microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation
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 an...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2022-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9707790/?tool=EBI |
| _version_ | 1797987323796783104 |
|---|---|
| author | Tim Scherr Johannes Seiffarth Bastian Wollenhaupt Oliver Neumann Marcel P. Schilling Dietrich Kohlheyer Hanno Scharr Katharina Nöh Ralf Mikut |
| author_facet | Tim Scherr Johannes Seiffarth Bastian Wollenhaupt Oliver Neumann Marcel P. Schilling Dietrich Kohlheyer Hanno Scharr Katharina Nöh Ralf Mikut |
| author_sort | Tim Scherr |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T07:45:55Z |
| format | Article |
| id | doaj.art-361c5c8b5b084cdab51b8a3374dbbded |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-11T07:45:55Z |
| publishDate | 2022-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-361c5c8b5b084cdab51b8a3374dbbded2022-12-22T04:36:16ZengPublic Library of Science (PLoS)PLoS ONE1932-62032022-01-011711microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentationTim ScherrJohannes SeiffarthBastian WollenhauptOliver NeumannMarcel P. SchillingDietrich KohlheyerHanno ScharrKatharina NöhRalf MikutIn 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.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9707790/?tool=EBI |
| spellingShingle | Tim Scherr Johannes Seiffarth Bastian Wollenhaupt Oliver Neumann Marcel P. Schilling Dietrich Kohlheyer Hanno Scharr Katharina Nöh Ralf Mikut microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation PLoS ONE |
| title | microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation |
| title_full | microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation |
| title_fullStr | microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation |
| title_full_unstemmed | microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation |
| title_short | microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation |
| title_sort | microbeseg a deep learning software tool with omero data management for efficient and accurate cell segmentation |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9707790/?tool=EBI |
| work_keys_str_mv | AT timscherr microbesegadeeplearningsoftwaretoolwithomerodatamanagementforefficientandaccuratecellsegmentation AT johannesseiffarth microbesegadeeplearningsoftwaretoolwithomerodatamanagementforefficientandaccuratecellsegmentation AT bastianwollenhaupt microbesegadeeplearningsoftwaretoolwithomerodatamanagementforefficientandaccuratecellsegmentation AT oliverneumann microbesegadeeplearningsoftwaretoolwithomerodatamanagementforefficientandaccuratecellsegmentation AT marcelpschilling microbesegadeeplearningsoftwaretoolwithomerodatamanagementforefficientandaccuratecellsegmentation AT dietrichkohlheyer microbesegadeeplearningsoftwaretoolwithomerodatamanagementforefficientandaccuratecellsegmentation AT hannoscharr microbesegadeeplearningsoftwaretoolwithomerodatamanagementforefficientandaccuratecellsegmentation AT katharinanoh microbesegadeeplearningsoftwaretoolwithomerodatamanagementforefficientandaccuratecellsegmentation AT ralfmikut microbesegadeeplearningsoftwaretoolwithomerodatamanagementforefficientandaccuratecellsegmentation |