scholarly journals The Natural Historian's Guide to the CT Galaxy: Step-by-Step Instructions for Preparing and Analyzing Computed Tomographic (CT) Data Using Cross-Platform, Open Access Software

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
T J Buser ◽  
O F Boyd ◽  
Á Cortés ◽  
C M Donatelli ◽  
M A Kolmann ◽  
...  
Keyword(s):  
Open Access ◽  
3D Printing ◽  
3D Visualization ◽  
3D Models ◽  
Digital Data ◽  
Anatomical Structures ◽  
Computed Tomographic ◽  
Biomechanical Models ◽  
Cross Platform ◽  
Ct Data

Synopsis The decreasing cost of acquiring computed tomographic (CT) data has fueled a global effort to digitize the anatomy of museum specimens. This effort has produced a wealth of open access digital three-dimensional (3D) models of anatomy available to anyone with access to the Internet. The potential applications of these data are broad, ranging from 3D printing for purely educational purposes to the development of highly advanced biomechanical models of anatomical structures. However, while virtually anyone can access these digital data, relatively few have the training to easily derive a desirable product (e.g., a 3D visualization of an anatomical structure) from them. Here, we present a workflow based on free, open source, cross-platform software for processing CT data. We provide step-by-step instructions that start with acquiring CT data from a new reconstruction or an open access repository, and progress through visualizing, measuring, landmarking, and constructing digital 3D models of anatomical structures. We also include instructions for digital dissection, data reduction, and exporting data for use in downstream applications such as 3D printing. Finally, we provide Supplementary Videos and workflows that demonstrate how the workflow facilitates five specific applications: measuring functional traits associated with feeding, digitally isolating anatomical structures, isolating regions of interest using semi-automated segmentation, collecting data with simple visual tools, and reducing file size and converting file type of a 3D model.

scholarly journals Visualizing Votive Practice: Exploring Limestone and Terracotta Sculpture from Athienou-Malloura through 3D Models

2020 ◽  
Author(s):  
Derek B. Counts ◽  
Erik Walcek Averett ◽  
Kevin Garstki ◽  
Michael K. Toumazou
Keyword(s):  
High Resolution ◽  
Open Access ◽  
3D Visualization ◽  
Contextual Information ◽  
3D Models ◽  
Data Publishing ◽  
Archaeological Data ◽  
Archaeological Project ◽  
High Resolution Models ◽  
Visualization Techniques

Visualizing Votive Practice is an innovative, open-access, digital monograph that explores the limestone and terracotta sculptures excavated from a rural sanctuary at the site of Athienou-Malloura (Cyprus) by the Athienou Archaeological Project. Chapters on the archaeology of the site, the historiography of Cypriot sculpture, and perspectives on archaeological visualization provide context for the catalogue of 50 representative examples of votive sculpture from the sanctuary. The catalogue not only includes formal and contextual information for each object, but also embeds 3D models directly onto the page. Readers can not only view, but also manipulate, measure, zoom, and rotate each model. Additionally, links at the bottom of each entry unleash high-resolution models with accompanying metadata on the Open Context archaeological data publishing platform and on via the Sketchfab 3D viewing platform as well. This innovative monograph is aimed at a variety of audiences, from Mediterranean archaeologists and students to specialists interested in 3D visualization techniques.

scholarly journals 3D printing of crystallographic models and open access databases

2014 ◽  
Vol 70 (a1) ◽  
pp. C1278-C1278 ◽  
Author(s):  
Werner Kaminsky ◽  
Trevor Snyder ◽  
Peter Moeck
Keyword(s):  
Open Access ◽  
3D Printing ◽  
College Education ◽  
Structural Data ◽  
Data Bank ◽  
3D Models ◽  
Crystal Defects ◽  
Crystallographic Structure ◽  
Performance Improvements ◽  
Basic Infrastructure

