pomBseen: An automated pipeline for analysis of fission yeast images.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2023
2023
Historique:
received:
06
01
2023
accepted:
25
08
2023
medline:
14
9
2023
pubmed:
12
9
2023
entrez:
12
9
2023
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 37699057
doi: 10.1371/journal.pone.0291391
pii: PONE-D-23-00477
pmc: PMC10497161
doi:
Substances chimiques
Coloring Agents
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0291391Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM134300
Pays : United States
Informations de copyright
Copyright: © 2023 Ohira, Rhind. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Sci Rep. 2020 Oct 6;10(1):16580
pubmed: 33024177
Yeast. 2017 Aug;34(8):323-334
pubmed: 28423198
PLoS One. 2013 Dec 06;8(12):e81434
pubmed: 24353754
Nat Methods. 2019 Dec;16(12):1226-1232
pubmed: 31570887
Nat Commun. 2020 Nov 12;11(1):5723
pubmed: 33184262
Nat Methods. 2021 Jan;18(1):100-106
pubmed: 33318659
BMC Biol. 2022 Aug 5;20(1):174
pubmed: 35932043
Nat Methods. 2012 Jul;9(7):671-5
pubmed: 22930834
Genome Biol. 2006;7(10):R100
pubmed: 17076895
MicroPubl Biol. 2022 Aug 4;2022:
pubmed: 35996688
Biol Open. 2019 Mar 12;8(3):
pubmed: 30814065
J Cell Biol. 2007 Nov 19;179(4):593-600
pubmed: 17998401
Genetics. 2016 Jun;203(2):621-9
pubmed: 27270696