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Yakovlev MA, Liang K, Zaino CR, Vanselow DJ, Sugarman AL, Lin AY, La Riviere PJ, Zheng Y, Silverman JD, Leichty JC, Huang SX, Cheng KC. Quantitative Geometric Modeling of Blood Cells from X-ray Histotomograms of Whole Zebrafish Larvae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541939. [PMID: 37292910 PMCID: PMC10245913 DOI: 10.1101/2023.05.23.541939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Tissue phenotyping is foundational to understanding and assessing the cellular aspects of disease in organismal context and an important adjunct to molecular studies in the dissection of gene function, chemical effects, and disease. As a first step toward computational tissue phenotyping, we explore the potential of cellular phenotyping from 3-Dimensional (3D), 0.74 µm isotropic voxel resolution, whole zebrafish larval images derived from X-ray histotomography, a form of micro-CT customized for histopathology. As proof of principle towards computational tissue phenotyping of cells, we created a semi-automated mechanism for the segmentation of blood cells in the vascular spaces of zebrafish larvae, followed by modeling and extraction of quantitative geometric parameters. Manually segmented cells were used to train a random forest classifier for blood cells, enabling the use of a generalized cellular segmentation algorithm for the accurate segmentation of blood cells. These models were used to create an automated data segmentation and analysis pipeline to guide the steps in a 3D workflow including blood cell region prediction, cell boundary extraction, and statistical characterization of 3D geometric and cytological features. We were able to distinguish blood cells at two stages in development (4- and 5-days-post-fertilization) and wild-type vs. polA2 huli hutu ( hht ) mutants. The application of geometric modeling across cell types to and across organisms and sample types may comprise a valuable foundation for computational phenotyping that is more open, informative, rapid, objective, and reproducible.
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Taphorn K, Busse M, Brantl J, Günther B, Diaz A, Holler M, Dierolf M, Mayr D, Pfeiffer F, Herzen J. X-ray Stain Localization with Near-Field Ptychographic Computed Tomography. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201723. [PMID: 35748171 PMCID: PMC9404393 DOI: 10.1002/advs.202201723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Although X-ray contrast agents offer specific characteristics in terms of targeting and attenuation, their accumulation in the tissue on a cellular level is usually not known and difficult to access, as it requires high resolution and sensitivity. Here, quantitative near-field ptychographic X-ray computed tomography is demonstrated to assess the location of X-ray stains at a resolution sufficient to identify intracellular structures by means of a basis material decomposition. On the example of two different X-ray stains, the nonspecific iodine potassium iodide, and eosin Y, which mostly interacts with proteins and peptides in the cell cytoplasm, the distribution of the stains within the cells in murine kidney samples is assessed and compared to unstained samples with similar structural features. Quantitative nanoscopic stain concentrations are in good agreement with dual-energy micro computed tomography measurements, the state-of-the-art modality for material-selective imaging. The presented approach can be applied to a variety of X-ray stains advancing the development of X-ray contrast agents.
