scholarly journals Reconstruction of Axial Tomographic High Resolution Data from Confocal Fluorescence Microscopy: A Method for Improving 3D FISH Images

2000 ◽  
Vol 20 (1) ◽  
pp. 7-15 ◽  
Author(s):  
R. Heintzmann ◽  
G. Kreth ◽  
C. Cremer
Keyword(s):  
High Resolution ◽  
Laser Scanning ◽  
Axial Direction ◽  
Laser Scanning Microscopy ◽  
Three Dimensions ◽  
Confocal Laser ◽  
Data Sets ◽  
Data Set ◽  
High Resolution Data ◽  
3D Data

Fluorescent confocal laser scanning microscopy allows an improved imaging of microscopic objects in three dimensions. However, the resolution along the axial direction is three times worse than the resolution in lateral directions. A method to overcome this axial limitation is tilting the object under the microscope, in a way that the direction of the optical axis points into different directions relative to the sample. A new technique for a simultaneous reconstruction from a number of such axial tomographic confocal data sets was developed and used for high resolution reconstruction of 3D‐data both from experimental and virtual microscopic data sets. The reconstructed images have a highly improved 3D resolution, which is comparable to the lateral resolution of a single deconvolved data set. Axial tomographic imaging in combination with simultaneous data reconstruction also opens the possibility for a more precise quantification of 3D data. The color images of this publication can be accessed from http://www.esacp.org/acp/2000/20‐1/heintzmann.htm. At this web address an interactive 3D viewer is additionally provided for browsing the 3D data. This java applet displays three orthogonal slices of the data set which are dynamically updated by user mouse clicks or keystrokes.

Imaging and Characterization of Microporous Carbonates Using Confocal and Electron Microscopy of Epoxy Pore Casts

SPE Journal ◽  
2019 ◽  
Vol 24 (03) ◽  
pp. 1220-1233 ◽  
Author(s):  
A.. Hassan ◽  
V.. Chandra ◽  
M. P. Yutkin ◽  
T. W. Patzek ◽  
D. N. Espinoza
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Oil Recovery ◽  
Laser Scanning ◽  
Two Dimensions ◽  
Laser Scanning Microscopy ◽  
Three Dimensions ◽  
Confocal Laser ◽  
Improved Oil Recovery ◽  
Imaging Approach

Summary Microporous carbonates contain perhaps 50% of the oil left behind in current projects in the giant carbonate fields in the Middle East and elsewhere. Pore geometry, connectivity, and wettability of the micropore systems in these carbonates are of paramount importance in finding new improved-oil-recovery methods. In this study, we present a robust pore-imaging approach that uses confocal laser scanning microscopy (CLSM) to obtain high-resolution 3D images of etched epoxy pore casts of the highly heterogeneous carbonates. In our approach, we have increased the depth of investigation for carbonates 20-fold, from 10 µm reported by Fredrich (1999) and Shah et al. (2013) to 200 µm. In addition, high-resolution 2D images from scanning electron microscopy (SEM) have been correlated with the 3D models from CLSM to develop a multiscale imaging approach that covers a range of scales, from millimeters in three dimensions to micrometers in two dimensions. The developed approach was implemented to identify various pore types [e.g., intercrystalline microporosity (IM), intragranular microporosity (IGM), and interboundary sheet pores (SPs)] in limestone and dolomite samples.

scholarly journals Direct determination of the area function for nanoindentation experiments

2021 ◽  
Author(s):  
Christian Saringer ◽  
Michael Tkadletz ◽  
Markus Kratzer ◽  
Megan J. Cordill
Keyword(s):  
Laser Scanning ◽  
Operation Mode ◽  
Direct Determination ◽  
Fused Silica ◽  
Laser Scanning Microscopy ◽  
Confocal Laser ◽  
Data Sets ◽  
Area Function ◽  
3D Data

