pomBseen: An automated pipeline for analysis of fission yeast images.
Fission yeast is a model organism widely used for studies of eukaryotic cell biology. As such, it is subject to bright-field and fluorescent microscopy. Manual analysis of such data can be laborious and subjective. Therefore, we have developed pomBseen, an image analysis pipeline for the quantitatio...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2023-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0291391 |
| _version_ | 1797682735881388032 |
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| author | Makoto Ohira Nicholas Rhind |
| author_facet | Makoto Ohira Nicholas Rhind |
| author_sort | Makoto Ohira |
| collection | DOAJ |
| description | Fission yeast is a model organism widely used for studies of eukaryotic cell biology. As such, it is subject to bright-field and fluorescent microscopy. Manual analysis of such data can be laborious and subjective. Therefore, we have developed pomBseen, an image analysis pipeline for the quantitation of fission yeast micrographs containing a bright-field channel and up to two fluorescent channels. It accepts a wide range of image formats and produces a table with the size and total and nuclear fluorescent intensities of the cells in the image. Benchmarking of the pipeline against manually annotated datasets demonstrates that it reliably segments cells and acquires their image parameters. Written in MATLAB, pomBseen is also available as a standalone application. |
| first_indexed | 2024-03-12T00:05:11Z |
| format | Article |
| id | doaj.art-6e0867d4f75541f1978f96ac6d9c4eb6 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-03-12T00:05:11Z |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-6e0867d4f75541f1978f96ac6d9c4eb62023-09-17T05:31:05ZengPublic Library of Science (PLoS)PLoS ONE1932-62032023-01-01189e029139110.1371/journal.pone.0291391pomBseen: An automated pipeline for analysis of fission yeast images.Makoto OhiraNicholas RhindFission yeast is a model organism widely used for studies of eukaryotic cell biology. As such, it is subject to bright-field and fluorescent microscopy. Manual analysis of such data can be laborious and subjective. Therefore, we have developed pomBseen, an image analysis pipeline for the quantitation of fission yeast micrographs containing a bright-field channel and up to two fluorescent channels. It accepts a wide range of image formats and produces a table with the size and total and nuclear fluorescent intensities of the cells in the image. Benchmarking of the pipeline against manually annotated datasets demonstrates that it reliably segments cells and acquires their image parameters. Written in MATLAB, pomBseen is also available as a standalone application.https://doi.org/10.1371/journal.pone.0291391 |
| spellingShingle | Makoto Ohira Nicholas Rhind pomBseen: An automated pipeline for analysis of fission yeast images. PLoS ONE |
| title | pomBseen: An automated pipeline for analysis of fission yeast images. |
| title_full | pomBseen: An automated pipeline for analysis of fission yeast images. |
| title_fullStr | pomBseen: An automated pipeline for analysis of fission yeast images. |
| title_full_unstemmed | pomBseen: An automated pipeline for analysis of fission yeast images. |
| title_short | pomBseen: An automated pipeline for analysis of fission yeast images. |
| title_sort | pombseen an automated pipeline for analysis of fission yeast images |
| url | https://doi.org/10.1371/journal.pone.0291391 |
| work_keys_str_mv | AT makotoohira pombseenanautomatedpipelineforanalysisoffissionyeastimages AT nicholasrhind pombseenanautomatedpipelineforanalysisoffissionyeastimages |