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Affiliation(s)
- Kirsten Taphorn
- Chair of Biomedical PhysicsDepartment of PhysicsSchool of Natural SciencesTechnical University of Munich85748GarchingGermany
- Munich Institute of Biomedical Engineering (MIBE)Technical University of Munich85748GarchingGermany
| | - Madleen Busse
- Chair of Biomedical PhysicsDepartment of PhysicsSchool of Natural SciencesTechnical University of Munich85748GarchingGermany
- Munich Institute of Biomedical Engineering (MIBE)Technical University of Munich85748GarchingGermany
| | - Johannes Brantl
- Chair of Biomedical PhysicsDepartment of PhysicsSchool of Natural SciencesTechnical University of Munich85748GarchingGermany
- Munich Institute of Biomedical Engineering (MIBE)Technical University of Munich85748GarchingGermany
| | - Benedikt Günther
- Chair of Biomedical PhysicsDepartment of PhysicsSchool of Natural SciencesTechnical University of Munich85748GarchingGermany
- Munich Institute of Biomedical Engineering (MIBE)Technical University of Munich85748GarchingGermany
| | - Ana Diaz
- Paul Scherrer InstituteVilligen5232Switzerland
| | | | - Martin Dierolf
- Chair of Biomedical PhysicsDepartment of PhysicsSchool of Natural SciencesTechnical University of Munich85748GarchingGermany
- Munich Institute of Biomedical Engineering (MIBE)Technical University of Munich85748GarchingGermany
| | - Doris Mayr
- Institute of PathologyLudwig‐Maximilians‐University80337MunichGermany
| | - Franz Pfeiffer
- Chair of Biomedical PhysicsDepartment of PhysicsSchool of Natural SciencesTechnical University of Munich85748GarchingGermany
- Munich Institute of Biomedical Engineering (MIBE)Technical University of Munich85748GarchingGermany
- Department of Diagnostic and Interventional RadiologySchool of Medicine & Klinikum rechts der IsarTechnical University of Munich81675MünchenGermany
- Institute for Advanced StudyTechnical University of Munich85748GarchingGermany
| | - Julia Herzen
- Chair of Biomedical PhysicsDepartment of PhysicsSchool of Natural SciencesTechnical University of Munich85748GarchingGermany
- Munich Institute of Biomedical Engineering (MIBE)Technical University of Munich85748GarchingGermany
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Yakovlev MA, Vanselow DJ, Ngu MS, Zaino CR, Katz SR, Ding Y, Parkinson D, Wang SY, Ang KC, La Riviere P, Cheng KC. A wide-field micro-computed tomography detector: micron resolution at half-centimetre scale. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:505-514. [PMID: 35254315 PMCID: PMC8900834 DOI: 10.1107/s160057752101287x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Ideal three-dimensional imaging of complex samples made up of micron-scale structures extending over mm to cm, such as biological tissues, requires both wide field of view and high resolution. For existing optics and detectors used for micro-CT (computed tomography) imaging, sub-micron pixel resolution can only be achieved for fields of view of <2 mm. This article presents a unique detector system with a 6 mm field-of-view image circle and 0.5 µm pixel size that can be used in micro-CT units utilizing both synchrotron and commercial X-ray sources. A resolution-test pattern with linear microstructures and whole adult Daphnia magna were imaged at beamline 8.3.2 of the Berkeley Advanced Light Source. Volumes of 10000 × 10000 × 7096 isotropic 0.5 µm voxels were reconstructed over a 5.0 mm × 3.5 mm field of view. Measurements in the projection domain confirmed a 0.90 µm measured spatial resolution that is largely Nyquist-limited. This unprecedented combination of field of view and resolution dramatically reduces the need for sectional scans and computational stitching for large samples, ultimately offering the means to elucidate changes in tissue and cellular morphology in the context of larger, whole, intact model organisms and specimens. This system is also anticipated to benefit micro-CT imaging in materials science, microelectronics, agricultural science and biomedical engineering.
