BAFFLE: A 3D Printable Device for Macroscopic Quantification of Fluorescent Bacteria in Space and Time
Despite the ubiquity and importance of microbial communities, understanding the population dynamics of mixed cultures in structured environments remains a fundamental problem in microbial ecology. Identifying bacterial strains within a complex microbial community represents a challenging technical p...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Ubiquity Press
2022-10-01
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| Series: | Journal of Open Hardware |
| Subjects: | |
| Online Access: | https://openhardware.metajnl.com/articles/44 |
| _version_ | 1798018589965418496 |
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| author | Carles Tardío Pi Daniela Reyes-González Andrea Fernández-Duque Ayari Fuentes-Hernández Fernando Santos-Escobar Rafael Peña-Miller |
| author_facet | Carles Tardío Pi Daniela Reyes-González Andrea Fernández-Duque Ayari Fuentes-Hernández Fernando Santos-Escobar Rafael Peña-Miller |
| author_sort | Carles Tardío Pi |
| collection | DOAJ |
| description | Despite the ubiquity and importance of microbial communities, understanding the population dynamics of mixed cultures in structured environments remains a fundamental problem in microbial ecology. Identifying bacterial strains within a complex microbial community represents a challenging technical problem. We describe a low-cost optomechanical device designed to acquire multi-channel time-lapse images of bacterial colonies growing in agar plates. This device uses a system of addressable LEDs and fluorescence filters to estimate the spatio-temporal distribution of different fluorescently-tagged cells from time-lapse images obtained using a standard DSLR camera with a macro lens. We demonstrate the potential of this device with a range of applications from experimental microbiology. METADATA OVERVIEW Main design files: https://github.com/ccg-esb-lab/baffle DOI archive: https://doi.org/10.5281/zenodo.6960207 Building instructions: https://www.penamiller.com/lab/baffle Scripts to produce figures: https://github.com/ccg-esb-lab/BAFFLE/tree/master/macros Raw data needed to produce figures: https://github.com/ccg-esb-lab/BAFFLE/tree/master/data Target group: school or academic staff, NGOs and scientific staff. Skills required for building the device: 3D printing – intermediate; mechanical assembly – intermediate; electrical assembly – intermediate. Replication: No builds known to the authors so far. |
| first_indexed | 2024-04-11T16:26:49Z |
| format | Article |
| id | doaj.art-349da71893fa484cb246cda8d51d7cad |
| institution | Directory Open Access Journal |
| issn | 2514-1708 |
| language | English |
| last_indexed | 2024-04-11T16:26:49Z |
| publishDate | 2022-10-01 |
| publisher | Ubiquity Press |
| record_format | Article |
| series | Journal of Open Hardware |
| spelling | doaj.art-349da71893fa484cb246cda8d51d7cad2022-12-22T04:14:09ZengUbiquity PressJournal of Open Hardware2514-17082022-10-016110.5334/joh.4444BAFFLE: A 3D Printable Device for Macroscopic Quantification of Fluorescent Bacteria in Space and TimeCarles Tardío Pi0Daniela Reyes-González1Andrea Fernández-Duque2Ayari Fuentes-Hernández3Fernando Santos-Escobar4Rafael Peña-Miller5Laboratorio de Biología de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210, CuernavacaLaboratorio de Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210, CuernavacaLaboratorio de Biología de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210, CuernavacaLaboratorio de Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210, CuernavacaLaboratorio de Biología de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210, CuernavacaLaboratorio de Biología de Sistemas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210, CuernavacaDespite the ubiquity and importance of microbial communities, understanding the population dynamics of mixed cultures in structured environments remains a fundamental problem in microbial ecology. Identifying bacterial strains within a complex microbial community represents a challenging technical problem. We describe a low-cost optomechanical device designed to acquire multi-channel time-lapse images of bacterial colonies growing in agar plates. This device uses a system of addressable LEDs and fluorescence filters to estimate the spatio-temporal distribution of different fluorescently-tagged cells from time-lapse images obtained using a standard DSLR camera with a macro lens. We demonstrate the potential of this device with a range of applications from experimental microbiology. METADATA OVERVIEW Main design files: https://github.com/ccg-esb-lab/baffle DOI archive: https://doi.org/10.5281/zenodo.6960207 Building instructions: https://www.penamiller.com/lab/baffle Scripts to produce figures: https://github.com/ccg-esb-lab/BAFFLE/tree/master/macros Raw data needed to produce figures: https://github.com/ccg-esb-lab/BAFFLE/tree/master/data Target group: school or academic staff, NGOs and scientific staff. Skills required for building the device: 3D printing – intermediate; mechanical assembly – intermediate; electrical assembly – intermediate. Replication: No builds known to the authors so far.https://openhardware.metajnl.com/articles/44microbiologyfluorescence imagingmacro photography |
| spellingShingle | Carles Tardío Pi Daniela Reyes-González Andrea Fernández-Duque Ayari Fuentes-Hernández Fernando Santos-Escobar Rafael Peña-Miller BAFFLE: A 3D Printable Device for Macroscopic Quantification of Fluorescent Bacteria in Space and Time Journal of Open Hardware microbiology fluorescence imaging macro photography |
| title | BAFFLE: A 3D Printable Device for Macroscopic Quantification of Fluorescent Bacteria in Space and Time |
| title_full | BAFFLE: A 3D Printable Device for Macroscopic Quantification of Fluorescent Bacteria in Space and Time |
| title_fullStr | BAFFLE: A 3D Printable Device for Macroscopic Quantification of Fluorescent Bacteria in Space and Time |
| title_full_unstemmed | BAFFLE: A 3D Printable Device for Macroscopic Quantification of Fluorescent Bacteria in Space and Time |
| title_short | BAFFLE: A 3D Printable Device for Macroscopic Quantification of Fluorescent Bacteria in Space and Time |
| title_sort | baffle a 3d printable device for macroscopic quantification of fluorescent bacteria in space and time |
| topic | microbiology fluorescence imaging macro photography |
| url | https://openhardware.metajnl.com/articles/44 |
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