Abstract The determination of a suitable correction for tip blunting is crucial in order to obtain useful mechanical properties from nanoindentation experiments. While typically the required area function is acquired from the indentation of a reference material, the direct imaging by suitable methods is an interesting alternative. In this paper, we investigate the applicability of confocal laser scanning microscopy (CLSM), atomic force microscopy (AFM), and self-imaging by scanning a sharp silicon tip using the scanning probe microscopy extension of the nanoindentation system and compare the results to the area function obtained by the indentation of fused silica. The important tip characteristics were determined by various methods based on the analysis of the obtained 3D data sets. It was found that the suitability of CLSM and AFM depend on the resolution and the operation mode, respectively. While for these methods only limited consistency of the determined tip characteristics was found, self-imaging resulted in an excellent overall agreement. Graphic abstract

scholarly journals Touching The Human Neuron: User-Centric Augmented Reality Viewing and Interaction of in-vivo Cellular Confocal Laser Scanning Microscopy (CLSM) Utilizing High Resolution zStack Data Sets

2017 ◽  
Vol 41 (1) ◽  
Author(s):  
Scott Riddle ◽  
Daniel Wasser ◽  
Michael McCarthy
Keyword(s):  
High Resolution ◽  
Augmented Reality ◽  
Confocal Laser Scanning Microscopy ◽  
Laser Scanning ◽  
Laser Scanning Microscopy ◽  
Confocal Laser ◽  
Data Sets ◽  
Time Interaction ◽  
User Centric

This is the first report of a prototype that allows for real-time interaction with high-resolution cellular modules using GLASS© technology. The prototype was developed* using zStack data sets which allow for real-time interaction of low polygon and direct surface models exported from primary source imaging. This paper also discusses potential educational and clinical applications of a wearable, interactive, user-centric, augmented reality visualization of cellular structures.Full article title: Touching The Human Neuron: User-Centric Augmented Reality Viewing and Interaction of in-vivo Cellular Confocal Laser Scanning Microscopy (CLSM) Utilizing High Resolution zStack Data Sets for Applications in Medical Education and Clinical Medicine Using GLASS and Motion Tracking Technology

Confocal laser scanning microscopy and Raman imagery of the late Neoproterozoic Chichkan microbiota of South Kazakhstan

2010 ◽  
Vol 84 (3) ◽  
pp. 402-416 ◽  
Author(s):  
J. William Schopf ◽  
Anatoliy B. Kudryavtsev ◽  
Vladimir N. Sergeev
Keyword(s):  
Confocal Laser Scanning Microscopy ◽  
Laser Scanning ◽  
Three Dimensional ◽  
Laser Scanning Microscopy ◽  
Three Dimensions ◽  
Confocal Laser Scanning ◽  
Scanning Microscopy ◽  
Confocal Laser ◽  
Depth Study ◽  
Late Neoproterozoic

Precambrian microbiotas, such as that permineralized in bedded and stromatolitic cherts of the late Neoproterozoic, 750- to 800-Ma-old, Chichkan Formation of South Kazakhstan, have traditionally been studied by optical microscopy only. Such studies, however, are incapable of documenting accurately either the three-dimensional morphology of such fossils or their chemical composition and that of their embedding minerals. As shown here by analyses of fossils of the Chichkan Lagerstätte, the solution to these long-standing problems is provided by two techniques recently introduced to paleontology: confocal laser scanning microscopy (CLSM) and Raman imagery. The two techniques are used together to characterize, in situ and at micron-scale resolution, the cellular and organismal morphology of the thin section-embedded organic-walled Chichkan fossils. In addition, Raman imagery is used to analyze the molecular-structural composition of the carbonaceous fossils and of their embedding mineral matrix, identify the composition of intracellular inclusions, and quantitatively assess the geochemical maturity of the Chichkan organic matter.CLSM and Raman imagery are both broadly applicable to the study of fossils, whether megascopic or microscopic and regardless of mode of preservation, and both are non-intrusive and non-destructive, factors that permit their use for analyses of archived specimens. They are especially useful for the study of microscopic fossils, as is demonstrated in this first in-depth study of diverse taxa of a single Precambrian microbiota for which they provide information in three dimensions at high spatial resolution about their organismal morphology, cellular anatomy, kerogenous composition, mode of preservation, and taphonomy and fidelity of preservation.