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Affiliation(s)
- Maksim A. Yakovlev
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania, USA
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania, USA
- Biomedical Sciences PhD Program, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Daniel J. Vanselow
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania, USA
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Mee Siing Ngu
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania, USA
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Carolyn R. Zaino
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania, USA
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Spencer R. Katz
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania, USA
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania, USA
- Medical Scientist Training Program, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Yifu Ding
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania, USA
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania, USA
- Medical Scientist Training Program, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Dula Parkinson
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Khai Chung Ang
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania, USA
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania, USA
- Penn State Zebrafish Functional Genomics Core, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | | | - Keith C. Cheng
- Department of Pathology, Penn State College of Medicine, Hershey, Pennsylvania, USA
- The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, Pennsylvania, USA
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Tkachev SY, Mitrin BI, Karnaukhov NS, Sadyrin EV, Voloshin MV, Maksimov AY, Goncharova AS, Lukbanova EA, Zaikina EV, Volkova AV, Khodakova DV, Mindar MV, Yengibarian MA, Protasova TP, Kit SO, Ermakov AM, Chapek SV, Tkacheva MS. Visualization of different anatomical parts of the enucleated human eye using X-ray micro-CT imaging. Exp Eye Res 2020; 203:108394. [PMID: 33310058 DOI: 10.1016/j.exer.2020.108394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 11/18/2020] [Accepted: 12/07/2020] [Indexed: 12/01/2022]
Abstract
Micro-CT visualization allows reconstruction of eye structures with the resolution of light microscopy and estimation of tissue densities. Moreover, this method excludes damaging procedures and allows further histological staining due to the similar steps in the beginning. We have shown the feasibility of the lab-based micro-CT machine usage for visualization of clinically important compartments of human eye such as trabecular outflow pathway, retina, iris and ciliary body after pre-treatment with iodine in ethanol. We also identified the challenges of applying this contrasting technique to lens, cornea, and retina and proposed alternative staining methods for these tissues. Thereby this work provides a starting point for other studies for imaging of human eyes in normal and pathological conditions using lab-based micro-CT systems.
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Affiliation(s)
- Sergey Y Tkachev
- National Medical Research Centre for Oncology, Rostov-on-Don, Russia.
| | | | | | | | | | - Alexey Y Maksimov
- National Medical Research Centre for Oncology, Rostov-on-Don, Russia
| | - Anna S Goncharova
- National Medical Research Centre for Oncology, Rostov-on-Don, Russia
| | | | | | | | - Darya V Khodakova
- National Medical Research Centre for Oncology, Rostov-on-Don, Russia
| | - Maria V Mindar
- National Medical Research Centre for Oncology, Rostov-on-Don, Russia
| | | | | | - Sergey O Kit
- National Medical Research Centre for Oncology, Rostov-on-Don, Russia
| | | | | | - Marina S Tkacheva
- National Medical Research Centre for Oncology, Rostov-on-Don, Russia
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Gabner S, Böck P, Fink D, Glösmann M, Handschuh S. The visible skeleton 2.0: phenotyping of cartilage and bone in fixed vertebrate embryos and foetuses based on X-ray microCT. Development 2020; 147:dev187633. [PMID: 32439754 DOI: 10.1242/dev.187633] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 04/23/2020] [Indexed: 01/14/2023]
Abstract
For decades, clearing and staining with Alcian Blue and Alizarin Red has been the gold standard to image vertebrate skeletal development. Here, we present an alternate approach to visualise bone and cartilage based on X-ray microCT imaging, which allows the collection of genuine 3D data of the entire developing skeleton at micron resolution. Our novel protocol is based on ethanol fixation and staining with Ruthenium Red, and efficiently contrasts cartilage matrix, as demonstrated in whole E16.5 mouse foetuses and limbs of E14 chicken embryos. Bone mineral is well preserved during staining, thus the entire embryonic skeleton can be imaged at high contrast. Differences in X-ray attenuation of ruthenium and calcium enable the spectral separation of cartilage matrix and bone by dual energy microCT (microDECT). Clearing of specimens is not required. The protocol is simple and reproducible. We demonstrate that cartilage contrast in E16.5 mouse foetuses is adequate for fast visual phenotyping. Morphometric skeletal parameters are easily extracted. We consider the presented workflow to be a powerful and versatile extension to the toolkit currently available for qualitative and quantitative phenotyping of vertebrate skeletal development.
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Affiliation(s)
- Simone Gabner
- Histology and Embryology, Department for Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Peter Böck
- Histology and Embryology, Department for Pathobiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Dieter Fink
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, Veterinaärplatz 1, A-1210 Vienna, Austria
| | - Martin Glösmann
- VetCore Facility for Research/Imaging Unit, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Stephan Handschuh
- VetCore Facility for Research/Imaging Unit, University of Veterinary Medicine Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
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Abstract
Recent developments within micro-computed tomography (μCT) imaging have combined to extend our capacity to image tissue in three (3D) and four (4D) dimensions at micron and sub-micron spatial resolutions, opening the way for virtual histology, live cell imaging, subcellular imaging and correlative microscopy. Pivotal to this has been the development of methods to extend the contrast achievable for soft tissue. Herein, we review the new capabilities within the field of life sciences imaging, and consider how future developments in this field could further benefit the life sciences community.
