Protocol for quantifying the germination properties of individual bacterial endospores using PySpore

PySpore is a Python program that tracks the germination of individual bacterial endospores. Here, we present a protocol for segmenting spores and quantifying the germination properties of individual bacterial endospores using PySpore. We describe steps for using GUI-based tools to optimize image pro...

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Detalles Bibliográficos
Autores principales: Ribis, John W., Shen, Aimee
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Protocol
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10630823/
https://www.ncbi.nlm.nih.gov/pubmed/37910513
http://dx.doi.org/10.1016/j.xpro.2023.102678
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author Ribis, John W.
Shen, Aimee
author_facet Ribis, John W.
Shen, Aimee
author_sort Ribis, John W.
collection PubMed
description PySpore is a Python program that tracks the germination of individual bacterial endospores. Here, we present a protocol for segmenting spores and quantifying the germination properties of individual bacterial endospores using PySpore. We describe steps for using GUI-based tools to optimize image processing, annotating data, setting gates, and joining datasets for downstream analyses. We then describe procedures for plotting functionality tools without the user needing to modify the underlying code. For complete details on the use and execution of this protocol, please refer to Ribis et al. (2023).(1)
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spelling pubmed-106308232023-10-30 Protocol for quantifying the germination properties of individual bacterial endospores using PySpore Ribis, John W. Shen, Aimee STAR Protoc Protocol PySpore is a Python program that tracks the germination of individual bacterial endospores. Here, we present a protocol for segmenting spores and quantifying the germination properties of individual bacterial endospores using PySpore. We describe steps for using GUI-based tools to optimize image processing, annotating data, setting gates, and joining datasets for downstream analyses. We then describe procedures for plotting functionality tools without the user needing to modify the underlying code. For complete details on the use and execution of this protocol, please refer to Ribis et al. (2023).(1) Elsevier 2023-10-30 /pmc/articles/PMC10630823/ /pubmed/37910513 http://dx.doi.org/10.1016/j.xpro.2023.102678 Text en © 2023 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Protocol
Ribis, John W.
Shen, Aimee
Protocol for quantifying the germination properties of individual bacterial endospores using PySpore
title Protocol for quantifying the germination properties of individual bacterial endospores using PySpore
title_full Protocol for quantifying the germination properties of individual bacterial endospores using PySpore
title_fullStr Protocol for quantifying the germination properties of individual bacterial endospores using PySpore
title_full_unstemmed Protocol for quantifying the germination properties of individual bacterial endospores using PySpore
title_short Protocol for quantifying the germination properties of individual bacterial endospores using PySpore
title_sort protocol for quantifying the germination properties of individual bacterial endospores using pyspore
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10630823/
https://www.ncbi.nlm.nih.gov/pubmed/37910513
http://dx.doi.org/10.1016/j.xpro.2023.102678
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