Towards a Scalable ESPINA for Neuroscience Data Analysis

2011 ◽  
Author(s):  
Juan Morales ◽  
Jorge G. Pen˜a ◽  
Jaime Ferna´ndez ◽  
Angel Rodri´guez
Keyword(s):  
Image Segmentation ◽  
Data Analysis ◽  
Response Times ◽  
Three Dimensional ◽  
3D Models ◽  
Volume Management ◽  
Data Volume ◽  
Computational Processes ◽  
Microscopy Images

ESPINA is an image segmentation tool designed to analyse microscopy images in order to identify neuronal structures and to produce 3D models of these structures. This tool allows to display three-dimensional volumes using auto-stereoscopic monitors. It was initially designed for workstations, but when data volume management or its processing complexity makes unfeasible the implementation of the new tools on these computers, it is necessary to resort to computing servers that delimit response times or by means of scalable solutions and algorithmic optimizations. This paper analyses the migration of this tool from the original implementation to a scalable solution and describes the experience achieved during the development of the workstation version. The proposed alternative is a distributed version of the tool that delegate heavy-computational processes to a cluster, improving the performance of the system in a master/slave architecture.

scholarly journals Structured-light 3D scanning of exhibited historical clothing—a first-ever methodical trial and its results

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Jerzy Montusiewicz ◽  
Marek Miłosz ◽  
Jacek Kęsik ◽  
Kamil Żyła
Keyword(s):  
Cultural Heritage ◽  
Information Technologies ◽  
Structured Light ◽  
Three Dimensional ◽  
3D Models ◽  
3D Scanning ◽  
Dimensional Representation ◽  
3D Scanner ◽  
Three Dimensional Representation ◽  
3D Scanners

AbstractHistorical costumes are part of cultural heritage. Unlike architectural monuments, they are very fragile, which exacerbates the problems of their protection and popularisation. A big help in this can be the digitisation of their appearance, preferably using modern techniques of three-dimensional representation (3D). The article presents the results of the search for examples and methodologies of implementing 3D scanning of exhibited historical clothes as well as the attendant problems. From a review of scientific literature it turns out that so far practically no one in the world has made any methodical attempts at scanning historical clothes using structured-light 3D scanners (SLS) and developing an appropriate methodology. The vast majority of methods for creating 3D models of clothes used photogrammetry and 3D modelling software. Therefore, an innovative approach was proposed to the problem of creating 3D models of exhibited historical clothes through their digitalisation by means of a 3D scanner using structural light technology. A proposal for the methodology of this process and concrete examples of its implementation and results are presented. The problems related to the scanning of 3D historical clothes are also described, as well as a proposal how to solve them or minimise their impact. The implementation of the methodology is presented on the example of scanning elements of the Emir of Bukhara's costume (Uzbekistan) from the end of the nineteenth century, consisting of the gown, turban and shoes. Moreover, the way of using 3D models and information technologies to popularise cultural heritage in the space of digital resources is also discussed.

scholarly journals Comparative Analysis of Digital Models of Objects of Cultural Heritage Obtained by the “3D SLS” and “SfM” Methods

2021 ◽  
Vol 11 (12) ◽  
pp. 5321
Author(s):  
Marcin Barszcz ◽  
Jerzy Montusiewicz ◽  
Magdalena Paśnikowska-Łukaszuk ◽  
Anna Sałamacha
Keyword(s):  
Cultural Heritage ◽  
Low Cost ◽  
Three Dimensional ◽  
3D Models ◽  
Silk Road ◽  
Digital Models ◽  
Global Pandemic ◽  
University Of Technology ◽  
Three Dimensional Models ◽  
3D Digitisation

