This paper describes the new open-source framework PyFLEXTRKR (Python FLEXible object TRacKeR), a flexible atmospheric feature tracking software package with specific capabilities to track convective clouds from a variety of observations and model simulations. This software can track any atmospheric 2D objects and handle merging and splitting explicitly. The package has a collection of multi-object identification algorithms, scalable parallelization options, and has been optimized for large datasets including global high-resolution data. We demonstrate applications of PyFLEXTRKR on tracking individual deep convective cells and mesoscale convective systems from observations and model simulations ranging from large-eddy resolving (∼100s m) to mesoscale (∼10s km) resolutions. Visualization, post-processing, and statistical analysis tools are included in the package. New Lagrangian analyses of convective clouds produced by PyFLEXTRKR applicable to a wide range of datasets and scales facilitate advanced model evaluation and development efforts as well as scientific discovery.