Harpy is a new Python workflow capable of accelerated processing of large spatial proteomics datasets, including state-of-the-art segmentation and feature extraction via parallel processing. Each analysis step is accompanied by appropriate quality control steps. Scalable clustering of cells and pixels allows identification of cell types, processed up to 27 times faster than previously reported. Secure remote storage options are supported, and processing and visualization can be performed locally or on high-performance computing servers. Additionally, Harpy integrates well with existing spatial single-cell analysis tools in the Python and R software ecosystem.
