Multiplex Immunofluorescence Image Quality Checking Using DAPI Channel-referenced Evaluation.

IF 16.4 1区化学 Q1 CHEMISTRY, MULTIDISCIPLINARY

Accounts of Chemical Research Pub Date : 2023-03-01 Epub Date: 2023-03-24 DOI:10.1369/00221554231161693

Jun Jiang, Raymond Moore, Clarissa E Jordan, Ruifeng Guo, Rachel L Maus, Hongfang Liu, Ellen Goode, Svetomir N Markovic, Chen Wang

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引用次数: 0

Abstract

Multiplex immunofluorescence (MxIF) images provide detailed information of cell composition and spatial context for biomedical research. However, compromised data quality could lead to research biases. Comprehensive image quality checking (QC) is essential for reliable downstream analysis. As a reliable and specific staining of cell nuclei, 4',6-diamidino-2-phenylindole (DAPI) signals were used as references for tissue localization and auto-focusing across MxIF staining-scanning-bleaching iterations and could potentially be reused for QC. To confirm the feasibility of using DAPI as QC reference, pixel-level DAPI values were extracted to calculate signal fluctuations and tissue content similarities in staining-scanning-bleaching iterations for identifying quality issues. Concordance between automatic quantification and human experts' annotations were evaluated on a data set consisting of 348 fields of view (FOVs) with 45 immune and tumor cell markers. Cell distribution differences between subsets of QC-pass vs QC-failed FOVs were compared to investigate the downstream effects. Results showed that 87.3% FOVs with tissue damage and 73.4% of artifacts were identified. QC-failed FOVs showed elevated regional gathering in cellular feature space compared with the QC-pass FOVs. Our results supported that DAPI signals could be used as references for MxIF image QC, and low-quality FOVs identified by our method must be cautiously considered for downstream analyses.

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利用 DAPI 通道参照评估进行多重免疫荧光图像质量检查

多重免疫荧光（MxIF）图像为生物医学研究提供了细胞组成和空间背景的详细信息。然而，数据质量的下降可能会导致研究偏差。全面的图像质量检查（QC）对于可靠的下游分析至关重要。4',6-二脒基-2-苯基吲哚（4',6-diamidino-2-phenylindole，DAPI）信号作为细胞核的可靠特异性染色，可在 MxIF 染色-扫描-漂白迭代过程中作为组织定位和自动聚焦的参考，并有可能重新用于质量控制。为了证实使用 DAPI 作为质量控制参考的可行性，提取了像素级 DAPI 值，以计算染色-扫描-漂白迭代中的信号波动和组织内容相似性，从而确定质量问题。自动定量与人类专家注释之间的一致性在一个数据集上进行了评估，该数据集由 348 个视场（FOV）组成，包含 45 种免疫和肿瘤细胞标记物。比较了通过 QC 与未通过 QC 的 FOVs 子集之间的细胞分布差异，以研究下游效应。结果显示，87.3% 的 FOV 有组织损伤，73.4% 的 FOV 有伪影。与QC通过的FOV相比，QC失败的FOV在细胞特征空间显示出更高的区域聚集。我们的结果表明，DAPI 信号可作为 MxIF 图像质控的参考，在下游分析中必须谨慎考虑用我们的方法识别出的低质量 FOV。

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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来源期刊

Accounts of Chemical Research 化学-化学综合

CiteScore

31.40

自引率

1.10%

发文量

312

审稿时长

2 months

期刊介绍： Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance. Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.