scholarly journals Micro-CT for Biological and Biomedical Studies: A Comparison of Imaging Techniques

2021 ◽  
Vol 7 (9) ◽  
pp. 172
Author(s):  
Kleoniki Keklikoglou ◽  
Christos Arvanitidis ◽  
Georgios Chatzigeorgiou ◽  
Eva Chatzinikolaou ◽  
Efstratios Karagiannidis ◽  
...  
Keyword(s):  
Laser Scanning ◽  
Imaging Techniques ◽  
Laser Scanning Microscopy ◽  
Three Dimensions ◽  
Morphological Data ◽  
Confocal Laser ◽  
Micro Ct ◽  
Micro Computed Tomography ◽  
Non Destructive ◽  
Great Resolution

Several imaging techniques are used in biological and biomedical studies. Micro-computed tomography (micro-CT) is a non-destructive imaging technique that allows the rapid digitisation of internal and external structures of a sample in three dimensions and with great resolution. In this review, the strengths and weaknesses of some common imaging techniques applied in biological and biomedical fields, such as optical microscopy, confocal laser scanning microscopy, and scanning electron microscopy, are presented and compared with the micro-CT technique through five use cases. Finally, the ability of micro-CT to create non-destructively 3D anatomical and morphological data in sub-micron resolution and the necessity to develop complementary methods with other imaging techniques, in order to overcome limitations caused by each technique, is emphasised.

Male terminalia of Ceraphronoidea: morphological diversity in an otherwise monotonous taxon

2013 ◽  
Vol 44 (3-4) ◽  
pp. 261-347 ◽  
Author(s):  
István Mikó ◽  
Lubomir Masner ◽  
Eva Johannes ◽  
Matthew J. Yoder ◽  
Andrew R. Deans
Keyword(s):  
Male Genitalia ◽  
Laser Scanning ◽  
Strong Support ◽  
Relevant Information ◽  
Laser Scanning Microscopy ◽  
Confocal Laser ◽  
Generic Level ◽  
Data Set ◽  
Anatomy Ontology ◽  
Equal Weighting

The skeletomuscular system of male terminalia in Evaniomorpha (Hymenoptera) is described and the functional morphology of male genitalia is discussed. Confocal laser scanning microscopy is the primary method used for illustrating anatomical phenotypes, and a domain-specific anatomy ontology is employed to more explicitly describe anatomical structures. A comprehensive data set of ceraphronoid male genitalia is analyzed, yielding the first phylogeny of the superfamily. One hundred and one taxa, including three outgroups, are scored for 48 characters. Ceraphronoidea are recovered as sister to the remaining Evaniomorpha in the implied weighting analyses. Numerous character states suggest that Ceraphronoidea is a relatively basal apocritan lineage. Ceraphronoidea, Ceraphronidae, and Megaspilinae are each retrieved as monophyletic in all analyses. Megaspilidae is not recovered as monophyletic. Lagynodinae is monophyletic in the implied weighting analyses with strong support and is a polytomy in the equal weighting analysis. Lagynodinae shares numerous plesiomorphies with both Megaspilinae and Ceraphronidae. Relationships among genera are weakly corroborated. Masner is sister of Ceraphronidae. Trassedia is nested within Ceraphronidae based on the present analysis. Because of this and numerous features shared between it and Ceraphron we transfer Trassedia from Megaspilidae to Ceraphronidae. Dendrocerus forms a single monophyletic clade, with modest support, together with some Conostigmus species. This result challenges the utility of such traditional diagnostic characters as ocellar arrangement and shape of the male flagellomeres. Aphanogmus is monophyletic in the implied weighting, but remains a polytomy with Ceraphron in the equal weighting analysis. Gnathoceraphron is always nested within a well-supported Aphanogmus clade. Cyoceraphron and Elysoceraphron are nested within Ceraphron and Aphanogmus, respectively. The male genitalia prove to be a substantial source of phylogenetically relevant information. Our results indicate that a reclassification of Ceraphronoidea both at the family and generic level is necessary but that more data are required.

