Dual-modality imaging of immunofluorescence and imaging mass cytometry for whole slide imaging with accurate single-cell segmentation

Kim, E. N.; Chen, P. Z.; Bressan, D.; Tripathi, M.; Miremadi, A.; di Pietro, M.; Coussens, L. M.; Hannon, G. J.; Fitzgerald, R. C.; Zhuang, L.; Chang, Y. H.

doi:10.1101/2023.02.23.529718

bioRxiv · 10.1101/2023.02.23.529718

Dual-modality imaging of immunofluorescence and imaging mass cytometry for whole slide imaging with accurate single-cell segmentation

Kim, E. N.·Chen, P. Z.·Bressan, D.·Tripathi, M.·Miremadi, A.·di Pietro, M.·Coussens, L. M.·Hannon, G. J.·Fitzgerald, R. C.·Zhuang, L.·Chang, Y. H.

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Abstract

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. MotivationHighly 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 mm2-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.

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Kim, E. N., Chen, P. Z., Bressan, D., Tripathi, M., Miremadi, A., di Pietro, M., Coussens, L. M., Hannon, G. J., Fitzgerald, R. C., Zhuang, L., Chang, Y. H.. 2023-02-23. Dual-modality imaging of immunofluorescence and imaging mass cytometry for whole slide imaging with accurate single-cell segmentation. https://doi.org/10.1101/2023.02.23.529718

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