scholarly journals When the Utility of Micro-Computed Tomography Collides with Insect Sample Preparation: An Entomologist User Guide to Solve Post-Processing Issues and Achieve Optimal 3D Models

2022 ◽  
Vol 12 (2) ◽  
pp. 769
Author(s):  
Francesco Simone Mensa ◽  
Maurizio Muzzi ◽  
Federica Spani ◽  
Giuliana Tromba ◽  
Christian Dullin ◽  
...  

Many techniques are used today to study insect morphology, including light and electron microscopy. Most of them require to specifically prepare the sample, precluding its use for further investigation. In contrast, micro-CT allows a sample to be studied in a non-destructive and rapid process, even without specific treatments that might hinder the use of rare and hard-to-find species in nature. We used synchrotron radiation (SR) micro-CT and conventional micro-CT to prepare 3D reconstructions of Diptera, Coleoptera, and Hymenoptera species that had been processed with 4 common preparation procedures: critical-point drying, sputter-coating, resin embedding, and air-drying. Our results showed that it is possible to further utilize insect samples prepared with the aforementioned preparation techniques for the creation of 3D models. Specimens dried at the critical point showed the best results, allowing us to faithfully reconstruct both their external surface and their internal structures, while sputter-coated insects were the most troublesome for the 3D reconstruction procedure. Air-dried specimens were suitable for external morphological analyses, while anatomical investigation of soft internal organs was not possible due to their shrinking and collapsing. The sample included in resin allowed us to reconstruct and appreciate the external cuticle and the internal parts. In this work, we demonstrate that insect samples destined to different analyses can be used for new micro-CT studies, further deepening the possibility of state-of-the-art morphological analyses.

2021 ◽  
Author(s):  
Dominik Göldner ◽  
Fotios Alexandros Karakostis ◽  
Armando Falcucci

This protocol presents the first detailed step-by-step pipeline for the 3D scanning and post processing of large batches of lithic artefacts using a micro-computed tomography (micro-CT) scanner (i.e., a Phoenix v-tome-x S model by General Electronics MCC, Boston MA) and an Artec Space Spider scanner (Artec Inc., Luxembourg). This protocol was used to scan and analyze ca. 700 lithic artefacts from the Protoaurignacian layers at Fumane Cave in north-eastern Italy (Falcucci et al., in preparation). For this study several costly scanners and proprietary software packages were employed. Although it is not easy to find a low-budget alternative for the scanners, it is possible to use free and open-source software programs, such as 3D-Slicer (https://www.slicer.org/) or MorphoDig (https://morphomuseum.com/morphodig), to process CT data as well as MeshLab (Cignoni et al. 2008) to interact with the 3D models in general. However, if alternative software is used, the steps and their order described in this protocol might diverge significantly. A cost-effective alternative to create 3D models is digital photogrammetry using commercial cameras and freely available software like Meshroom (https://alicevision.org). Although photogrammetry is an affordable technique to create accurate 3D models of objects, this method might not be useful when scanning large batches of artefacts, as it will require a lot of computation time and processing capacity. Likewise, it could be difficult to generate accurate 3D models of very small and/or detailed tool shapes using 3D surface scanners because stone tools are often much smaller than the recommended minimum field of view. Similarly, the resolution of conventional medical CT scanners might not be sufficient to capture minor details of stone tools, such as the outline or dorsal scars. Thus, high-resolution micro-CT technology is the only reliable way to accurately capture the overall morphology of small stone tools. This protocol aims at providing the first detailed procedure dedicated to the scanning of small lithic implements for further three-dimensional analysis. Note that some of the steps must be repeated at different working stages throughout this protocol. In cases where a task must be done in the exact same way as described in a previous step, a reference to that step is provided. When slight changes were made, the step was modified and reported entirely. This protocol contains a few red and green colours (e.g., arrows or within-program colours) which might be perceived differently by people with dyschromatopsia. However, the display of these colours has been kept to a minimum. We recommend the reader to go over the entire protocol carefully, even if only some specific parts are required. A few points are in fact interdependent, and some of them must be applied simultaneously. Content: Part 1 – Styrofoam preparation Part 2 – Micro-CT scanning Part 3 – 3D model extraction of CT scanned stone artifacts using Avizo Part 4 – Cropping extracted surface model to separate Face A and B in Artec Studio Part 5 – Cropping Face A to separate the lines in Artec Studio Part 6 – Cropping each stone artefact from the lines in Artec Studio Part 7 – Virtually control measurements in MeshLab Part 8 – Artec scanning of larger artifacts Part 9 – Export meshes as non-binary ply models for successive analysis in geomorph Three-dimensional example (in ply format) of the effectivity of the StyroStone Protocol: You can download an example of one Styrofoam line in 3D obtained using our protocol to appreciate the result that can be achieved. We have selected a line where objects are characterized by different metric and morphological attributes. Notice the retouching well visible in the last five smaller artifacts (counting from the left when artifact are oriented with the dorsal face in front of the observer and the butt down), as well as the platforms and bulbs of all artifacts. For more information and examples, feel free to contact us!