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Affiliation(s)
- Shelley D Rawson
- The Henry Royce Institute and School of Materials, The University of Manchester, Manchester, M13 9PL, UK
| | - Jekaterina Maksimcuka
- The Henry Royce Institute and School of Materials, The University of Manchester, Manchester, M13 9PL, UK
| | - Philip J Withers
- The Henry Royce Institute and School of Materials, The University of Manchester, Manchester, M13 9PL, UK
| | - Sarah H Cartmell
- The Henry Royce Institute and School of Materials, The University of Manchester, Manchester, M13 9PL, UK.
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Whitaker J, Neji R, Byrne N, Puyol-Antón E, Mukherjee RK, Williams SE, Chubb H, O’Neill L, Razeghi O, Connolly A, Rhode K, Niederer S, King A, Tschabrunn C, Anter E, Nezafat R, Bishop MJ, O’Neill M, Razavi R, Roujol S. Improved co-registration of ex-vivo and in-vivo cardiovascular magnetic resonance images using heart-specific flexible 3D printed acrylic scaffold combined with non-rigid registration. J Cardiovasc Magn Reson 2019; 21:62. [PMID: 31597563 PMCID: PMC6785908 DOI: 10.1186/s12968-019-0574-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 09/02/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Ex-vivo cardiovascular magnetic resonance (CMR) imaging has played an important role in the validation of in-vivo CMR characterization of pathological processes. However, comparison between in-vivo and ex-vivo imaging remains challenging due to shape changes occurring between the two states, which may be non-uniform across the diseased heart. A novel two-step process to facilitate registration between ex-vivo and in-vivo CMR was developed and evaluated in a porcine model of chronic myocardial infarction (MI). METHODS Seven weeks after ischemia-reperfusion MI, 12 swine underwent in-vivo CMR imaging with late gadolinium enhancement followed by ex-vivo CMR 1 week later. Five animals comprised the control group, in which ex-vivo imaging was undertaken without any support in the LV cavity, 7 animals comprised the experimental group, in which a two-step registration optimization process was undertaken. The first step involved a heart specific flexible 3D printed scaffold generated from in-vivo CMR, which was used to maintain left ventricular (LV) shape during ex-vivo imaging. In the second step, a non-rigid co-registration algorithm was applied to align in-vivo and ex-vivo data. Tissue dimension changes between in-vivo and ex-vivo imaging were compared between the experimental and control group. In the experimental group, tissue compartment volumes and thickness were compared between in-vivo and ex-vivo data before and after non-rigid registration. The effectiveness of the alignment was assessed quantitatively using the DICE similarity coefficient. RESULTS LV cavity volume changed more in the control group (ratio of cavity volume between ex-vivo and in-vivo imaging in control and experimental group 0.14 vs 0.56, p < 0.0001) and there was a significantly greater change in the short axis dimensions in the control group (ratio of short axis dimensions in control and experimental group 0.38 vs 0.79, p < 0.001). In the experimental group, prior to non-rigid co-registration the LV cavity contracted isotropically in the ex-vivo condition by less than 20% in each dimension. There was a significant proportional change in tissue thickness in the healthy myocardium (change = 29 ± 21%), but not in dense scar (change = - 2 ± 2%, p = 0.034). Following the non-rigid co-registration step of the process, the DICE similarity coefficients for the myocardium, LV cavity and scar were 0.93 (±0.02), 0.89 (±0.01) and 0.77 (±0.07) respectively and the myocardial tissue and LV cavity volumes had a ratio of 1.03 and 1.00 respectively. CONCLUSIONS The pattern of the morphological changes seen between the in-vivo and the ex-vivo LV differs between scar and healthy myocardium. A 3D printed flexible scaffold based on the in-vivo shape of the LV cavity is an effective strategy to minimize morphological changes in the ex-vivo LV. The subsequent non-rigid registration step further improved the co-registration and local comparison between in-vivo and ex-vivo data.
