5.50
自引率
9.40%
发文量
257
审稿时长
1 months
期刊介绍: The Journal of the American Society for Mass Spectrometry presents research papers covering all aspects of mass spectrometry, incorporating coverage of fields of scientific inquiry in which mass spectrometry can play a role. Comprehensive in scope, the journal publishes papers on both fundamentals and applications of mass spectrometry. Fundamental subjects include instrumentation principles, design, and demonstration, structures and chemical properties of gas-phase ions, studies of thermodynamic properties, ion spectroscopy, chemical kinetics, mechanisms of ionization, theories of ion fragmentation, cluster ions, and potential energy surfaces. In addition to full papers, the journal offers Communications, Application Notes, and Accounts and Perspectives
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