In the era of the global pandemic caused by the COVID-19 virus, 3D digitisation of selected museum artefacts is becoming more and more frequent practice, but the vast majority is performed by specialised teams. The paper presents the results of comparative studies of 3D digital models of the same museum artefacts from the Silk Road area generated by two completely different technologies: Structure from Motion (SfM)—a method belonging to the so-called low-cost technologies—and by Structured-light 3D Scanning (3D SLS). Moreover, procedural differences in data acquisition and their processing to generate three-dimensional models are presented. Models built using a point cloud were created from data collected in the Afrasiyab museum in Samarkand (Uzbekistan) during “The 1st Scientific Expedition of the Lublin University of Technology to Central Asia” in 2017. Photos for creating 3D models in SfM technology were taken during a virtual expedition carried out under the “3D Digital Silk Road” program in 2021. The obtained results show that the quality of the 3D models generated with SfM differs from the models from the technology (3D SLS), but they may be placed in the galleries of the vitrual museum. The obtained models from SfM do not have information about their size, which means that they are not fully suitable for archiving purposes of cultural heritage, unlike the models from SLS.

scholarly journals 3D-Volume Rendering of the Pelvis with Emphasis on Paraurethral Structures Based on MRI Scans and Comparisons between 3D Slicer and OsiriX®

2021 ◽  
Vol 45 (3) ◽  
Author(s):  
C. M. Durnea ◽  
S. Siddiqi ◽  
D. Nazarian ◽  
G. Munneke ◽  
P. M. Sedgwick ◽  
...  
Keyword(s):  
Image Processing ◽  
Secondary Analysis ◽  
Three Dimensional ◽  
3D Models ◽  
Clinical Role ◽  
Cross Sectional ◽  
3D Slicer ◽  
Mri Scans ◽  
3D Volume ◽  
Good Agreement

AbstractThe feasibility of rendering three dimensional (3D) pelvic models of vaginal, urethral and paraurethral lesions from 2D MRI has been demonstrated previously. To quantitatively compare 3D models using two different image processing applications: 3D Slicer and OsiriX. Secondary analysis and processing of five MRI scan based image sets from female patients aged 29–43 years old with vaginal or paraurethral lesions. Cross sectional image sets were used to create 3D models of the pelvic structures with 3D Slicer and OsiriX image processing applications. The linear dimensions of the models created using the two different methods were compared using Bland-Altman plots. The comparisons demonstrated good agreement between measurements from the two applications. The two data sets obtained from different image processing methods demonstrated good agreement. Both 3D Slicer and OsiriX can be used interchangeably and produce almost similar results. The clinical role of this investigation modality remains to be further evaluated.

scholarly journals Improving 3D-3D facial registration methods: potential role of three-dimensional models in personal identification of the living

2021 ◽  
Author(s):  
Daniele Gibelli ◽  
Andrea Palamenghi ◽  
Pasquale Poppa ◽  
Chiarella Sforza ◽  
Cristina Cattaneo ◽  
...  
Keyword(s):  
Three Dimensional ◽  
3D Models ◽  
Personal Identification ◽  
Surveillance Systems ◽  
3D Registration ◽  
Three Dimensional Models ◽  
Point To Point ◽  
Point Distance ◽  
Male Subjects

AbstractPersonal identification of the living from video surveillance systems usually involves 2D images. However, the potentiality of three-dimensional facial models in gaining personal identification through 3D-3D comparison still needs to be verified. This study aims at testing the reliability of a protocol for 3D-3D registration of facial models, potentially useful for personal identification. Fifty male subjects aged between 18 and 45 years were randomly chosen from a database of 3D facial models acquired through stereophotogrammetry. For each subject, two acquisitions were available; the 3D models of faces were then registered onto other models belonging to the same and different individuals according to the least point-to-point distance on the entire facial surface, for a total of 50 matches and 50 mismatches. RMS value (root mean square) of point-to-point distance between the two models was then calculated through the VAM® software. Intra- and inter-observer errors were assessed through calculation of relative technical error of measurement (rTEM). Possible statistically significant differences between matches and mismatches were assessed through Mann–Whitney test (p < 0.05). Both for intra- and inter-observer repeatability rTEM was between 2.2 and 5.2%. Average RMS point-to-point distance was 0.50 ± 0.28 mm in matches, 2.62 ± 0.56 mm in mismatches (p < 0.01). An RMS threshold of 1.50 mm could distinguish matches and mismatches in 100% of cases. This study provides an improvement to existing 3D-3D superimposition methods and confirms the great advantages which may derive to personal identification of the living from 3D facial analysis.

