micromorph: a Python toolkit for measurement of microbial morphology

Detection of morphological phenotypes from light microscopy is a key part of microbiology. Despite advances in automated morphological analysis, accurate measurements still often require significant user input. To address this, we have developed micromorph, a Python package to measure bacterial morphological properties from multiple types of light microscopy data. micromorph is available as a Python package with a documented API, or as napari plugin, thus appealing to a range of users regardless of their coding proficiency. The micromorph API allows easy integration into custom analysis pipelines. We demonstrate a range of scenarios in which micromorph demonstrates excellent performance and introduce a new approach for reliably measuring the widths and lengths of quasi-circular cells.