microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation

Clicks: 73
ID: 276972
2022
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Abstract
In biotechnology, cell growth is one of the most important properties for the characterization and optimization of microbial cultures. Novel live-cell imaging methods are leading to an ever better understanding of cell cultures and their development. The key to analyzing acquired data is accurate and automated cell segmentation at the single-cell level. Therefore, we present microbeSEG, a user-friendly Python-based cell segmentation tool with a graphical user interface and OMERO data management. microbeSEG utilizes a state-of-the-art deep learning-based segmentation method and can be used for instance segmentation of a wide range of cell morphologies and imaging techniques, e.g., phase contrast or fluorescence microscopy. The main focus of microbeSEG is a comprehensible, easy, efficient, and complete workflow from the creation of training data to the final application of the trained segmentation model. We demonstrate that accurate cell segmentation results can be obtained within 45 minutes of user time. Utilizing public segmentation datasets or pre-labeling further accelerates the microbeSEG workflow. This opens the door for accurate and efficient data analysis of microbial cultures.
Reference Key
scherr2022microbesegplos Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Scherr, T.
Journal PloS one
Year 2022
DOI
10.1371/journal.pone.0277601
URL
Keywords Keywords not found

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