scholarly journals Intercomparison of photogrammetry software for three-dimensional vegetation modelling

2018 ◽  
Vol 5 (7) ◽  
pp. 172192 ◽  
Author(s):  
Alexandra Probst ◽  
Demetrios Gatziolis ◽  
Nikolay Strigul
Keyword(s):  
A Priori ◽  
Three Dimensional ◽  
Type I ◽  
Receiver Operating Characteristic Curves ◽  
Research Areas ◽  
Vegetation Modelling ◽  
Dimensional Reconstruction ◽  
Tree Models ◽  
Type Ii Errors

Photogrammetry-based three-dimensional reconstruction of objects is becoming increasingly appealing in research areas unrelated to computer vision. It has the potential to facilitate the assessment of forest inventory-related parameters by enabling or expediting resource measurements in the field. We hereby compare several implementations of photogrammetric algorithms (CMVS/PMVS, CMPMVS, MVE, OpenMVS, SURE and Agisoft PhotoScan) with respect to their performance in vegetation assessment. The evaluation is based on (i) a virtual scene where the precise location and dimensionality of objects is known a priori and is thus conducive to a quantitative comparison and (ii) using series of in situ acquired photographs of vegetation with overlapping field of view where the photogrammetric outcomes are compared qualitatively. Performance is quantified by computing receiver operating characteristic curves that summarize the type-I and type-II errors between the reference and reconstructed tree models. Similar artefacts are observed in synthetic- and in situ -based reconstructions.

scholarly journals A guided approach for subtomogram averaging of challenging macromolecular assemblies

2020 ◽  
Author(s):  
Danielle Grotjahn ◽  
Saikat Chowdhury ◽  
Gabriel C. Lander
Keyword(s):  
Electron Tomography ◽  
A Priori ◽  
Three Dimensional ◽  
Structural Heterogeneity ◽  
Dimensional Structure ◽  
Diverse Range ◽  
Macromolecular Assemblies ◽  
Cryo Electron Tomography ◽  
Subtomogram Averaging

AbstractCryo-electron tomography is a powerful biophysical technique enabling three-dimensional visualization of complex biological systems. Macromolecular targets of interest identified within cryo-tomograms can be computationally extracted, aligned, and averaged to produce a better-resolved structure through a process called subtomogram averaging (STA). However, accurate alignment of macromolecular machines that exhibit extreme structural heterogeneity and conformational flexibility remains a significant challenge with conventional STA approaches. To expand the applicability of STA to a broader range of pleomorphic complexes, we developed a user-guided, focused refinement approach that can be incorporated into the standard STA workflow to facilitate the robust alignment of particularly challenging samples. We demonstrate that it is possible to align visually recognizable portions of multi-subunit complexes by providing a priori information regarding their relative orientations within cryo-tomograms, and describe how this strategy was applied to successfully elucidate the first three-dimensional structure of the dynein-dynactin motor protein complex bound to microtubules. Our approach expands the application of STA for solving a more diverse range of heterogeneous biological structures, and establishes a conceptual framework for the development of automated strategies to deconvolve the complexity of crowded cellular environments and improve in situ structure determination technologies.

scholarly journals A virtual diorama. Mapping archives in situ at places of cultural significance

1970 ◽  
pp. 22-36
Author(s):  
Jonathan Westin ◽  
Gunnar Almevik
Keyword(s):  
Spatial Information ◽  
Three Dimensional ◽  
Physical Space ◽  
Cultural Significance ◽  
Dimensional Reconstruction ◽  
Historical Photographs ◽  
New Applications ◽  
Archive Material

Using the wooden church of Södra Råda as a case study, this article concerns new applications of technology to contextualise and activate archive material in situ at places of cultural significance. Using a combination of augmented reality and virtual reality, we describe a process of turning historical photographs and two-dimensional reconstruction drawings into three-dimensional virtual models that can be lined up to a physical space. The leading questions for our investigation concern how archive material can be contextualised, and how the result may be made accessible in situ and contribute to place development. The result of this research suggests possibilities for using historical photographs to faithfully reconstruct lost historical spaces as three-dimensional surfaces that contextualise documentation and offer spatial information.

