scholarly journals Improving distribution models of riparian vegetation with mobile laser scanning and hydraulic modelling

PLoS ONE ◽  
2019 ◽  
Vol 14 (12) ◽  
pp. e0225936
Author(s):  
Tua Nylén ◽  
Elina Kasvi ◽  
Jouni Salmela ◽  
Harri Kaartinen ◽  
Antero Kukko ◽  
...  
Keyword(s):  
Riparian Vegetation ◽  
Laser Scanning ◽  
Hydraulic Modelling ◽  
Distribution Models

Exploring the 4D scales of vegetation-morphological interactions along a river corridor using repeat UAV Laser Scanning (ULS), multispectral imagery, and a functional traits framework.

2021 ◽  
Author(s):  
Chris Tomsett ◽  
Julian Leyland
Keyword(s):  
High Resolution ◽  
Functional Traits ◽  
Riparian Vegetation ◽  
Laser Scanning ◽  
Temporal Dynamics ◽  
Spatial Scales ◽  
Morphological Data ◽  
Multispectral Imagery ◽  
Vegetation Diversity ◽  
River Corridor

<p>Interactions between riparian vegetation and river morphology are complex as they are often co-dependent, highly dynamic, and vary across both space and time. Vegetation diversity can be partially attributed to factors such as flood regimes and morphology, whilst simultaneously influencing the flow of water and sediment, ultimately impacting morphology and floodplain connectivity. As such, the importance of vegetation within the river corridor is well recognised and has been the subject of a considerable volume of research. However, within ecogeomorphology, most studies to date have been scale invariant, focusing either on characterisation of fine scale hydraulic roughness (e.g. using Terrestrial Laser Scanning; TLS) or on >reach scale patterns of riparian vegetation (using airborne or satellite imagery). Similarly, less attention has been paid to the temporal dynamics of vegetation beyond some appreciation of seasonality in controlling flow dynamics. This leaves a number of unresolved questions relating to the nested spatial and temporal (i.e. 4-dimensional; 4D) interactions of riparian vegetation and river flow.</p><p>In this study we seek to establish the temporal and spatial scales of riparian vegetation interaction within a river corridor using a traits based framework. Traits based research characterises plants with similar functional traits into guilds (groups) as opposed to by species or types, and as such provides a more useful basis to group vegetation according to the potential geomorphic impact that they exhibit. Traits based research for ecogeomorphic processes is relatively new in fluvial geomorphology, but has shown promise in its applicability, albeit existing applications are yet to investigate the temporal changes in vegetation. The need for extensive ground survey currently limits the application of traits based methods at reach scale and greater, highlighting the requirement for an approach that is able to classify a range of vegetation sizes and types into appropriate guilds.</p><p>Using a novel ULS and multispectral imaging systems, we have collected repeat high resolution (~1000 points per m<sup>3</sup>) surveys over a 1 km reach of the River Teme, UK, which has a wide variety of seasonally dynamic riparian vegetation. For each survey we use the point cloud data and multispectral imagery to classify vegetation into guilds. We use these in conjunction with the morphological data from the survey to create spatially varying surfaces of ecogeomorphic interactions, allowing us to establish links between guild coverage and morphological evolution across the reach throughout the year. The results show that vegetation-morphological co-evolution exists across scales and that high resolution survey methods are highly beneficial for resolving such interactions. The methods are designed to be transferable to other eco-geomorphic domains in any morpho-climatic regions, highlighting the flexibility and potential of a high resolution 4D traits based approach.</p>

scholarly journals Riparian vegetation classification from airborne laser scanning data with an emphasis on cottonwood trees

2006 ◽  
Vol 32 (1) ◽  
pp. 15-18 ◽  
Author(s):  
A. Farid ◽  
D. Rautenkranz ◽  
D C Goodrich ◽  
S E Marsh ◽  
S. Sorooshian
Keyword(s):  
Riparian Vegetation ◽  
Laser Scanning ◽  
Vegetation Classification ◽  
Airborne Laser Scanning ◽  
Airborne Laser ◽  
Cottonwood Trees

3-D imaging of cells using a confocal laser scanning microscope and digital image processing

1988 ◽  
Vol 46 ◽  
pp. 96-97
Author(s):  
Thomas M. Jovin ◽  
Michel Robert-Nicoud ◽  
Donna J. Arndt-Jovin ◽  
Thorsten Schormann
Keyword(s):  
Laser Scanning ◽  
Confocal Laser Scanning Microscope ◽  
Laser Scanning Microscopy ◽  
Confocal Laser Scanning ◽  
Confocal Laser ◽  
Scanning Microscope ◽  
Laser Scanning Microscope ◽  
Biochemical Processes ◽  
Adjacent Structures

Light microscopic techniques for visualizing biomolecules and biochemical processes in situ have become indispensable in studies concerning the structural organization of supramolecular assemblies in cells and of processes during the cell cycle, transformation, differentiation, and development. Confocal laser scanning microscopy offers a number of advantages for the in situ localization and quantitation of fluorescence labeled targets and probes: (i) rejection of interfering signals emanating from out-of-focus and adjacent structures, allowing the “optical sectioning” of the specimen and 3-D reconstruction without time consuming deconvolution; (ii) increased spatial resolution; (iii) electronic control of contrast and magnification; (iv) simultanous imaging of the specimen by optical phenomena based on incident, scattered, emitted, and transmitted light; and (v) simultanous use of different fluorescent probes and types of detectors.We currently use a confocal laser scanning microscope CLSM (Zeiss, Oberkochen) equipped with 3-laser excitation (u.v - visible) and confocal optics in the fluorescence mode, as well as a computer-controlled X-Y-Z scanning stage with 0.1 μ resolution.

