A low cost harmonically modulated chlorophyll fluorescence imaging system and frequency domain analysis of chlorophyll fluorescence

2021 ◽  
Author(s):  
Dingle Jose
Keyword(s):  
Chlorophyll Fluorescence ◽  
Frequency Domain ◽  
Fluorescence Imaging ◽  
Imaging System ◽  
Low Cost ◽  
Domain Analysis ◽  
Frequency Domain Analysis ◽  
Chlorophyll Fluorescence Imaging ◽  
Fluorescence Imaging System ◽  
Modulated Chlorophyll Fluorescence

scholarly journals Democratising “Microscopi”: a 3D printed automated XYZT fluorescence imaging system for teaching, outreach and fieldwork

2020 ◽  
Author(s):  
Matthew Wincott ◽  
Andrew Jefferson ◽  
Ian M. Dobbie ◽  
Martin J. Booth ◽  
Ilan Davis ◽  
...  
Keyword(s):  
Open Source ◽  
Fluorescence Imaging ◽  
Imaging System ◽  
Low Cost ◽  
Dark Field ◽  
List Type ◽  
Image Capture ◽  
Fluorescence Imaging System ◽  
3D Printed ◽  
Open Source Hardware

ABSTRACTCommercial fluorescence microscope stands and fully automated XYZt fluorescence imaging systems are generally beyond the limited budgets available for teaching and outreach. We have addressed this problem by developing “Microscopi”, an accessible, affordable, DIY automated imaging system that is built from 3D printed and commodity off-the-shelf hardware, including electro-mechanical, computer and optical components. Our design features automated sample navigation and image capture with a simple web-based graphical user interface, accessible with a tablet or other mobile device. The light path can easily be switched between different imaging modalities. The open source Python-based control software allows the hardware to be driven as an integrated imaging system. Furthermore, the microscope is fully customisable, which also enhances its value as a learning tool. Here, we describe the basic design and demonstrate imaging performance for a range of easily sourced specimens.HighlightsPortable, low cost, self-build from 3D printed and commodity componentsMultimodal imaging: bright field, dark field, pseudo-phase and fluorescenceAutomated XYZt imaging from a tablet or smartphone via a simple GUIWide ranging applications in teaching, outreach and fieldworkOpen source hardware and software design, allowing user modification

Distinction and characterisation of rice genotypes tolerant to combined stresses of salinity and partial submergence, proved by a high-resolution chlorophyll fluorescence imaging system

2019 ◽  
Vol 46 (3) ◽  
pp. 248 ◽  
Author(s):  
Bhubaneswar Pradhan ◽  
Koushik Chakraborty ◽  
Nibedita Prusty ◽  
Deepa ◽  
Arup Kumar Mukherjee ◽  
...  
Keyword(s):  
Chlorophyll Fluorescence ◽  
Quantum Yield ◽  
Fluorescence Imaging ◽  
Imaging System ◽  
Oryza Sativa L ◽  
Photochemical Efficiency ◽  
Combined Effect ◽  
Chlorophyll Fluorescence Imaging ◽  
Photochemical Quenching ◽  
Submergence Stress

Chlorophyll a fluorescence (ChlF) parameters measured with fluorescence imaging techniques were used to investigate the combined effect of salt and partial submergence stress to understand photosynthetic performance in rice (Oryza sativa L.). ChlF parameters such as maximal fluorescence (Fm), variable fluorescence (Fv=Fm –F0), the maximal photochemical efficiency of PSII (Fv/Fm) and the quantum yield of nonregulated energy dissipation of PSII (Y(NO)) were able to distinguish genotypes precisely based on their sensitivity to stress. Upon analysis, we found the images of F0 were indistinguishable among the genotypes, irrespective of their tolerance to salt and partial submergence stress. On the contrary, the images of Fm and Fv/Fm showed marked differences between the tolerant and susceptible genotypes in terms of tissue greenness and the appearance of dark spots as stress symptoms. The images of effective PSII quantum yield, the coefficient of nonphotochemical quenching (qN) and the coefficient of photochemical quenching (qP) captured under different PAR were able to distinguish the tolerant and susceptible genotypes, and were also quite effective for differentiating the tolerant and moderately tolerant ones. Similarly, the values of electron transport rate, qN, qP and Y(NO) were also able to distinguish the genotypes based on their sensitivity to stress. Overall, this investigation indicates the suitability of chlorophyll fluorescence imaging technique for precise phenotyping of rice based on their sensitivity to the combined effect of salt and partial submergence.

scholarly journals Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering

PLoS ONE ◽  
2017 ◽  
Vol 12 (11) ◽  
pp. e0187163 ◽  
Author(s):  
Isaac Nuñez ◽  
Tamara Matute ◽  
Roberto Herrera ◽  
Juan Keymer ◽  
Timothy Marzullo ◽  
...  
Keyword(s):  
Open Source ◽  
Fluorescence Imaging ◽  
Imaging System ◽  
Low Cost ◽  
Teaching And Research ◽  
Fluorescence Imaging System

scholarly journals Low-Cost Chlorophyll Fluorescence Imaging for Stress Detection

Sensors ◽  
2021 ◽  
Vol 21 (6) ◽  
pp. 2055
Author(s):  
Reeve Legendre ◽  
Nicholas T. Basinger ◽  
Marc W. van Iersel
Keyword(s):  
Chlorophyll Fluorescence ◽  
Photosystem Ii ◽  
Fluorescence Imaging ◽  
Low Cost ◽  
Pulse Amplitude ◽  
Chlorophyll Fluorescence Imaging ◽  
Stress Index ◽  
Pam Fluorometry ◽  
Pixel Intensity ◽  
Pam Fluorometer

Plants naturally contain high levels of the stress-responsive fluorophore chlorophyll. Chlorophyll fluorescence imaging (CFI) is a powerful tool to measure photosynthetic efficiency in plants and provides the ability to detect damage from a range of biotic and abiotic stresses before visible symptoms occur. However, most CFI systems are complex, expensive systems that use pulse amplitude modulation (PAM) fluorometry. Here, we test a simple CFI system, that does not require PAM fluorometry, but instead simply images fluorescence emitted by plants. We used this technique to visualize stress induced by the photosystem II-inhibitory herbicide atrazine. After applying atrazine as a soil drench, CFI and color images were taken at 15-minute intervals, alongside measurements from a PAM fluorometer and a leaf reflectometer. Pixel intensity of the CFI images was negatively correlated with the quantum yield of photosystem II (ΦPSII) (p < 0.0001) and positively correlated with the measured reflectance in the spectral region of chlorophyll fluorescence emissions (p < 0.0001). A fluorescence-based stress index was developed using the reflectometer measurements based on wavelengths with the highest (741.2 nm) and lowest variability (548.9 nm) in response to atrazine damage. This index was correlated with ΦPSII (p < 0.0001). Low-cost CFI imaging can detect herbicide-induced stress (and likely other stressors) before there is visual damage.

scholarly journals Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering

2017 ◽  
Author(s):  
Nuñez Isaac ◽  
Matute Tamara ◽  
Herrera Roberto ◽  
Keymer Juan ◽  
Marzullo Tim ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Open Source ◽  
Fluorescence Imaging ◽  
Imaging System ◽  
Fluorescent Proteins ◽  
Low Cost ◽  
Fluorescent Imaging ◽  
Diverse Range ◽  
Fluorescence Imaging System ◽  
Open Source Hardware

AbstractThe advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential for STEM teaching in a high school environment, using it to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for STEM education, scientific research and bioengineering. All the resources developed here are available under open source licenses.

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