scholarly journals Automated Quantification and Sizing of Unbranched Filamentous Cyanobacteria by Model-Based Object-Oriented Image Analysis

2010 ◽  
Vol 76 (5) ◽  
pp. 1615-1622 ◽  
Author(s):  
Michael Zeder ◽  
Silke Van den Wyngaert ◽  
Oliver K�ster ◽  
Kathrin M. Felder ◽  
Jakob Pernthaler
Keyword(s):  
Image Analysis ◽  
Length Distribution ◽  
Object Oriented ◽  
Microscopic Analysis ◽  
Basic Research ◽  
Filament Length ◽  
Filamentous Cyanobacteria ◽  
Water Quality Control ◽  
Data Set ◽  
Field Samples

ABSTRACT Quantification and sizing of filamentous cyanobacteria in environmental samples or cultures are time-consuming and are often performed by using manual or semiautomated microscopic analysis. Automation of conventional image analysis is difficult because filaments may exhibit great variations in length and patchy autofluorescence. Moreover, individual filaments frequently cross each other in microscopic preparations, as deduced by modeling. This paper describes a novel approach based on object-oriented image analysis to simultaneously determine (i) filament number, (ii) individual filament lengths, and (iii) the cumulative filament length of unbranched cyanobacterial morphotypes in fluorescent microscope images in a fully automated high-throughput manner. Special emphasis was placed on correct detection of overlapping objects by image analysis and on appropriate coverage of filament length distribution by using large composite images. The method was validated with a data set for Planktothrix rubescens from field samples and was compared with manual filament tracing, the line intercept method, and the Uterm�hl counting approach. The computer program described allows batch processing of large images from any appropriate source and annotation of detected filaments. It requires no user interaction, is available free, and thus might be a useful tool for basic research and drinking water quality control.

scholarly journals Development of Genus-Specific PCR Primers for Molecular Monitoring of Invasive Nostocalean Cyanobacteria

2021 ◽  
Vol 18 (11) ◽  
pp. 5703
Author(s):  
In-Soo Kim ◽  
Hae-Kyung Park ◽  
Yong-Jin Kim
Keyword(s):  
Microscopic Analysis ◽  
Pcr Primers ◽  
Molecular Monitoring ◽  
Water Quality Control ◽  
Accurate Identification ◽  
Specific Pcr ◽  
Pcr Product ◽  
Field Samples ◽  
Cell Densities ◽  
The Nakdong River

The geographical range of invasive cyanobacteria with high toxigenic potential is widening because of eutrophication and global warming, thus, monitoring their appearance is necessary for safe water quality control. Most invasive cyanobacteria are nostocalean species, and their accurate identification by classical morphological methods may be problematic. In this study, we developed polymerase chain reaction (PCR) primers to selectively identify five invasive cyanobacterial genera, namely, Chrysosporum, Cuspidothrix, Cylindrospermopsis, Raphidiopsis, and Sphaerospermopsis, using genetic markers such as rbcLX, rpoB, rpoC1, and cpcBA, and determined the amplification conditions for each pair of primers. The primer performances were verified on single or mixed nostocalean cyanobacterial isolates. The five primers allowed selective identification of all the target genera. In field samples collected during summer, when cyanobacteria flourished in the Nakdong River, the respective PCR product was observed in all samples where the target genus was detected by microscopic analysis. Besides, weak bands corresponding to Sphaerospermopsis and Raphidiopsis were observed in some samples in which these genera were not detected by microscopy, suggesting that the cell densities were below the detection limit of the microscopic method used. Thus, the genus-specific primers developed in this study enable molecular monitoring to supplement the current microscopy-based monitoring.

Algorithms for automated montage synthesis of images from laser-scanning confocal microscopes

1995 ◽  
Vol 53 ◽  
pp. 650-651
Author(s):  
D. E. Becker
Keyword(s):  
Image Analysis ◽  
High Resolution ◽  
Laser Scanning ◽  
Cell Counting ◽  
Wide Area ◽  
Data Set ◽  
Computational Synthesis ◽  
Automated Cell Counting ◽  
Partial View ◽  
The Individual

An efficient, robust, and widely-applicable technique is presented for computational synthesis of high-resolution, wide-area images of a specimen from a series of overlapping partial views. This technique can also be used to combine the results of various forms of image analysis, such as segmentation, automated cell counting, deblurring, and neuron tracing, to generate representations that are equivalent to processing the large wide-area image, rather than the individual partial views. This can be a first step towards quantitation of the higher-level tissue architecture. The computational approach overcomes mechanical limitations, such as hysterisis and backlash, of microscope stages. It also automates a procedure that is currently done manually. One application is the high-resolution visualization and/or quantitation of large batches of specimens that are much wider than the field of view of the microscope.The automated montage synthesis begins by computing a concise set of landmark points for each partial view. The type of landmarks used can vary greatly depending on the images of interest. In many cases, image analysis performed on each data set can provide useful landmarks. Even when no such “natural” landmarks are available, image processing can often provide useful landmarks.