scholarly journals Heritage Artefacts in the COVID-19 Era: The Aura and Authenticity of 3D Models

2021 ◽  
Vol 7 (1) ◽  
pp. 519-539
Author(s):  
Thiago Minete Cardozo ◽  
Costas Papadopoulos
Keyword(s):  
User Experience ◽  
Three Dimensional ◽  
3D Models ◽  
Essential Elements ◽  
The Other ◽  
Social Distancing ◽  
The Public ◽  
Affective Experiences ◽  
The One ◽  
Digital Engagement

Abstract Museums have been increasingly investing in their digital presence. This became more pressing during the COVID-19 pandemic since heritage institutions had, on the one hand, to temporarily close their doors to visitors while, on the other, find ways to communicate their collections to the public. Virtual tours, revamped websites, and 3D models of cultural artefacts were only a few of the means that museums devised to create alternative ways of digital engagement and counteract the physical and social distancing measures. Although 3D models and collections provide novel ways to interact, visualise, and comprehend the materiality and sensoriality of physical objects, their mediation in digital forms misses essential elements that contribute to (virtual) visitor/user experience. This article explores three-dimensional digitisations of museum artefacts, particularly problematising their aura and authenticity in comparison to their physical counterparts. Building on several studies that have problematised these two concepts, this article establishes an exploratory framework aimed at evaluating the experience of aura and authenticity in 3D digitisations. This exploration allowed us to conclude that even though some aspects of aura and authenticity are intrinsically related to the physicality and materiality of the original, 3D models can still manifest aura and authenticity, as long as a series of parameters, including multimodal contextualisation, interactivity, and affective experiences are facilitated.

scholarly journals Virtual Archaeology of Death and Burial: A Procedure for Integrating 3D Visualization and Analysis in Archaeothanatology

2021 ◽  
Vol 7 (1) ◽  
pp. 540-555
Author(s):  
Hayley L. Mickleburgh ◽  
Liv Nilsson Stutz ◽  
Harry Fokkens
Keyword(s):  
Spatial Information ◽  
3D Visualization ◽  
Rapid Development ◽  
Three Dimensional ◽  
3D Models ◽  
The Body ◽  
Test Case ◽  
Archaeology Of Death ◽  
Human Burials ◽  
3D Information

Abstract The reconstruction of past mortuary rituals and practices increasingly incorporates analysis of the taphonomic history of the grave and buried body, using the framework provided by archaeothanatology. Archaeothanatological analysis relies on interpretation of the three-dimensional (3D) relationship of bones within the grave and traditionally depends on elaborate written descriptions and two-dimensional (2D) images of the remains during excavation to capture this spatial information. With the rapid development of inexpensive 3D tools, digital replicas (3D models) are now commonly available to preserve 3D information on human burials during excavation. A procedure developed using a test case to enhance archaeothanatological analysis and improve post-excavation analysis of human burials is described. Beyond preservation of static spatial information, 3D visualization techniques can be used in archaeothanatology to reconstruct the spatial displacement of bones over time, from deposition of the body to excavation of the skeletonized remains. The purpose of the procedure is to produce 3D simulations to visualize and test archaeothanatological hypotheses, thereby augmenting traditional archaeothanatological analysis. We illustrate our approach with the reconstruction of mortuary practices and burial taphonomy of a Bell Beaker burial from the site of Oostwoud-Tuithoorn, West-Frisia, the Netherlands. This case study was selected as the test case because of its relatively complete context information. The test case shows the potential for application of the procedure to older 2D field documentation, even when the amount and detail of documentation is less than ideal.

scholarly journals 3D Culture Systems for Exploring Cancer Immunology

Cancers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 56
Author(s):  
Allison A. Fitzgerald ◽  
Eric Li ◽  
Louis M. Weiner
Keyword(s):  
Immune Cell ◽  
Three Dimensional ◽  
3D Culture ◽  
3D Models ◽  
Therapeutic Benefit ◽  
Cancer Immunology ◽  
Microfluidic Chips ◽  
Murine Models ◽  
Human Immune System ◽  
Culture Systems