2003 ◽  
Vol 44 (5) ◽  
pp. 532-537
Author(s):  
A. Mohr ◽  
C. Heiss ◽  
I. Bergmann ◽  
C. Schrader ◽  
F. W. Roemer ◽  
...  

Purpose: To evaluate micro computed tomography (micro-CT) for the assessment of osteochondritis dissecans in comparison with histology. Material and Methods: Osteochondritis dissecans lesions of 3 patients were evaluated using micro-CT (0.125 mA, 40 keV, 60 μm slice thickness, 60 μm isotropic resolution, entire sample) and light microscopy (toluidine blue, 3–5 μm slice thickness). The methods were compared regarding preparation time, detectability of tissue types and morphologic features of bone and cartilage. Results: Non-destructive micro-CT imaging of the entire sample was faster than histologic preparation of a single slice for light microscopy. Morphologic features of bone and cartilage could be imaged in a comparable way to histology. It was not possible to image cells or different tissue types of bone and cartilage with micro-CT. Conclusion: Micro-CT is a fast, non-destructive tool that may be a supplement or, if detailed histologic information is not necessary, an alternative to light microscopy for the investigation of osteochondritis dissecans.


2021 ◽  
Vol 7 (9) ◽  
pp. 172
Author(s):  
Kleoniki Keklikoglou ◽  
Christos Arvanitidis ◽  
Georgios Chatzigeorgiou ◽  
Eva Chatzinikolaou ◽  
Efstratios Karagiannidis ◽  
...  

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.


Author(s):  
William G. Henk ◽  
Ben O. Spurlock

The increased depth of focus and superior resolving power of the scanning electron microscope provide advantages over the light microscope in viewing the external morphology of cultured cells and protists. Internal structures have, however, proved more difficult to observe. Freeze drying adequately preserves surface structures but results in poorly preserved cytoplasmic elements due to ice crystal damage. Critical point drying results in good preservation of both surface and cytoplasmic fine structure. Attempts to cut or break critical point dried material, however, result in plastic deformation of the cells. Humphreys, et al, recently introduced freeze fracturing of ethanol infiltrated tissues for biological scanning electron microscopy. We have modified and applied their technique and obtained similar results with Paramecium sp. obtained from mass cultures.


2016 ◽  
Vol 722 ◽  
pp. 235-240 ◽  
Author(s):  
Martin Lidmila ◽  
Tomáš Zikmund ◽  
Jindřich Dvořák ◽  
Jozef Kaiser ◽  
Vít Lojda

The extent of the use of asphalt concrete in track bed layers is minimal in contrast to the application of granular materials mostly represented by coarse/fine crushed stone mixture. This article summarizes advantages and disadvantages of the use of asphalt concrete in the track bed construction and provides relevant literature research. The main part of this article focuses on the application of recycled asphalt concrete (so called R-material) in the track bed layer and its following non-destructive X-ray Micro Computed Tomography Method (Micro-CT) for the description of its structural parameters. The contribution of this research is based on the evaluation of the air void and soluble binder content of chosen recycled asphalt concrete. First, it was obtained from laboratory geotechnical models of a railway track, and then from the following implementation in a trial section of an operating railway track. The conclusion contains results of the R-material practical application and findings from Micro-CT.