scholarly journals Micromagnetic Simulations of Fe and Ni Nanodot Arrays Surrounded by Magnetic or Non-Magnetic Matrices

Nanomaterials ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 349
Author(s):  
Devika Sudsom ◽  
Andrea Ehrmann
Keyword(s):  
Magnetic Materials ◽  
Data Storage ◽  
Magnetization Reversal ◽  
Hysteresis Loops ◽  
Object Oriented ◽  
Basic Research ◽  
Memory Systems ◽  
The Other ◽  
Micromagnetic Simulations ◽  
Nanodot Arrays

Combining clusters of magnetic materials with a matrix of other magnetic materials is very interesting for basic research because new, possibly technologically applicable magnetic properties or magnetization reversal processes may be found. Here we report on different arrays combining iron and nickel, for example, by surrounding circular nanodots of one material with a matrix of the other or by combining iron and nickel nanodots in air. Micromagnetic simulations were performed using the OOMMF (Object Oriented MicroMagnetic Framework). Our results show that magnetization reversal processes are strongly influenced by neighboring nanodots and the magnetic matrix by which the nanodots are surrounded, respectively, which becomes macroscopically visible by several steps along the slopes of the hysteresis loops. Such material combinations allow for preparing quaternary memory systems, and are thus highly relevant for applications in data storage and processing.

Snippet Counting for Cotton Length Distribution Measurement Using Image Analysis

2008 ◽  
Vol 78 (4) ◽  
pp. 336-341 ◽  
Author(s):  
Weilin Xu ◽  
Bugao Xu ◽  
Wenbin Li ◽  
Weigang Cui
Keyword(s):  
Image Analysis ◽  
Length Distribution ◽  
Distribution Measurement

Vimentin Intermediate Filament Formation: In Vitro Measurement and Mathematical Modeling of the Filament Length Distribution during Assembly†

Langmuir ◽  
2009 ◽  
Vol 25 (15) ◽  
pp. 8817-8823 ◽  
Author(s):  
Stéphanie Portet ◽  
Norbert Mücke ◽  
Robert Kirmse ◽  
Jörg Langowski ◽  
Michael Beil ◽  
...  
Keyword(s):  
Mathematical Modeling ◽  
Intermediate Filament ◽  
Length Distribution ◽  
Filament Length ◽  
Filament Formation ◽  
Vimentin Intermediate Filament

scholarly journals Phylogenetic and Morphological Diversity of Cyanobacteria in Soil Desert Crusts from the Colorado Plateau

2001 ◽  
Vol 67 (4) ◽  
pp. 1902-1910 ◽  
Author(s):  
Ferran Garcia-Pichel ◽  
Alejandro López-Cortés ◽  
Ulrich Nübel
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Colorado Plateau ◽  
Morphological Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Filamentous Cyanobacteria ◽  
Phylogenetic Cluster ◽  
Field Samples ◽  
Gradient Gel Electrophoresis ◽  
Well Differentiated

ABSTRACT We compared the community structures of cyanobacteria in four biological desert crusts from Utah's Colorado Plateau developing on different substrata. We analyzed natural samples, cultures, and cyanobacterial filaments or colonies retrieved by micromanipulation from field samples using microscopy, denaturing gradient gel electrophoresis, and sequencing of 16S rRNA genes. While microscopic analyses apparently underestimated the biodiversity of thin filamentous cyanobacteria, molecular analyses failed to retrieve signals for otherwise conspicuous heterocystous cyanobacteria with thick sheaths. The diversity found in desert crusts was underrepresented in currently available nucleotide sequence databases, and several novel phylogenetic clusters could be identified. Morphotypes fitting the description of Microcoleus vaginatus Gomont, dominant in most samples, corresponded to a tight phylogenetic cluster of probable cosmopolitan distribution, which was well differentiated from other cyanobacteria traditionally classified within the same genus. A new, diverse phylogenetic cluster, named “Xeronema,” grouped a series of thin filamentousPhormidium-like cyanobacteria. These were also ubiquitous in our samples and probably correspond to various botanicalPhormidium and Schizothrix spp., but they are phylogenetically distant from thin filamentous cyanobacteria from other environments. Significant differences in community structure were found among soil types, indicating that soil characteristics may select for specific cyanobacteria. Gypsum crusts were most deviant from the rest, while sandy, silt, and shale crusts were relatively more similar among themselves.

scholarly journals Ecological and hydrogeological factors of qualitative composition destabilization of drinking groundwater within the central part of DDAB

2019 ◽  
Keyword(s):  
Water Quality ◽  
Groundwater Quality ◽  
Water Withdrawal ◽  
Geological Environment ◽  
Qualitative Composition ◽  
Total Water ◽  
Water Quality Control ◽  
Data Set ◽  
Factors Of Influence ◽  
First Time

