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Brunet J, Walsh CL, Wagner WL, Bellier A, Werlein C, Marussi S, Jonigk DD, Verleden SE, Ackermann M, Lee PD, Tafforeau P. Preparation of large biological samples for high-resolution, hierarchical, synchrotron phase-contrast tomography with multimodal imaging compatibility. Nat Protoc 2023; 18:1441-1461. [PMID: 36859614 DOI: 10.1038/s41596-023-00804-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 12/12/2022] [Indexed: 03/03/2023]
Abstract
Imaging across different scales is essential for understanding healthy organ morphology and pathophysiological changes. The macro- and microscale three-dimensional morphology of large samples, including intact human organs, is possible with X-ray microtomography (using laboratory or synchrotron sources). Preparation of large samples for high-resolution imaging, however, is challenging due to limitations such as sample shrinkage, insufficient contrast, movement of the sample and bubble formation during mounting or scanning. Here, we describe the preparation, stabilization, dehydration and mounting of large soft-tissue samples for X-ray microtomography. We detail the protocol applied to whole human organs and hierarchical phase-contrast tomography at the European Synchrotron Radiation Facility, yet it is applicable to a range of biological samples, including complete organisms. The protocol enhances the contrast when using X-ray imaging, while preventing sample motion during the scan, even with different sample orientations. Bubbles trapped during mounting and those formed during scanning (in the case of synchrotron X-ray imaging) are mitigated by multiple degassing steps. The sample preparation is also compatible with magnetic resonance imaging, computed tomography and histological observation. The sample preparation and mounting require 24-36 d for a large organ such as a whole human brain or heart. The preparation time varies depending on the composition, size and fragility of the tissue. Use of the protocol enables scanning of intact organs with a diameter of 150 mm with a local voxel size of 1 μm. The protocol requires users with expertise in handling human or animal organs, laboratory operation and X-ray imaging.
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Affiliation(s)
- J Brunet
- Department of Mechanical Engineering, University College London, London, UK.
- European Synchrotron Radiation Facility, Grenoble, France.
| | - C L Walsh
- Department of Mechanical Engineering, University College London, London, UK.
| | - W L Wagner
- Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany
- Translational Lung Research Centre Heidelberg (TLRC), German Lung Research Centre (DZL), Heidelberg, Germany
| | - A Bellier
- Laboratoire d'Anatomie des Alpes Françaises (LADAF), Université Grenoble Alpes, Grenoble, France
| | - C Werlein
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - S Marussi
- Department of Mechanical Engineering, University College London, London, UK
| | - D D Jonigk
- Institute of Pathology, Hannover Medical School, Hannover, Germany
- Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), German Lung Research Centre (DZL), Hannover, Germany
| | - S E Verleden
- Antwerp Surgical Training, Anatomy and Research Centre (ASTARC), University of Antwerp, Antwerp, Belgium
| | - M Ackermann
- Institute of Pathology and Molecular Pathology, Helios University Clinic Wuppertal, University of Witten/Herdecke, Wuppertal, Germany
- Institute of Functional and Clinical Anatomy, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Peter D Lee
- Department of Mechanical Engineering, University College London, London, UK.
- Research Complex at Harwell, Didcot, UK.
| | - Paul Tafforeau
- European Synchrotron Radiation Facility, Grenoble, France.
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de Carvalho AC, Dias CSB, Coimbra LD, Rocha RPF, Borin A, Fontoura MA, Carvalho M, Proost P, Nogueira ML, Consonni SR, Sesti-Costa R, Marques RE. Characterization of Systemic Disease Development and Paw Inflammation in a Susceptible Mouse Model of Mayaro Virus Infection and Validation Using X-ray Synchrotron Microtomography. Int J Mol Sci 2023; 24:4799. [PMID: 36902230 PMCID: PMC10003659 DOI: 10.3390/ijms24054799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/03/2023] [Accepted: 01/12/2023] [Indexed: 03/06/2023] Open
Abstract
Mayaro virus (MAYV) is an emerging arthropod-borne virus endemic in Latin America and the causative agent of arthritogenic febrile disease. Mayaro fever is poorly understood; thus, we established an in vivo model of infection in susceptible type-I interferon receptor-deficient mice (IFNAR-/-) to characterize the disease. MAYV inoculations in the hind paws of IFNAR-/- mice result in visible paw inflammation, evolve into a disseminated infection and involve the activation of immune responses and inflammation. The histological analysis of inflamed paws indicated edema at the dermis and between muscle fibers and ligaments. Paw edema affected multiple tissues and was associated with MAYV replication, the local production of CXCL1 and the recruitment of granulocytes and mononuclear leukocytes to muscle. We developed a semi-automated X-ray microtomography method to visualize both soft tissue and bone, allowing for the quantification of MAYV-induced paw edema in 3D with a voxel size of 69 µm3. The results confirmed early edema onset and spreading through multiple tissues in inoculated paws. In conclusion, we detailed features of MAYV-induced systemic disease and the manifestation of paw edema in a mouse model extensively used to study infection with alphaviruses. The participation of lymphocytes and neutrophils and expression of CXCL1 are key features in both systemic and local manifestations of MAYV disease.
