scholarly journals A novel laboratory method for the detection and identification of cyanobacteria using hyperspectral imaging : hyperspectral imaging for cyanobacteria detection

2021 ◽  
Author(s):  
Kaytee Pokrzywinski ◽  
Cliff Morgan ◽  
Scott Bourne ◽  
Molly Reif ◽  
Kenneth Matheson ◽  
...  
Keyword(s):  
Hyperspectral Imaging ◽  
Laboratory Method ◽  
Army Corps ◽  
Imaging Method ◽  
Accurate Identification ◽  
Active Growth ◽  
Detection And Identification ◽  
Aerial Platforms ◽  
Field Deployment ◽  
The Stability

To assist US Army Corps of Engineers resource managers in monitoring for cyanobacteria bloom events, a laboratory method using hyperspectral imaging has been developed. This method enables the rapid detection of cyanobacteria in large volumes and has the potential to be transitioned to aerial platforms for field deployment. Prior to field data collection, validation of the technology in the laboratory using monocultures was needed. This report describes the development of the detection method using hyperspectral imaging and the stability/reliability of these signatures for identification purposes. Hyperspectral signatures of different cyanobacteria were compared to evaluate spectral deviations between genera to assess the feasibility of using this imaging method in the field. Algorithms were then developed to spectrally deconvolute mixtures of cyanobacteria to determine relative abundances of each species. Last, laboratory cultures of Microcystis aeruginosa and Anabaena sp. were subjected to varying macro (nitrate and phosphate) and micro-nutrient (iron and magnesium) stressors to establish the stability of signatures within each species. Based on the findings, hyperspectral imaging can be a valuable tool for the detection and monitoring of cyanobacteria. However, it should be used with caution and only during stages of active growth for accurate identification and limited interference owing to stress.

Hyperspectral imaging for the elimination of visual ambiguity in corrosion detection and identification of corrosion sources

2021 ◽  
pp. 147592172110416
Author(s):  
Dayakar N Lavadiya ◽  
Hizb Ullah Sajid ◽  
Ravi K Yellavajjala ◽  
Xin Sun
Keyword(s):  
Hyperspectral Imaging ◽  
Near Infrared ◽  
Sulfate Solution ◽  
Vital Role ◽  
Mitigation Strategies ◽  
Svm Classifier ◽  
Corrosive Media ◽  
Detection And Identification ◽  
Coated Surfaces ◽  
Visual Ambiguity

The similarity in the hue of corroded surfaces and coated surfaces, dust, vegetation, etc. leads to visual ambiguity which is challenging to eliminate using existing image classification/segmentation techniques. Furthermore, existing methods lack the ability to identify the source of corrosion, which plays a vital role in framing the corrosion mitigation strategies. The goal of this study to employ hyperspectral imaging (1) to detect corroded surfaces under visually ambiguous scenarios and (2) identify the source of corrosion in such scenarios. To this end, three different corrosive media, namely, (1) 1M hydrochloric acid (HCl), 2) 3.5 wt.% sodium chloride solution (NaCl), and (3) 3 wt.% sodium sulfate solution (Na2SO4), are employed to generate chemically distinctive corroded surfaces. The hyperspectral imaging sensor is employed to obtain the visible and near infrared (VNIR) spectra (397 nm–1004 nm) reflected by the corroded/coated surfaces. The intensity of the reflectance in various spectral bands are considered as the descriptive features in this study, and the training and test datasets were generated consisting of 35,000 and 15,000 data points, respectively. SVM classifier is trained and then its efficacy on the test data is assessed. Furthermore, validation datasets are employed and the generalization ability of the trained SVM classifier is verified. The results from this study revealed that the SVM classifier achieved an overall accuracy of 94% with the misclassifications of 18% and 13% in the case of NaCl and Na2SO4 corrosion, respectively. Reflectance spectra obtained in the VNIR region was found to eliminate the visual ambiguity between the corroded and coated surfaces and, identify the source of corrosion accurately. Further, the range of key wavelengths of the spectra that play an important role in the distinguishability of coating and chemically distinctive corroded surface were identified to be 500–520 nm, 660–680 nm, 760–770 nm, and 830–850 nm.

scholarly journals Evaluation of Anti-biofilm Potential of Biosurfactant Extracted from Nocardia Species