Although introduced 30 years ago, cost and performance improvements have only recently made 3D printing affordable. The industry wide input file format for 3D printers incorporates explicit mesh - `STL' data. Molecules and crystal structures, when including symmetry, crystal morphologies, or crystal defects are encoded in the parametrical `CIF' syntax. Free software for converting directly CIF data to STL files has just been developed, available online [1]. First examples of printed 3D models from STL-files created with these programs include molecules of sucrose, herapathite [2a], caffeine, humulone [2b], an alpha-quartz crystal and its Japanese {112} twin or a brilliant cut diamond. Far more CIF encoded models are available, even open access. The Crystallography Open Database (COD) features over 245,000 entries and has recently developed into the world's premier open-access source for structures of small to medium unit cell-sized inorganic and molecular crystals [3a], complementing the well-established open-access Worldwide Protein Data Bank [3b]. The Cambridge Crystallographic Data Centre in the United Kingdom provides crystal structure data of small (organic) molecules free for bona fide research [3c]. Structural data on inorganic crystals, metals and alloys can be obtained free of charge from the Inorganic Material Database (AtomWork) [3d]. Related to the COD, the crystallographic open-access databases [3e] ("COD offspring") provide CIF data for interdisciplinary college education. With this basic infrastructure in place, any interested college educator may print out her or his favorite crystallographic structure model in 3D and use it in hands on class room demonstrations [3f].

scholarly journals A multidisciplinary approach to digital mapping of dinosaurian tracksites in the Lower Cretaceous (Valanginian–Barremian) Broome Sandstone of the Dampier Peninsula, Western Australia

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3013 ◽  
Author(s):  
Anthony Romilio ◽  
Jorg M. Hacker ◽  
Robert Zlot ◽  
George Poropat ◽  
Michael Bosse ◽  
...  
Keyword(s):  
High Resolution ◽  
Western Australia ◽  
Lower Cretaceous ◽  
3D Visualization ◽  
3D Models ◽  
Unmanned Aircraft ◽  
Digital Data ◽  
3D Data ◽  
National Heritage ◽  
Mapping Techniques

The abundant dinosaurian tracksites of the Lower Cretaceous (Valanginian–Barremian) Broome Sandstone of the Dampier Peninsula, Western Australia, form an important part of the West Kimberley National Heritage Place. Previous attempts to document these tracksites using traditional mapping techniques (e.g., surface overlays, transects and gridlines combined with conventional photography) have been hindered by the non-trivial challenges associated with working in this area, including, but not limited to: (1) the remoteness of many of the tracksites; (2) the occurrence of the majority of the tracksites in the intertidal zone; (3) the size and complexity of many of the tracksites, with some extending over several square kilometres. Using the historically significant and well-known dinosaurian tracksites at Minyirr (Gantheaume Point), we show how these issues can be overcome through the use of an integrated array of remote sensing tools. A combination of high-resolution aerial photography with both manned and unmanned aircraft, airborne and handheld high-resolution lidar imaging and handheld photography enabled the collection of large amounts of digital data from which 3D models of the tracksites at varying resolutions were constructed. The acquired data encompasses a very broad scale, from the sub-millimetre level that details individual tracks, to the multiple-kilometre level, which encompasses discontinuous tracksite exposures and large swathes of coastline. The former are useful for detailed ichnological work, while the latter are being employed to better understand the stratigraphic and temporal relationship between tracksites in a broader geological and palaeoecological context. These approaches and the data they can generate now provide a means through which digital conservation and temporal monitoring of the Dampier Peninsula’s dinosaurian tracksites can occur. As plans for the on-going management of the tracks in this area progress, analysis of the 3D data and 3D visualization will also likely provide an important means through which the broader public can experience these spectacular National Heritage listed landscapes.

scholarly journals Computed Tomographic Image Analysis Based on FEM Performance Comparison of Segmentation on Knee Joint Reconstruction

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Seong-Wook Jang ◽  
Young-Jin Seo ◽  
Yon-Sik Yoo ◽  
Yoon Sang Kim
Keyword(s):  
Image Segmentation ◽  
Knee Joint ◽  
Movement Analysis ◽  
3D Models ◽  
Performance Comparison ◽  
Fe Analysis ◽  
Joint Movement ◽  
Computed Tomographic ◽  
Ct Data ◽  
Scan Data