Formulation of the problem. The paper is devoted to a topical environmental theme – a study of the destabilization of drinking groundwater quality in the conditions of modern intensive technogenesis of geological environment. The purpose of the article is 2 components of a study of the groundwater quality deterioration of buchak-kaniv aquifer: - an identification of the ecological and hydrogeological factors of influence on the water qualitative composition; - an ensuring of the environmentally safe use of groundwater. Materials and methods. The research is based on an analysis of the results of over 700 groundwater chemical analyses of the target aquifer within the region. The chemical researches have been carried out during the period of active man-made pressure on the geological environment of studied territory (1960-2015). The available current data of geological, ecological and neotectonic conditions of studied area have been also used. The following methods of obtaining, processing and interpretation of necessary ecological-hydrogeological data have been used in the paper: field, chemical-analytical, comparative and graphical methods. A number of the common research methods have been used for the information processing – an analysis, a synthesis, a systematization, a classification, a modeling. The mathematical and statistical methods have been also used in the processing of received large data set. The interpolation and analogy methods have been used to simulate changes in the groundwater hydrochemical features using MapInfo Professional 10.0. Results and scientific novelty. For the first time on the basis of analysis of geological, ecological-hydrogeological and neotectonic conditions of region, the factors of influence on the qualitative composition of groundwater at the buchak-kaniv water intakes were revealed. On the basis of these factors – the priority indicators of buchak-kaniv aquifer water quality for its systematic hydrogeochemical monitoring under the infiltration of pollutants from the surface and their inflow from below in the zones of influence of tectonic structures have been proposed. For the first time a direct positive correlation between a change of the content of characteristic indicator elements of influence on the ecological-hydrogeological state of groundwater (mineralization, Cl-, F-, Fetotal, Br-, B3 +, J-) and the value of total water withdrawal in the zone of direct influence of tectonic faults of East-Poltava tectonic structure has been found. An approach for the ecologically safe use of target aquifer waters within the buchak-kaniv water intakes of Eastern Ukraine, which is based on the established correlation between the factors of influence and the qualitative composition of waters, has been developed. Practical significance. Due to an approbation of the proposed water quality control system at the Poltava water intakes network, which is strategically important within the region of research, an optimization of the total water withdrawal at the water intakes has been justified (the recommended limit is 50-60 thousand m3/day). The perspective areas for location of new water intakes within a 40 km radius around Poltava city have been identified (a total area – 750 km2). The estimated resources of drinking groundwater (54.5 thousand m3/day) have been calculated. Due to the using of these resources it is possible to gradually replace the current water supply of urban agglomeration with high-quality groundwater.

scholarly journals Lateral flow assays for the detection of African swine fever virus antigen are not fit for field diagnosis of wild boar carcasses

2021 ◽  
Author(s):  
Paul Deutschmann ◽  
Jutta Pikalo ◽  
Martin Beer ◽  
Sandra Blome
Keyword(s):  
Wild Boar ◽  
Point Of Care ◽  
African Swine Fever ◽  
Virus Antigen ◽  
Lateral Flow ◽  
Lateral Flow Assay ◽  
Field Conditions ◽  
Real Field ◽  
Data Set ◽  
Field Samples

African swine fever (ASF) is one of the most important viral diseases of domestic pigs and wild boar. Apart from endemic cycles in Africa, ASF is now continuously spreading in Europe and Asia. As ASF leads to severe but unspecific clinical signs and high lethality, early pathogen detection is of utmost importance. Recently, “point-of-care” (POC) tests have been intensively discussed for the use in remote areas but also in the context of on-farm epidemiological investigations and wild boar carcass screening. Along these lines, the INGEZIM ASFV CROM Ag lateral flow assay (Eurofins Technologies Ingenasa) promises virus antigen detection under field conditions within minutes. In the present study, we evaluated the performance of the assay with selected high-quality reference blood samples, and also with real field samples from wild boar carcasses in different stages of decay from the ongoing ASF outbreak in Germany. While we observed a sensitivity of roughly 77% in freeze-thawed matrices of close to ideal quality, our approach to simulate field conditions in direct carcass testing without any modification resulted in a drastically reduced sensitivity of only 12.5%. Freeze thawing increased the sensitivity to roughly 44% which mirrored the overall sensitivity of 49% in the total data set of carcass samples. A diagnostic specificity of 100% was observed. However, most of the German ASF cases in wild boar would have been missed using the lateral flow assay (LFA) alone. Therefore, the antigen-specific LFA should not be regarded as a substitute for any OIE listed diagnostic method and has very limited use for carcass testing at the point of care. For optimized LFA antigen tests, the sensitivity with field samples must be significantly increased. An improved sensitivity is seen with freeze-thawed samples, which may indicate problems in the accessibility of ASFV antigen.

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