Folia Medica ◽  
2021 ◽  
Vol 63 (3) ◽  
pp. 392-399
Author(s):  
Ali Javadi ◽  
Mohamad Reza Pourmand ◽  
Javad Hamedi ◽  
Fatemeh Gharebaghi ◽  
Zohre Baseri ◽  
...  
Keyword(s):  
Agar Plate ◽  
Compositional Analysis ◽  
16S Rrna Gene Sequencing ◽  
Hydrocarbon Chain ◽  
Laboratory Method ◽  
Rrna Gene ◽  
Surface Active Agents ◽  
Rrna Gene Sequencing ◽  
The Stability ◽  
Spreading Test

Introduction: Bacterial natural products such as biosurfactants and surface-active agents are important compounds which exhibit many applications in the fields of medicine.Aim: The aim of the present study was to isolate and identify Nocardia strains with high biosurfactant production and antibiofilm ability.Materials and methods: In the present study, a biosurfactant producing Nocardia species was isolated and identified by a laboratory method. Nocardia species were initially screened and then tested for their ability to produce biosurfactant. The oil spreading test and the surface tension measurements showed that one strain was a biosurfactant producer. The strain with the best surface activity results was selected for further studies and identified by 16S rRNA gene sequencing method. Fourier transform infrared spectroscopy (FTIR) and compositional analysis proved a biosurfactant structure.Results: Oil spreading test and blue agar plate test confirmed biosurfactants and extracellular anionic glycolipids. E24% assay using olive oil revealed strong emulsifying characteristic of the extracted biosurfactant with 100% emulsifying strength. FTIR spectrum indicated the presence of aliphatic hydrocarbon chain (lipid) along with the polysaccharide portion, confirming the glycolipid nature of the biosurfactant. The stability of the biosurfactant produced in different conditions was significant. Increasing concentration of BS significantly inhibited Pseudomonas aeruginosa biofilm.Conclusions: N. coubleae can be a representative of the genus Nocardia for the production of biosurfactants with beneficial physicochemical properties.

Measurement Tools for Non-Invasive Monitoring of the Plants Growth Conditions by Using Hyperspectral Imaging Methods: a Review

2021 ◽  
Vol 2 (43) ◽  
pp. 54-61
Author(s):  
Dmitriy A. Burynin ◽  
◽  
Aleksandr A. Smirnov
Keyword(s):  
Hyperspectral Imaging ◽  
Physiological State ◽  
Effective Means ◽  
Research Problem ◽  
High Spectral Resolution ◽  
Research Purpose ◽  
Imaging Method ◽  
Invasive Monitoring ◽  
Imaging Methods ◽  
Non Invasive

Portable spectroradiometers and hyperspectral cameras are increasingly being used to quickly assess the physiological state of plants. The operation of these devices is based on the registration of reflection or reflection and transmission spectra. (Research purpose) The research purpose is in analyzing the technical means and methods of non-invasive monitoring of the plant state based on the registration of the reflection spectra of leaves. (Materials and methods) The article presents a review of the work on the application of hyperspectral imaging methods. Authors classified and analyzed materials on spectroscopic radiometers and hyperspectral cameras, and outlined the prospects for implementation. Authors applied the methods of a systematic approach to the research problem. (Results and discussion) Hyperspectral imaging methods serve as an effective means of monitoring plants. It is possible to determine the pigment composition of plants, lack of nutrition, and detect biotic stress through hyperspectral imaging. The article presents methods of application of portable spectroradiometers and hyperspectral cameras. With the help of these devices it is possible to carry out measurements with high spectral resolution. The difficulty of accurately detecting the content of pigments in the leaves lies in the mutual overlap of the areas of light absorption by them. The main drawback of spectroradiometers is that they measure only at one point on a single sheet. The article presents the difficulties encountered in interpreting the results obtained by the hyperspectral camera. The background reflectivity of the soil, the geometry of the vegetation cover, and the uneven lighting can make errors in the measurements. (Conclusions) The article presents the disadvantages of the hyperspectral imaging method when using only the reflection spectrum. In order to increase the accuracy of the determination of pigments and stresses of various origins, it is necessary to develop a portable device that combines the methods of recording reflection and fluorescence.