The demand for an accurate and accessible image segmentation to generate 3D models from CT scan data has been increasing as such models are required in many areas of orthopedics. In this paper, to find the optimal image segmentation to create a 3D model of the knee CT data, we compared and validated segmentation algorithms based on both objective comparisons and finite element (FE) analysis. For comparison purposes, we used 1 model reconstructed in accordance with the instructions of a clinical professional and 3 models reconstructed using image processing algorithms (Sobel operator, Laplacian of Gaussian operator, and Canny edge detection). Comparison was performed by inspecting intermodel morphological deviations with the iterative closest point (ICP) algorithm, and FE analysis was performed to examine the effects of the segmentation algorithm on the results of the knee joint movement analysis.

scholarly journals 3D printing of crystallographic models for interdisciplinary college education

2014 ◽  
Vol 70 (a1) ◽  
pp. C1379-C1379 ◽  
Author(s):  
Peter Moeck ◽  
Werner Kaminsky ◽  
Trevor Snyder
Keyword(s):  
Open Access ◽  
3D Printing ◽  
Small Molecules ◽  
Point Group ◽  
College Education ◽  
3D Models ◽  
Crystal Defects ◽  
File Format ◽  
Performance Improvements ◽  
College Educators

Crystallographic models of molecule and crystal structures, crystal morphologies, Bravais lattices, space and point group symmetries, highly local and extended crystal defects, ... can all be encoded in the Crystallographic Information Framework (CIF) file format. While 3D printing has been available for at least 20 years, cost and performance improvements have only recently made 3D printing practical for usage by college educators and the general public. There is also an industry wide 3D printing standard, the STL file format. Virtual reality freeware programs that include conversions from CIF to STL are openly available [1]. The more than 250,000 entries Crystallography Open Database (COD) has in recent years developed into the world's premier open-access source for CIFs of structures of small molecules and small to medium sized unit cell crystals [2]. The International Advisory Board of the COD also supports a related project [3a], which provides CIFs for interdisciplinary college education. Three of these "COD offspring" databases have started to provide for free downloads of STL files of small molecules, crystal morphologies, and grain boundaries [3b]. These 3D printing files were created directly from the CIFs in these databases. It is now up to interested college educators to develop new pedagogy in teaching crystallography on the basis of 3D models that can be printed out from these files. To facilitate further developments in this field, there is a web portal of open-access crystallography resources to which all interested college educators are invited to contribute [3c].

scholarly journals Automatic Unfolding of CityGML Buildings to Paper Models

Geographies ◽  
2021 ◽  
Vol 1 (3) ◽  
pp. 333-345
Author(s):  
Steffen Goebbels ◽  
Regina Pohle-Fröhlich
Keyword(s):  
3D Printing ◽  
3D Visualization ◽  
3D Models ◽  
Perspective Projection ◽  
3D City Models ◽  
Building Models ◽  
Color Printing ◽  
Over Time ◽  
City Models

3D city models are mainly viewed on computer screens, but many municipalities also use 3D printing to make urban planning tangible. Since 3D color printing is still comparatively expensive and the colors often fade over time, many of these models are monochrome. Here, color textured paper models offer an inexpensive and under-appreciated alternative. In this paper, a greedy algorithm adapted to CityGML building models is presented, which creates print templates for such paper models. These 2D layouts consist of cut edges and fold edges that bound polygons of a building. The polygons can be textured or left blank depending on the existence of CityGML textures. Glue tabs are attached to cut edges. In addition to the haptic 3D visualization, the quality of the 3D models can sometimes be better assessed on the basis of the print templates than from a perspective projection. The unfolding procedure was applied to parts of the freely available CityGML model of Berlin as well as to parts of models of the cities of Dortmund and Krefeld.