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Affiliation(s)
- Ana Carolina de Carvalho
- Brazilian National Biosciences Laboratory—LNBio, Brazilian Center for Research in Energy and Materials—CNPEM, R. Giuseppe Máximo Scolfaro, 10000-Bosque das Palmeiras, Campinas 13083-100, Brazil
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Rua Bertrand Russel, Campinas 13083-970, Brazil
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven (KU Leuven), Herestraat 49 Box 1042, 3000 Leuven, Belgium
| | - Carlos Sato B. Dias
- Institut Für Photonenforschung und Synchrotronstrahlung (IPS), Karlsruher Institut Für Technologie (KIT), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, 76344 Karlsruhe, Germany
| | - Laís D. Coimbra
- Brazilian National Biosciences Laboratory—LNBio, Brazilian Center for Research in Energy and Materials—CNPEM, R. Giuseppe Máximo Scolfaro, 10000-Bosque das Palmeiras, Campinas 13083-100, Brazil
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Rua Bertrand Russel, Campinas 13083-970, Brazil
| | - Rebeca P. F. Rocha
- Brazilian National Biosciences Laboratory—LNBio, Brazilian Center for Research in Energy and Materials—CNPEM, R. Giuseppe Máximo Scolfaro, 10000-Bosque das Palmeiras, Campinas 13083-100, Brazil
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Rua Bertrand Russel, Campinas 13083-970, Brazil
| | - Alexandre Borin
- Brazilian National Biosciences Laboratory—LNBio, Brazilian Center for Research in Energy and Materials—CNPEM, R. Giuseppe Máximo Scolfaro, 10000-Bosque das Palmeiras, Campinas 13083-100, Brazil
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Rua Bertrand Russel, Campinas 13083-970, Brazil
| | - Marina A. Fontoura
- Brazilian National Biosciences Laboratory—LNBio, Brazilian Center for Research in Energy and Materials—CNPEM, R. Giuseppe Máximo Scolfaro, 10000-Bosque das Palmeiras, Campinas 13083-100, Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, s/n, Campinas 13083-970, Brazil
| | - Murilo Carvalho
- Brazilian National Biosciences Laboratory—LNBio, Brazilian Center for Research in Energy and Materials—CNPEM, R. Giuseppe Máximo Scolfaro, 10000-Bosque das Palmeiras, Campinas 13083-100, Brazil
- Brazilian Synchrotron Light Laboratory—LNLS, Brazilian Center for Research in Energy and Materials—CNPEM, R. Giuseppe Máximo Scolfaro, 10000-Bosque das Palmeiras, Campinas 13083-100, Brazil
| | - Paul Proost
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven (KU Leuven), Herestraat 49 Box 1042, 3000 Leuven, Belgium
| | - Maurício L. Nogueira
- Laboratório de Pesquisas em Virologia (LPV), São José do Rio Preto Medical School (FAMERP), Av. Brigadeiro Faria Lima, 5416-Vila São Pedro, São José do Rio Preto 15090-000, Brazil
| | - Sílvio R. Consonni
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, s/n, Campinas 13083-970, Brazil
| | - Renata Sesti-Costa
- Brazilian National Biosciences Laboratory—LNBio, Brazilian Center for Research in Energy and Materials—CNPEM, R. Giuseppe Máximo Scolfaro, 10000-Bosque das Palmeiras, Campinas 13083-100, Brazil
| | - Rafael Elias Marques
- Brazilian National Biosciences Laboratory—LNBio, Brazilian Center for Research in Energy and Materials—CNPEM, R. Giuseppe Máximo Scolfaro, 10000-Bosque das Palmeiras, Campinas 13083-100, Brazil
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Dinsley JM, Davies HS, Gomez‐Gonzalez MA, Robinson CH, Pittman JK. The value of synchrotron radiation X‐ray techniques to explore microscale chemistry for ecology and evolution research. Ecosphere 2022. [DOI: 10.1002/ecs2.4312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- James M. Dinsley
- Department of Earth and Environmental Sciences The University of Manchester Manchester UK
| | - Helena S. Davies
- Department of Earth and Environmental Sciences The University of Manchester Manchester UK
| | | | - Clare H. Robinson
- Department of Earth and Environmental Sciences The University of Manchester Manchester UK
| | - Jon K. Pittman
- Department of Earth and Environmental Sciences The University of Manchester Manchester UK