scholarly journals High-Throughput Sequencing Facilitates Discovery of New Plant Viruses in Poland

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 820
Author(s):  
Julia Minicka ◽  
Aleksandra Zarzyńska-Nowak ◽  
Daria Budzyńska ◽  
Natasza Borodynko-Filas ◽  
Beata Hasiów-Jaroszewska
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Plant Viruses ◽  
Yellow Mosaic Virus ◽  
Virus Species ◽  
Phylogenetic Groups ◽  
Accurate Identification ◽  
Detection And Identification ◽  
New Finding ◽  
Recent Occurrence

Viruses cause epidemics on all major crops of agronomic importance, and a timely and accurate identification is essential for control. High throughput sequencing (HTS) is a technology that allows the identification of all viruses without prior knowledge on the targeted pathogens. In this paper, we used HTS technique for the detection and identification of different viral species occurring in single and mixed infections in plants in Poland. We analysed various host plants representing different families. Within the 20 tested samples, we identified a total of 13 different virus species, including those whose presence has not been reported in Poland before: clover yellow mosaic virus (ClYMV) and melandrium yellow fleck virus (MYFV). Due to this new finding, the obtained sequences were compared with others retrieved from GenBank. In addition, cucurbit aphid-borne yellows virus (CABYV) was also detected, and due to the recent occurrence of this virus in Poland, a phylogenetic analysis of these new isolates was performed. The analysis revealed that CABYV population is highly diverse and the Polish isolates of CABYV belong to two different phylogenetic groups. Our results showed that HTS-based technology is a valuable diagnostic tool for the identification of different virus species originating from variable hosts, and can provide rapid information about the spectrum of plant viruses previously not detected in a region.

scholarly journals The Future of Hyperspectral Imaging

2019 ◽  
Vol 5 (11) ◽  
pp. 84 ◽  
Author(s):  
Stefano Selci
Keyword(s):  
Hyperspectral Imaging ◽  
Age Determination ◽  
Plant Diseases ◽  
Potato Tubers ◽  
Dynamic Scenes ◽  
New Methods ◽  
The Future ◽  
Using Data ◽  
The Stability

The Special Issue on hyperspectral imaging (HSI), entitled “The Future of Hyperspectral Imaging”, has published 12 papers. Nine papers are related to specific current research and three more are review contributions: In both cases, the request is to propose those methods or instruments so as to show the future trends of HSI. Some contributions also update specific methodological or mathematical tools. In particular, the review papers address deep learning methods for HSI analysis, while HSI data compression is reviewed by using liquid crystals spectral multiplexing as well as DMD-based Raman spectroscopy. Specific topics explored by using data obtained by HSI include alert on the sprouting of potato tubers, the investigation on the stability of painting samples, the prediction of healing diabetic foot ulcers, and age determination of blood-stained fingerprints. Papers showing advances on more general topics include video approach for HSI dynamic scenes, localization of plant diseases, new methods for the lossless compression of HSI data, the fusing of multiple multiband images, and mixed modes of laser HSI imaging for sorting and quality controls.

scholarly journals Optical imaging of single-protein size, charge, mobility, and binding

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Guangzhong Ma ◽  
Zijian Wan ◽  
Yunze Yang ◽  
Pengfei Zhang ◽  
Shaopeng Wang ◽  
...  
Keyword(s):  
Optical Imaging ◽  
Single Molecule ◽  
Near Field ◽  
Disease Diagnosis ◽  
Imaging Method ◽  
Charge Mobility ◽  
Single Molecule Level ◽  
Protein Size ◽  
Flexible Polymer ◽  
Detection And Identification

Abstract Detection and identification of proteins are typically achieved by analyzing protein size, charge, mobility and binding to antibodies, which are critical for biomedical research and disease diagnosis and treatment. Despite the importance, measuring these quantities with one technology and at the single-molecule level has not been possible. Here we tether a protein to a surface with a flexible polymer, drive it into oscillation with an electric field, and image the oscillation with a near field optical imaging method, from which we determine the size, charge, and mobility of the protein. We also measure antibody binding and conformation changes in the protein. The work demonstrates a capability for comprehensive protein analysis and precision protein biomarker detection at the single molecule level.

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