Dual-modality imaging of immunofluorescence and imaging mass cytometry for whole-slide imaging and accurate segmentation
Eun Na Kim, Phyllis Zixuan Chen, Dario Bressan, Monika Tripathi, Ahmad Miremadi, Massimiliano di Pietro, Lisa M. Coussens, Gregory J. Hannon, Rebecca C. Fitzgerald, Lizhe Zhuang, Young Hwan Chang
Abstract
Imaging mass cytometry (IMC) is a powerful technique capable of detecting over 30 markers on a single slide. It has been increasingly used for single-cell-based spatial phenotyping in a wide range of samples. However, it only acquires a rectangle field of view (FOV) with a relatively small size and low image resolution, which 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-FOV 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.