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Einarsson E, Pierantoni M, Novak V, Svensson J, Isaksson H, Englund M. Phase-contrast enhanced synchrotron micro-tomography of human meniscus tissue. Osteoarthritis Cartilage 2022; 30:1222-1233. [PMID: 35750240 DOI: 10.1016/j.joca.2022.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/27/2022] [Accepted: 06/13/2022] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To investigate the feasibility of synchrotron radiation-based phase contrast enhanced micro-computed tomography (SR-PhC-μCT) for imaging of human meniscus. Quantitative parameters related to fiber orientation and crimping were evaluated as potential markers of tissue degeneration. DESIGN Human meniscus specimens from 10 deceased donors were prepared using different preparation schemes: fresh frozen and thawed before imaging or fixed and paraffin-embedded. The samples were imaged using SR-PhC-μCT with an isotropic voxel size of 1.625 μm. Image quality was evaluated by visual inspection and spatial resolution. Fiber voxels were defined using a grey level threshold and a structure tensor analysis was applied to estimate collagen fiber orientation. The area at half maximum (FAHM) was calculated from angle histograms to quantify orientation distribution. Crimping period was calculated from the power spectrum of image profiles of crimped fibers. Parameters were compared to degenerative stage as evaluated by Pauli histopathological scoring. RESULTS Image quality was similar between frozen and embedded samples and spatial resolutions ranged from 5.1 to 5.8 μm. Fiber structure, including crimping, was clearly visible in the images. Fibers appeared to be less organized closer to the tip of the meniscus. Fiber density might decrease slightly with degeneration. FAHM and crimping period did not show any clear association with histopathological scoring. CONCLUSION SR-PhC-μCT is a feasible technique for high-resolution 3D imaging of fresh frozen meniscus tissue. Further work is needed to establish quantitative parameters that relate to tissue degeneration, but this imaging technique is promising for future studies of meniscus structure and biomechanical response.
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Affiliation(s)
- E Einarsson
- Medical Radiation Physics, Department of Translational Medicine, Lund University, Malmö, Sweden; Clinical Epidemiology Unit, Orthopedics, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
| | - M Pierantoni
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - V Novak
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - J Svensson
- Medical Radiation Physics, Department of Translational Medicine, Lund University, Malmö, Sweden; Medical Imaging and Physiology, Skåne University Hospital, Lund, Sweden
| | - H Isaksson
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - M Englund
- Clinical Epidemiology Unit, Orthopedics, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
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Paiva K, Meneses AADM, Barcellos R, Moura MSDS, Mendes G, Fidalgo G, Sena G, Colaço G, Silva HR, Braz D, Colaço MV, Barroso RC. Performance evaluation of segmentation methods for assessing the lens of the frog Thoropa miliaris from synchrotron-based phase-contrast micro-CT images. Phys Med 2022; 94:43-52. [PMID: 34995977 DOI: 10.1016/j.ejmp.2021.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/16/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
PURPOSE In the context of synchrotron microtomography using propagation-based phase-contrast imaging (XSPCT), we evaluated the performance of semiautomatic and automatic image segmentation of soft biological structures by means of Dice Similarity Coefficient (DSC) and volume quantification. METHODS We took advantage of the phase-contrast effects of XSPCT to provide enhanced object boundaries and improved visualization of the lenses of the frog Thoropa miliaris. Then, we applied semiautomatic segmentation methods 1 and 2 (Interpolation and Watershed, respectively) and method 3, an automatic segmentation algorithm using the U-Net architecture, to the reconstructed images. DSC and volume quantification of the lenses were used to quantify the performance of image segmentation methods. RESULTS Comparing the lenses segmented by the three methods, the most pronounced difference in volume quantification was between methods 1 and 3: a reduction of 4.24%. Method 1, 2 and 3 obtained the global average DSC of 97.02%, 95.41% and 89.29%, respectively. Although it obtained the lowest DSC, method 3 performed the segmentation in a matter of seconds, while the semiautomatic methods had the average time to segment the lenses around 1 h and 30 min. CONCLUSIONS Our results suggest that the performance of U-Net was impaired due to the irregularities of the ROI edges mainly in its lower and upper regions, but it still showed high accuracy (DSC = 89.29%) with significantly reduced segmentation time compared to the semiautomatic methods. Besides, with the present work we have established a baseline for future assessments of Deep Neural Networks applied to XSPCT volumes.
