Kim Eun Na, Chen Phyllis Zixuan, Bressan Dario, Tripathi Monika, Miremadi Ahmad, di Pietro Massimiliano, Coussens Lisa M, Hannon Gregory J, Fitzgerald Rebecca C, Zhuang Lizhe, Chang Young Hwan
Department of Biomedical Engineering and Computational Biology Program, Oregon Health and Science University, Portland, OR, USA.
Early Cancer Institute, University of Cambridge, Cambridge, UK.
bioRxiv. 2023 Feb 23:2023.02.23.529718. doi: 10.1101/2023.02.23.529718.
Imaging mass cytometry (IMC) is a powerful multiplexed tissue imaging technology that allows simultaneous detection of more than 30 makers on a single slide. It has been increasingly used for singlecell-based spatial phenotyping in a wide range of samples. However, it only acquires a small, rectangle field of view (FOV) with a low image resolution that hinders downstream analysis. Here, we reported a highly practical dual-modality imaging method that combines high-resolution immunofluorescence (IF) and high-dimensional IMC on the same tissue slide. Our computational pipeline uses the whole slide image (WSI) of IF as a spatial reference and integrates small FOVs IMC into a WSI of IMC. The high-resolution IF images enable accurate single-cell segmentation to extract robust high-dimensional IMC features for downstream analysis. We applied this method in esophageal adenocarcinoma of different stages, identified the single-cell pathology landscape via reconstruction of WSI IMC images, and demonstrated the advantage of the dual-modality imaging strategy.
Highly multiplexed tissue imaging allows visualization of the spatially resolved expression of multiple proteins at the single-cell level. Although imaging mass cytometry (IMC) using metal isotope-conjugated antibodies has a significant advantage of low background signal and absence of autofluorescence or batch effect, it has a low resolution that hampers accurate cell segmentation and results in inaccurate feature extraction. In addition, IMC only acquires mm -sized rectangle regions, which limits its application and efficiency when studying larger clinical samples with non-rectangle shapes. To maximize the research output of IMC, we developed the dual-modality imaging method based on a highly practical and technical improvement requiring no extra specialized equipment or agents and proposed a comprehensive computational pipeline that combines IF and IMC. The proposed method greatly improves the accuracy of cell segmentation and downstream analysis and is able to obtain whole slide image IMC to capture the comprehensive cellular landscape of large tissue sections.
成像质谱流式细胞术（IMC）是一种强大的多重组织成像技术，可在一张载玻片上同时检测30多种标志物。它已越来越多地用于各种样本中基于单细胞的空间表型分析。然而，它只能获取小的矩形视野（FOV），图像分辨率低，这阻碍了下游分析。在此，我们报告了一种高度实用的双模态成像方法，该方法在同一组织载玻片上结合了高分辨率免疫荧光（IF）和高维IMC。我们的计算流程将IF的全玻片图像（WSI）用作空间参考，并将小视野IMC整合到IMC的WSI中。高分辨率IF图像能够进行准确的单细胞分割，以提取强大的高维IMC特征用于下游分析。我们将此方法应用于不同阶段的食管腺癌，通过重建WSI IMC图像识别单细胞病理格局，并证明了双模态成像策略的优势。
高度多重的组织成像允许在单细胞水平可视化多种蛋白质的空间分辨表达。尽管使用金属同位素偶联抗体的成像质谱流式细胞术（IMC）具有低背景信号、无自发荧光或批次效应的显著优势，但它具有低分辨率，这妨碍了准确的细胞分割并导致特征提取不准确。此外，IMC仅获取毫米大小的矩形区域，这在研究具有非矩形形状的较大临床样本时限制了其应用和效率。为了最大化IMC的研究产出，我们基于一项高度实用且无需额外专门设备或试剂的技术改进开发了双模态成像方法，并提出了一种结合IF和IMC的综合计算流程。所提出的方法大大提高了细胞分割和下游分析的准确性，并且能够获得全玻片图像IMC以捕获大组织切片的综合细胞格局。