Cancer immunotherapy has revolutionized cancer treatment, spurring extensive investigation into cancer immunology and how to exploit this biology for therapeutic benefit. Current methods to investigate cancer-immune cell interactions and develop novel drug therapies rely on either two-dimensional (2D) culture systems or murine models. However, three-dimensional (3D) culture systems provide a potentially superior alternative model to both 2D and murine approaches. As opposed to 2D models, 3D models are more physiologically relevant and better replicate tumor complexities. Compared to murine models, 3D models are cheaper, faster, and can study the human immune system. In this review, we discuss the most common 3D culture systems—spheroids, organoids, and microfluidic chips—and detail how these systems have advanced our understanding of cancer immunology.

scholarly journals Extending In-Plane Impedance Measurements from 2D to 3D Cultures: Design Considerations

2021 ◽  
Vol 8 (1) ◽  
pp. 11
Author(s):  
Sorel E. De Leon ◽  
Lana Cleuren ◽  
Zay Yar Oo ◽  
Paul R. Stoddart ◽  
Sally L. McArthur
Keyword(s):  
Three Dimensional ◽  
3D Culture ◽  
Collagen Gel ◽  
Impedance Measurement ◽  
Impedance Spectrum ◽  
3D Models ◽  
Low Frequencies ◽  
3D Cell Cultures ◽  
3D Collagen ◽  
2D And 3D

Three-dimensional (3D) cell cultures have recently emerged as tools for biologically modelling the human body. As 3D models make their way into laboratories there is a need to develop characterisation techniques that are sensitive enough to monitor the cells in real time and without the need for chemical labels. Impedance spectroscopy has been shown to address both of these challenges, but there has been little research into the full impedance spectrum and how the different components of the system affect the impedance signal. Here we investigate the impedance of human fibroblast cells in 2D and 3D collagen gel cultures across a broad range of frequencies (10 Hz to 5 MHz) using a commercial well with in-plane electrodes. At low frequencies in both 2D and 3D models it was observed that protein adsorption influences the magnitude of the impedance for the cell-free samples. This effect was eliminated once cells were introduced to the systems. Cell proliferation could be monitored in 2D at intermediate frequencies (30 kHz). However, the in-plane electrodes were unable to detect any changes in the impedance at any frequency when the cells were cultured in the 3D collagen gel. The results suggest that in designing impedance measurement devices, both the nature and distribution of the cells within the 3D culture as well as the architecture of the electrodes are key variables.

Prevascularized, Co-Culture Model for Breast Cancer Drug Development

2012 ◽  
Author(s):  
Lauren Marshall ◽  
Isabel Löwstedt ◽  
Paul Gatenholm ◽  
Joel Berry
Keyword(s):  
Breast Cancer ◽  
Drug Development ◽  
Three Dimensional ◽  
Human Tumor ◽  
3D Models ◽  
Cancer Drug ◽  
Cancer Therapies ◽  
Anti Cancer

The objective of this study was to create 3D engineered tissue models to accelerate identification of safe and efficacious breast cancer drug therapies. It is expected that this platform will dramatically reduce the time and costs associated with development and regulatory approval of anti-cancer therapies, currently a multi-billion dollar endeavor [1]. Existing two-dimensional (2D) in vitro and in vivo animal studies required for identification of effective cancer therapies account for much of the high costs of anti-cancer medications and health insurance premiums borne by patients, many of whom cannot afford it. An emerging paradigm in pharmaceutical drug development is the use of three-dimensional (3D) cell/biomaterial models that will accurately screen novel therapeutic compounds, repurpose existing compounds and terminate ineffective ones. In particular, identification of effective chemotherapies for breast cancer are anticipated to occur more quickly in 3D in vitro models than 2D in vitro environments and in vivo animal models, neither of which accurately mimic natural human tumor environments [2]. Moreover, these 3D models can be multi-cellular and designed with extracellular matrix (ECM) function and mechanical properties similar to that of natural in vivo cancer environments [3].

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