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.

3-Dimensional immunolabeling and in situ hybridization detection using fluorescence photooxidation and intermediate-voltage Electron Microscopy

1994 ◽  
Vol 52 ◽  
pp. 164-165
Author(s):  
Thomas J. Deerinck ◽  
Maryann E. Martone ◽  
Varda Lev-Ram ◽  
David P. L. Green ◽  
Roger Y. Tsien ◽  
...  
Keyword(s):  
Laser Scanning ◽  
Reactive Oxygen ◽  
Confocal Laser Scanning Microscope ◽  
Fluorescent Dye ◽  
Confocal Laser ◽  
3 Dimensional ◽  
Voltage Electron ◽  
Dimensional Distribution ◽  
Electron Microscopes ◽  
New Generation

The confocal laser scanning microscope has become a powerful tool in the study of the 3-dimensional distribution of proteins and specific nucleic acid sequences in cells and tissues. This is also proving to be true for a new generation of high contrast intermediate voltage electron microscopes (IVEM). Until recently, the number of labeling techniques that could be employed to allow examination of the same sample with both confocal and IVEM was rather limited. One method that can be used to take full advantage of these two technologies is fluorescence photooxidation. Specimens are labeled by a fluorescent dye and viewed with confocal microscopy followed by fluorescence photooxidation of diaminobenzidine (DAB). In this technique, a fluorescent dye is used to photooxidize DAB into an osmiophilic reaction product that can be subsequently visualized with the electron microscope. The precise reaction mechanism by which the photooxidation occurs is not known but evidence suggests that the radiationless transfer of energy from the excited-state dye molecule undergoing the phenomenon of intersystem crossing leads to the formation of reactive oxygen species such as singlet oxygen. It is this reactive oxygen that is likely crucial in the photooxidation of DAB.

Five-Dimensional Microscopy using Widefield-Deconvolution: Practical Considerations and Biological Applications

1996 ◽  
Vol 54 ◽  
pp. 268-269
Author(s):  
W.F. Marshall ◽  
K. Oegema ◽  
J. Nunnari ◽  
A.F. Straight ◽  
D.A. Agard ◽  
...  
Keyword(s):  
Confocal Microscopy ◽  
High Speed ◽  
Laser Scanning ◽  
Ccd Camera ◽  
Image Plane ◽  
Time Lapse ◽  
Laser Scanning Confocal Microscopy ◽  
Three Dimensions ◽  
Excitation Light ◽  
Cooled Ccd

The ability to image cells in three dimensions has brought about a revolution in biological microscopy, enabling many questions to be asked which would be inaccessible without this capability. There are currently two major methods of three dimensional microscopy: laser-scanning confocal microscopy and widefield-deconvolution microscopy. The method of widefield-deconvolution uses a cooled CCD to acquire images from a standard widefield microscope, and then computationally removes out of focus blur. Using such a scheme, it is easy to acquire time-lapse 3D images of living cells without killing them, and to do so for multiple wavelengths (using computer-controlled filter wheels). Thus, it is now not only feasible, but routine, to perform five dimensional microscopy (three spatial dimensions, plus time, plus wavelength).Widefield-deconvolution has several advantages over confocal microscopy. The two main advantages are high speed of acquisition (because there is no scanning, a single optical section is acquired at a time by using a cooled CCD camera) and the use of low excitation light levels Excitation intensity can be much lower than in a confocal microscope for three reasons: 1) longer exposures can be taken since the entire 512x512 image plane is acquired in parallel, so that dwell time is not an issue, 2) the higher quantum efficiently of a CCD detect over those typically used in confocal microscopy (although this is expected to change due to advances in confocal detector technology), and 3) because no pinhole is used to reject light, a much larger fraction of the emitted light is collected. Thus we can typically acquire images with thousands of photons per pixel using a mercury lamp, instead of a laser, for illumination. The use of low excitation light is critical for living samples, and also reduces bleaching. The high speed of widefield microscopy is also essential for time-lapse 3D microscopy, since one must acquire images quickly enough to resolve interesting events.

Vacuoles Induced in Mammalian Cells by Helicobacter Cytotoxin are Acidic Organelles

1990 ◽  
Vol 48 (3) ◽  
pp. 168-169
Author(s):  
M. H. Chestnut ◽  
C. E. Catrenich
Keyword(s):  
Acridine Orange ◽  
Mammalian Cells ◽  
Laser Scanning ◽  
Laser Scanning Microscopy ◽  
Confocal Laser ◽  
Ulcer Disease ◽  
Gastroduodenal Disease ◽  
H Pylori

Helicobacter pylori is a non-invasive, Gram-negative spiral bacterium first identified in 1983, and subsequently implicated in the pathogenesis of gastroduodenal disease including gastritis and peptic ulcer disease. Cytotoxic activity, manifested by intracytoplasmic vacuolation of mammalian cells in vitro, was identified in 55% of H. pylori strains examined. The vacuoles increase in number and size during extended incubation, resulting in vacuolar and cellular degeneration after 24 h to 48 h. Vacuolation of gastric epithelial cells is also observed in vivo during infection by H. pylori. A high molecular weight, heat labile protein is believed to be responsible for vacuolation and to significantly contribute to the development of gastroduodenal disease in humans. The mechanism by which the cytotoxin exerts its effect is unknown, as is the intracellular origin of the vacuolar membrane and contents. Acridine orange is a membrane-permeant weak base that initially accumulates in low-pH compartments. We have used acridine orange accumulation in conjunction with confocal laser scanning microscopy of toxin-treated cells to begin probing the nature and origin of these vacuoles.

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