Pytometry: Flow and mass cytometry analytics in Python

Flow and mass cytometry data are commonly analyzed via manual gating strategies which requires prior knowledge, expertise and time. With increasingly complex experiments with many parameters and samples, traditional manual flow and mass cytometry data analysis becomes cumbersome if not inefficient. At the same time, computational tools developed for the analysis of single-cell RNA-sequencing data have made single cell genomics analysis highly efficient, yet they are mostly inaccessible for the analysis of flow and mass cytometry data due to different data formats, noise assumptions and scales. To bring the advantages of both fields together, we developed Pytometry as an extension to the popular scanpy framework for the analysis of flow and mass cytometry data. We showcase a standard analysis workflow on healthy human bone marrow data, illustrating the applicability of tools developed for the larger feature space of single cell genomics data. Pytometry combines joint analysis of multiple samples and advanced computational applications, ranging from automated pre-processing, cell type annotation and disease classification.