Protocol for quantifying the germination properties of individual bacterial endospores using PySpore
Summary: 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...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2023-12-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166723006457 |
| _version_ | 1797643569497899008 |
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| author | John W. Ribis Aimee Shen |
| author_facet | John W. Ribis Aimee Shen |
| author_sort | John W. Ribis |
| collection | DOAJ |
| description | Summary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-03-11T14:17:15Z |
| format | Article |
| id | doaj.art-6c58d204987249aeb1edad8925aed2ef |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-03-11T14:17:15Z |
| publishDate | 2023-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-6c58d204987249aeb1edad8925aed2ef2023-11-01T04:48:02ZengElsevierSTAR Protocols2666-16672023-12-0144102678Protocol for quantifying the germination properties of individual bacterial endospores using PySporeJohn W. Ribis0Aimee Shen1Tufts University School of Medicine, Boston, MA 02111, USA; Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA; Corresponding authorTufts University School of Medicine, Boston, MA 02111, USA; Corresponding authorSummary: 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 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166723006457Cell BiologyDevelopmental BiologyMicrobiologyMicroscopyComputer Sciences |
| spellingShingle | John W. Ribis Aimee Shen Protocol for quantifying the germination properties of individual bacterial endospores using PySpore STAR Protocols Cell Biology Developmental Biology Microbiology Microscopy Computer Sciences |
| 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 | Cell Biology Developmental Biology Microbiology Microscopy Computer Sciences |
| url | http://www.sciencedirect.com/science/article/pii/S2666166723006457 |
| work_keys_str_mv | AT johnwribis protocolforquantifyingthegerminationpropertiesofindividualbacterialendosporesusingpyspore AT aimeeshen protocolforquantifyingthegerminationpropertiesofindividualbacterialendosporesusingpyspore |