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Affiliation(s)
- Katrine Paiva
- Laboratory of Applied Physics to Biomedical and Environmental Sciences, Physics Institute, State University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | | | - Renan Barcellos
- Laboratory of Applied Physics to Biomedical and Environmental Sciences, Physics Institute, State University of Rio de Janeiro, Rio de Janeiro, Brazil; Nuclear Engineering Program/COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Gabriela Mendes
- Laboratory of Applied Physics to Biomedical and Environmental Sciences, Physics Institute, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriel Fidalgo
- Laboratory of Applied Physics to Biomedical and Environmental Sciences, Physics Institute, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriela Sena
- Nuclear Engineering Program/COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gustavo Colaço
- Laboratory of Herpetology, Institute of Biological and Health Sciences, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Hélio Ricardo Silva
- Laboratory of Herpetology, Institute of Biological and Health Sciences, Federal Rural University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Delson Braz
- Nuclear Engineering Program/COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcos Vinicius Colaço
- Laboratory of Applied Physics to Biomedical and Environmental Sciences, Physics Institute, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Regina Cely Barroso
- Laboratory of Applied Physics to Biomedical and Environmental Sciences, Physics Institute, State University of Rio de Janeiro, Rio de Janeiro, Brazil
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Pierantoni M, Silva Barreto I, Hammerman M, Verhoeven L, Törnquist E, Novak V, Mokso R, Eliasson P, Isaksson H. A quality optimization approach to image Achilles tendon microstructure by phase-contrast enhanced synchrotron micro-tomography. Sci Rep 2021; 11:17313. [PMID: 34453067 PMCID: PMC8397765 DOI: 10.1038/s41598-021-96589-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 08/06/2021] [Indexed: 12/19/2022] Open
Abstract
Achilles tendons are mechanosensitive, and their complex hierarchical structure is in part the result of the mechanical stimulation conveyed by the muscles. To fully understand how their microstructure responds to mechanical loading a non-invasive approach for 3D high resolution imaging suitable for soft tissue is required. Here we propose a protocol that can capture the complex 3D organization of the Achilles tendon microstructure, using phase-contrast enhanced synchrotron micro-tomography (SR-PhC-μCT). We investigate the effects that sample preparation and imaging conditions have on the resulting image quality, by considering four types of sample preparations and two imaging setups (sub-micrometric and micrometric final pixel sizes). The image quality is assessed using four quantitative parameters. The results show that for studying tendon collagen fibers, conventional invasive sample preparations such as fixation and embedding are not necessary or advantageous. Instead, fresh frozen samples result in high-quality images that capture the complex 3D organization of tendon fibers in conditions as close as possible to natural. The comprehensive nature of this innovative study by SR-PhC-μCT breaks ground for future studies of soft complex biological tissue in 3D with high resolution in close to natural conditions, which could be further used for in situ characterization of how soft tissue responds to mechanical stimuli on a microscopic level.
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Affiliation(s)
- Maria Pierantoni
- Department of Biomedical Engineering, Lund University, Box 118, 221 00, Lund, Sweden.
| | | | - Malin Hammerman
- Department of Biomedical Engineering, Lund University, Box 118, 221 00, Lund, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83, Linköping, Sweden
| | - Lissa Verhoeven
- Department of Biomedical Engineering, Lund University, Box 118, 221 00, Lund, Sweden
| | - Elin Törnquist
- Department of Biomedical Engineering, Lund University, Box 118, 221 00, Lund, Sweden
| | - Vladimir Novak
- Swiss Light Source, Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Rajmund Mokso
- Swiss Light Source, Paul Scherrer Institute, 5232, Villigen, Switzerland
- Division of Solid Mechanics, Lund University, Box 118, 221 00, Lund, Sweden
| | - Pernilla Eliasson
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83, Linköping, Sweden
| | - Hanna Isaksson
- Department of Biomedical Engineering, Lund University, Box 118, 221 00, Lund, Sweden
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Rodrigues PV, Tostes K, Bosque BP, de Godoy JVP, Amorim Neto DP, Dias CSB, Fonseca MDC. Illuminating the Brain With X-Rays: Contributions and Future Perspectives of High-Resolution Microtomography to Neuroscience. Front Neurosci 2021; 15:627994. [PMID: 33815039 PMCID: PMC8010130 DOI: 10.3389/fnins.2021.627994] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/26/2021] [Indexed: 12/27/2022] Open
Abstract
The assessment of three-dimensional (3D) brain cytoarchitecture at a cellular resolution remains a great challenge in the field of neuroscience and constant development of imaging techniques has become crucial, particularly when it comes to offering direct and clear obtention of data from macro to nano scales. Magnetic resonance imaging (MRI) and electron or optical microscopy, although valuable, still face some issues such as the lack of contrast and extensive sample preparation protocols. In this context, x-ray microtomography (μCT) has become a promising non-destructive tool for imaging a broad range of samples, from dense materials to soft biological specimens. It is a new supplemental method to be explored for deciphering the cytoarchitecture and connectivity of the brain. This review aims to bring together published works using x-ray μCT in neurobiology in order to discuss the achievements made so far and the future of this technique for neuroscience.
