micromorph: a Python toolkit for measurement of microbial morphology
Coppola, S.; Holden, S.
Show abstract
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 outperforms currently available bacterial morphology algorithms and introduce a new approach for reliably measuring the widths and lengths of quasi-circular cells.
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