Challenges of three-dimensional reconstruction of ribonucleoprotein complexes from electron spectroscopic images - Reconstructing ribosomal RNA

1996 ◽  
Vol 54 ◽  
pp. 52-53
Author(s):  
D.R. Beniac ◽  
G.J. Czarnota ◽  
T.A. Bartlett ◽  
F.P. Ottensmeyer ◽  
G. Harauz
Keyword(s):  
Ribosomal Rna ◽  
Correlation Functions ◽  
Three Dimensional ◽  
Three Dimensional Reconstruction ◽  
Mutual Correlation ◽  
Ribosomal Subunits ◽  
E Coli ◽  
Ribonucleoprotein Complexes ◽  
Dimensional Reconstruction

Transmission electron microscopy has been dominant in structural studies of the ribosome and its constituent ribonucleic acids and proteins. Ribosomal RNA (rRNA) has central importance in the architecture of this complex and in protein synthesis. Our work has entailed using electron spectroscopic imaging (ESI) to probe the tertiary structure of rRNA in situ in a prokaryote (Escherichia coli) and in a eukaryote (Thermomyces lanuginosus). ESI uses only electrons which have lost a specific amount of energy due to specific inner-shell ionisation interactions with the specimen to form an elemental map. In nucleoprotein complexes, a map of the phosphorus distribution represents primarily a projection of the phosphate backbone of the nucleic acid component. The visualisation of rRNA in situ in the intact ribosomal subunit by ESI was demonstrated almost a decade ago to be feasible. Our work on quantitative image analysis of ES images of E. coli and Th. lanuginosus ribosomal subunits has presented unique challenges and has resulted in new algorithmic developments generally applicable to such images. These innovations include a singular pretreatment procedure, the use of mutual correlation functions rather than cross correlation functions to reduce the effect of low spatial frequency components, and angular determination using iterative quaternion-assisted angular reconstitution to compute a three-dimensional reconstruction. These investigations have produced direct information regarding ribosomal rRNA localisation in the ribosomal subunits of E. coli and Th. lanuginosus, and the position of non-conserved sequences.

Three-dimensional reconstruction of axonemal outer dynein arms in situ by electron tomography

2005 ◽  
Vol 62 (2) ◽  
pp. 69-83 ◽  
Author(s):  
Pietro Lupetti ◽  
Salvatore Lanzavecchia ◽  
David Mercati ◽  
Francesca Cantele ◽  
Romano Dallai ◽  
...  
Keyword(s):  
Electron Tomography ◽  
Three Dimensional ◽  
Three Dimensional Reconstruction ◽  
Dimensional Reconstruction ◽  
Dynein Arms

scholarly journals Value of CT and three-dimensional reconstruction revealing specific radiological signs for screening causative high jugular bulb in patients with Menière's disease

2020 ◽  
Author(s):  
Junjiao Hu ◽  
Anquan Peng ◽  
Kai Deng ◽  
Chao Huang ◽  
Qin Wang ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Jugular Bulb ◽  
Type I ◽  
Three Dimensional Reconstruction ◽  
Inferior Margin ◽  
Type Iii ◽  
High Jugular Bulb ◽  
Imaging Results ◽  
Significant Difference ◽  
Dimensional Reconstruction

Abstract Background The aim of the present study was to investigate the pathological features of vestibular aqueduct (VA) related high jugular bulb (HJB) and explore the possible cause-consequence relation between HJB and endolymphatic hydrops (EH), and the potential specific radiological signs for screening causative HJB in MD. Methods High-resolution computed tomography (HRCT) and three-dimensional reconstruction (3DRC) were used to detect the anatomical variables associated with VA and jugular bulb (JB) in hydropic and non-hydropic ears. The presence or absence of EH in the inner ear was determined by gadopentetate dimeglumine-enhanced magnetic resonance imaging. Results JB was classified as: Type 1, no bulb; type 2, below the inferior margin of the posterior semicircular canal (PSCC); type 3, between the inferior margin of the PSCC and the inferior margin of the internal auditory canal (IAC); type 4, above the inferior margin of the IAC. There were no significant differences in the presence of types 1, 2 and 3 JB between two groups. The presence of type 4 JB, average height of the JB and prevalence of the non-visualization of the VA in CT scans showed significant differences between two groups. The morphological pattern between the JB and VA revealing by 3DRC was classified as: Type I, the JB was not in contact with the VA; type II, the JB was in contact with the VA, but the latter was intact without obstruction; type III, the VA was obliterated by HJB encroachment. There were no significant differences in the presence of type I and II between two groups. Type III was identified in 5 hydropic ears but no non-hydropic ears, with a significant difference observed between the two groups.Conclusion The present results showed that JB height and non-visualization of the VA on Pöschl's plane could render patients susceptible to the development of EH. A jugular bulb reaching above the inferior margin of the IAC (type 4 JB) could obstruct VA, resulting in EH in a few isolated patients with MD. VA obliteration revealed by 3DRC, as a specific radiological sign, may have the potential for screening causative HJB in MD.

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