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Affiliation(s)
- Paulla Vieira Rodrigues
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Katiane Tostes
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Beatriz Pelegrini Bosque
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - João Vitor Pereira de Godoy
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Dionisio Pedro Amorim Neto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Carlos Sato Baraldi Dias
- Brazilian Synchrotron Light National Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Matheus de Castro Fonseca
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
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A correlation analysis of Light Microscopy and X-ray MicroCT imaging methods applied to archaeological plant remains' morphological attributes visualization. Sci Rep 2020; 10:15105. [PMID: 32934262 PMCID: PMC7493802 DOI: 10.1038/s41598-020-71726-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/30/2020] [Indexed: 12/05/2022] Open
Abstract
In this work, several attributes of the internal morphology of drupaceous fruits found in the archaeological site Monte Castelo (Rondonia, Brazil) are analyzed by means of two different imaging methods. The aim is to explore similarities and differences in the visualization and analytical properties of the images obtained via High Resolution Light Microscopy and X-ray micro-computed tomography (X-ray MicroCT) methods. Both provide data about the three-layered pericarp (exo-, meso- and endocarp) of the studied exemplars, defined by cell differentiation, vascularisation, cellular contents, presence of sclerenchyma cells and secretory cavities. However, it is possible to identify a series of differences between the information that can be obtained through each of the methods. These variations are related to the definition of contours and fine details of some characteristics, their spatial distribution, size attributes, optical properties and material preservation. The results obtained from both imaging methods are complementary, contributing to a more exhaustive morphological study of the plant remains. X-ray MicroCT in phase-contrast mode represents a suitable non-destructive analytic technique when sample preservation is required.
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Ortega-Gil A, Vaquero JJ, Gonzalez-Arjona M, Rullas J, Muñoz-Barrutia A. X-ray-based virtual slicing of TB-infected lungs. Sci Rep 2019; 9:19404. [PMID: 31852973 PMCID: PMC6920455 DOI: 10.1038/s41598-019-55986-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 12/03/2019] [Indexed: 11/14/2022] Open
Abstract
Hollow organs such as the lungs pose a considerable challenge for post-mortem imaging in preclinical research owing to their extremely low contrast and high structural complexity. The aim of our study was to enhance the contrast of tuberculosis lesions for their stratification by 3D x-ray-based virtual slicing. Organ samples were taken from five control and five tuberculosis-infected mice. Micro-Computed Tomography (CT) scans of the subjects were acquired in vivo (without contrast agent) and post-mortem (with contrast agent). The proposed contrast-enhancing technique consists of x-ray contrast agent uptake (silver nitrate and iodine) by immersion. To create the histology ground-truth, the CT scan of the paraffin block guided the sectioning towards specific planes of interest. The digitalized histological slides reveal the presence, extent, and appearance of the contrast agents in lung structures and organized aggregates of immune cells. These findings correlate with the contrast-enhanced micro-CT slice. The abnormal densities in the lungs due to tuberculosis disease are concentrated in the right tail of the lung intensity histograms. The increase in the width of the right tail (~376%) indicates a contrast enhancement of the details of the abnormal densities. Postmortem contrast agents enhance the x-ray attenuation in tuberculosis lesions to allow 3D visualization by polychromatic x-ray CT, providing an advantageous tool for virtual slicing of whole lungs. The proposed contrast-enhancing technique combined with computational methods and the diverse micro-CT modalities will open the doors to the stratification of lesion types associated with infectious diseases.
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Affiliation(s)
- Ana Ortega-Gil
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Leganés, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
- Diseases of the Developing World, Infectious Diseases-Centre for Excellence in Drug Discovery (ID CEDD), GlaxoSmithKline, Madrid, Spain
| | - Juan José Vaquero
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Leganés, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | | | - Joaquín Rullas
- Diseases of the Developing World, Infectious Diseases-Centre for Excellence in Drug Discovery (ID CEDD), GlaxoSmithKline, Madrid, Spain
| | - Arrate Muñoz-Barrutia
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Leganés, Spain.
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain.
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