Observation of the Pulp Chamber of Maxillary First Premolars: A Micro-computed Tomographic Study

2020 ◽  
Vol 16 (3) ◽  
pp. 224-230
Author(s):  
Gozde Serindere ◽  
Ceren Aktuna Belgin ◽  
Kaan Orhan
Keyword(s):  
Root Canal ◽  
Age Groups ◽  
Slice Thickness ◽  
Micro Ct ◽  
Micro Computed Tomography ◽  
Pulp Chamber ◽  
Anatomical Structures ◽  
Computed Tomographic ◽  
The Mean ◽  
Chamber Floor

Background: There are a few studies about the evaluation of maxillary first premolars internal structure with micro-computed tomography (micro-CT). The aim of this study was to assess morphological features of the pulp chamber in maxillary first premolar teeth using micro- CT. Methods: Extracted 15 maxillary first premolar teeth were selected from the patients who were in different age groups. The distance between the pulp orifices, the diameter of the pulp and the width of the pulp chamber floor were measured on the micro-CT images with the slice thickness of 13.6 µm. The number of root canal orifices and the presence of isthmus were evaluated. Results: The mean diameter of orifices was 0.73 mm on the buccal side while it was 0.61 mm on palatinal side. The mean distance between pulp orifices was 2.84 mm. The mean angle between pulp orifices was -21.53°. The mean height of pulp orifices on the buccal side was 4.32 mm while the mean height of pulp orifices on the palatinal side was 3.56 mm. The most observed shape of root canal orifices was flattened ribbon. No isthmus was found in specimens. Conclusion: Minor anatomical structures can be evaluated in more detail with micro-CT. The observation of the pulp cavity was analyzed using micro-CT.

scholarly journals MeshSlicer: A 3D-Printing software for printing 3D-models with a 6-axis industrial robot

Procedia CIRP ◽  
2021 ◽  
Vol 99 ◽  
pp. 110-115
Author(s):  
Jan Werner ◽  
Mohamed Aburaia ◽  
Alexander Raschendorfer ◽  
Maximilian Lackner
Keyword(s):  
3D Printing ◽  
Industrial Robot ◽  
3D Models

scholarly journals An Anatomical Thermal 3D Model in Preclinical Research: Combining CT and Thermal Images

Sensors ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1200
Author(s):  
Franziska Schollemann ◽  
Carina Barbosa Pereira ◽  
Stefanie Rosenhain ◽  
Andreas Follmann ◽  
Felix Gremse ◽  
...  
Keyword(s):  
Image Processing ◽  
Temperature Profile ◽  
3D Models ◽  
Animal Suffering ◽  
Preclinical Research ◽  
Thermal Images ◽  
Animal Trials ◽  
Superficial Skin ◽  
Ct Data ◽  
3D Information

Even though animal trials are a controversial topic, they provide knowledge about diseases and the course of infections in a medical context. To refine the detection of abnormalities that can cause pain and stress to the animal as early as possible, new processes must be developed. Due to its noninvasive nature, thermal imaging is increasingly used for severity assessment in animal-based research. Within a multimodal approach, thermal images combined with anatomical information could be used to simulate the inner temperature profile, thereby allowing the detection of deep-seated infections. This paper presents the generation of anatomical thermal 3D models, forming the underlying multimodal model in this simulation. These models combine anatomical 3D information based on computed tomography (CT) data with a registered thermal shell measured with infrared thermography. The process of generating these models consists of data acquisition (both thermal images and CT), camera calibration, image processing methods, and structure from motion (SfM), among others. Anatomical thermal 3D models were successfully generated using three anesthetized mice. Due to the image processing improvement, the process was also realized for areas with few features, which increases the transferability of the process. The result of this multimodal registration in 3D space can be viewed and analyzed within a visualization tool. Individual CT slices can be analyzed axially, sagittally, and coronally with the corresponding superficial skin temperature distribution. This is an important and successfully implemented milestone on the way to simulating the internal temperature profile. Using this temperature profile, deep-seated infections and inflammation can be detected in order to reduce animal suffering.

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