scholarly journals Automated Confocal Laser Scanning Microscopy and Semiautomated Image Processing for Analysis of Biofilms

1998 ◽  
Vol 64 (11) ◽  
pp. 4115-4127 ◽  
Author(s):  
Martin Kuehn ◽  
Martina Hausner ◽  
Hans-Joachim Bungartz ◽  
Michael Wagner ◽  
Peter A. Wilderer ◽  
...  
Keyword(s):  
Image Analysis ◽  
Laser Scanning ◽  
Fluorescent Protein ◽  
Image Acquisition ◽  
Three Dimensional ◽  
Laser Scanning Microscopy ◽  
Three Dimensions ◽  
Confocal Laser ◽  
Cross Sectional ◽  
In Situ Conditions

ABSTRACT The purpose of this study was to develop and apply a quantitative optical method suitable for routine measurements of biofilm structures under in situ conditions. A computer program was designed to perform automated investigations of biofilms by using image acquisition and image analysis techniques. To obtain a representative profile of a growing biofilm, a nondestructive procedure was created to study and quantify undisturbed microbial populations within the physical environment of a glass flow cell. Key components of the computer-controlled processing described in this paper are the on-line collection of confocal two-dimensional (2D) cross-sectional images from a preset 3D domain of interest followed by the off-line analysis of these 2D images. With the quantitative extraction of information contained in each image, a three-dimensional reconstruction of the principal biological events can be achieved. The program is convenient to handle and was generated to determine biovolumes and thus facilitate the examination of dynamic processes within biofilms. In the present study, Pseudomonas fluorescens or a green fluorescent protein-expressing Escherichia coli strain, EC12, was inoculated into glass flow cells and the respective monoculture biofilms were analyzed in three dimensions. In this paper we describe a method for the routine measurements of biofilms by using automated image acquisition and semiautomated image analysis.

scholarly journals EcoDes-DK15: High-resolution ecological descriptors of vegetation and terrain derived from Denmark's national airborne laser scanning data set

2021 ◽  
Author(s):  
Jakob J. Assmann ◽  
Jesper E. Moeslund ◽  
Urs A. Treier ◽  
Signe Normand
Keyword(s):  
Remote Sensing ◽  
High Resolution ◽  
Laser Scanning ◽  
Three Dimensional ◽  
Airborne Laser Scanning ◽  
Data Sets ◽  
Ecosystem Structure ◽  
Data Set ◽  
Vegetation Height ◽  
Airborne Laser

Abstract. Biodiversity studies could strongly benefit from three-dimensional data on ecosystem structure derived from contemporary remote sensing technologies, such as Light Detection and Ranging (LiDAR). Despite the increasing availability of such data at regional and national scales, the average ecologist has been limited in accessing them due to high requirements on computing power and remote-sensing knowledge. We processed Denmark's publicly available national Airborne Laser Scanning (ALS) data set acquired in 2014/15 together with the accompanying elevation model to compute 70 rasterized descriptors of interest for ecological studies. With a grain size of 10 m, these data products provide a snapshot of high-resolution measures including vegetation height, structure and density, as well as topographic descriptors including elevation, aspect, slope and wetness across more than forty thousand square kilometres covering almost all of Denmark's terrestrial surface. The resulting data set is comparatively small (~ 87 GB, compressed 16.4 GB) and the raster data can be readily integrated into analytical workflows in software familiar to many ecologists (GIS software, R, Python). Source code and documentation for the processing workflow are openly available via a code repository, allowing for transfer to other ALS data sets, as well as modification or re-calculation of future instances of Denmark’s national ALS data set. We hope that our high-resolution ecological vegetation and terrain descriptors (EcoDes-DK15) will serve as an inspiration for the publication of further such data sets covering other countries and regions and that our rasterized data set will provide a baseline of the ecosystem structure for current and future studies of biodiversity, within Denmark and beyond.

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