2012 ◽  
Vol 229-231 ◽  
pp. 1445-1448
Author(s):  
Wei Yun Huang ◽  
Chang Da Chen ◽  
Yen Nien Chen ◽  
Wei Jen Shih ◽  
Chih Han Chang

Metal injection molding (MIM) is a combination of metal powder and injection molding technology. The main advantage of this technology for material parts with small and complex shape is to manufacture cost-effective and high-volume products. The main processing steps include mixing, injection molding, debinding , sintering, and hot isostatic pressing (HIP) in order to reduce internal porosity of metals, then to improve mechanical properties. This study is based on non-destructive testing method to determine the possible defect inside the internal structure of the MIM parts. Three types of parts with and without HIP were evaluated investigated in this study. The micro computed tomography (Micro-CT) is used to scan these parts. Based the reconstructed section images from CT, the defects can be identified. It showed that with HIP the much of detects could be reduced. To conclude, Micro CT could be used to detect, in a non-destructive way, the internal detect within MIM parts can be found out in the micro-CT images, so that the manufacturing process could be modified to improve the quality of MIM parts.


2020 ◽  
Vol 21 (12) ◽  
pp. 4538
Author(s):  
Samantha J. Borland ◽  
Julia Behnsen ◽  
Nick Ashton ◽  
Sheila E. Francis ◽  
Keith Brennan ◽  
...  

Vascular calcification describes the formation of mineralized tissue within the blood vessel wall, and it is highly associated with increased cardiovascular morbidity and mortality in patients with chronic kidney disease, diabetes, and atherosclerosis. In this article, we briefly review different rodent models used to study vascular calcification in vivo, and critically assess the strengths and weaknesses of the current techniques used to analyze and quantify calcification in these models, namely 2-D histology and the o-cresolphthalein assay. In light of this, we examine X-ray micro-computed tomography (µCT) as an emerging complementary tool for the analysis of vascular calcification in animal models. We demonstrate that this non-destructive technique allows us to simultaneously quantify and localize calcification in an intact vessel in 3-D, and we consider recent advances in µCT sample preparation techniques. This review also discusses the potential to combine 3-D µCT analyses with subsequent 2-D histological, immunohistochemical, and proteomic approaches in correlative microscopy workflows to obtain rich, multifaceted information on calcification volume, calcification load, and signaling mechanisms from within the same arterial segment. In conclusion we briefly discuss the potential use of µCT to visualize and measure vascular calcification in vivo in real-time.


2011 ◽  
Vol 1319 ◽  
Author(s):  
Rui M.S. Martins ◽  
Felix Beckmann ◽  
Rui Castanhinha ◽  
Octávio Mateus ◽  
Philipp Klaus Pranzas

ABSTRACTPortugal is ranked within the 10 countries with the most dinosaur taxa and the Lourinhã Formation is known by the Late Jurassic findings of dinosaurs and other fossils. In many cases, studies of the external morphological characteristics of the fossils are not sufficient to extract all the information for a paleontological study and, thus, observations of internal structures, using non-destructive techniques, are required. The fossils studied in the present work belong to the Museum of Lourinhã. The access to the Geesthacht Neutron Facility in Germany allowed us to characterize a jaw of the dinosaur Baryonyx walkeri specimen and the jaw of a crocodile (possibly a Tomistomidae) by Neutron Tomography. The study allowed us to detect the presence of teeth inside the jaws and it provides valuable information about the development of its dental characteristics. Synchrotron radiation based micro-computed tomography studies on tiny samples have been performed at the beamline HARWI II operated by the Helmholtz-Zentrum Geesthacht at the storage ring DORIS III at the Deutsches Elektronen–Synchrotron DESY in Hamburg, Germany. The first data recorded for eggshells collected in the Lourinhã Formation is shown. It allowed us to visualize the morphology of the pores and their connectivity in the eggshells, providing information that is either exceedingly difficult or impossible to obtain by traditional methods based on section cutting.


Author(s):  
Kleoniki Keklikoglou ◽  
Sarah Faulwetter ◽  
Eva Chatzinikolaou ◽  
Patricia Wils ◽  
Jonathan Brecko ◽  
...  

Micro-computed tomography (micro-CT or microtomography) is a non-destructive imaging technique using X-rays which allows the digitisation of an object in three dimensions. The ability of micro-CT imaging to visualise both internal and external features of an object, without destroying the specimen, makes the technique ideal for the digitisation of valuable natural history collections. This handbook serves as a comprehensive guide to laboratory micro-CT imaging of different types of natural history specimens, including zoological, botanical, palaeontological and geological samples. The basic principles of the micro-CT technology are presented, as well as protocols, tips and tricks and use cases for each type of natural history specimen. Finally, data management protocols and a comprehensive list of institutions with micro-CT facilities, micro-CT manufacturers and relative software are included.


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