Automated Cell Phenotyping for Imaging Mass Cytometry

Imaging mass cytometry (IMC) is a new advancement in tissue imaging that is quickly gaining wider usage since its recent launch. It improves upon current tissue imaging methods by allowing for a significantly higher number of proteins to be imaged at once on a single tissue slide. For most analyses of IMC data, determining the phenotype of each cell is a crucial step. Current methods of phenotyping require sufficient biological knowledge regarding the protein expression profile of the various cell types. Here, we develop a deep convolutional autoencoder-classifier to automate the cell phenotyping process into four basic cell types. Biopsy tissue from bladder cancer patients is used to evaluate the efficacy of the classification. The model is evaluated and validated through feature importance, confirming that the significant features are biologically relevant. Our results demonstrate the potential of deep learning to automate the task of cell phenotyping for high-dimensional IMC data.