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Affiliation(s)
- John Whitaker
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
| | - Radhouene Neji
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
- Siemens Healthcare Limited, Frimley, UK
| | - Nicholas Byrne
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
- Medical Physics, Guy’s and St. Thomas’ NHS Foundation Trust, London, UK
| | - Esther Puyol-Antón
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
| | - Rahul K. Mukherjee
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
| | - Steven E. Williams
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
| | - Henry Chubb
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
| | - Louisa O’Neill
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
| | - Orod Razeghi
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
| | - Adam Connolly
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
| | - Kawal Rhode
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
| | - Steven Niederer
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
| | - Andrew King
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
| | - Cory Tschabrunn
- Cardiology Department, University of Pennsylvania, Philadelphia, PA USA
| | - Elad Anter
- Cardiology Department, Beth Israel Deaconess Medical Centre / Harvard Medical School, Boston, MA USA
| | - Reza Nezafat
- Cardiology Department, Beth Israel Deaconess Medical Centre / Harvard Medical School, Boston, MA USA
| | - Martin J. Bishop
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
| | - Mark O’Neill
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
| | - Reza Razavi
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
| | - Sébastien Roujol
- School of Biomedical Engineering and Imaging Sciences, King’s College, London, Fourth Floor Lambeth Wing, St Thomas’ Hospital, London, SE1 7EH UK
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Contrast-Enhanced MicroCT for Virtual 3D Anatomical Pathology of Biological Tissues: A Literature Review. CONTRAST MEDIA & MOLECULAR IMAGING 2019; 2019:8617406. [PMID: 30944550 PMCID: PMC6421764 DOI: 10.1155/2019/8617406] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/07/2019] [Indexed: 11/17/2022]
Abstract
To date, the combination of histological sectioning, staining, and microscopic assessment of the 2D sections is still the golden standard for structural and compositional analysis of biological tissues. X-ray microfocus computed tomography (microCT) is an emerging 3D imaging technique with high potential for 3D structural analysis of biological tissues with a complex and heterogeneous 3D structure, such as the trabecular bone. However, its use has been mostly limited to mineralized tissues because of the inherently low X-ray absorption of soft tissues. To achieve sufficient X-ray attenuation, chemical compounds containing high atomic number elements that bind to soft tissues have been recently adopted as contrast agents (CAs) for contrast-enhanced microCT (CE-CT); this novel technique is very promising for quantitative "virtual" 3D anatomical pathology of both mineralized and soft biological tissues. In this paper, we provided a review of the advances in CE-CT since the very first reports on the technology to date. Perfusion CAs for in vivo imaging have not been discussed, as the focus of this review was on CAs that bind to the tissue of interest and that are, thus, used for ex vivo imaging of biological tissues. As CE-CT has mostly been applied for the characterization of musculoskeletal tissues, we have put specific emphasis on these tissues. Advantages and limitations of multiple CAs for different musculoskeletal tissues have been highlighted, and their reproducibility has been discussed. Additionally, the advantages of the "full" 3D CE-CT information have been pinpointed, and its importance for more detailed structural, spatial, and functional characterization of the tissues of interest has been shown. Finally, the remaining challenges that are still hampering a broader adoption of CE-CT have been highlighted, and suggestions have been made to move the field of CE-CT imaging one step further towards a standard accepted tool for quantitative virtual 3D anatomical pathology.
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Koç MM, Aslan N, Kao AP, Barber AH. Evaluation of X-ray tomography contrast agents: A review of production, protocols, and biological applications. Microsc Res Tech 2019; 82:812-848. [PMID: 30786098 DOI: 10.1002/jemt.23225] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/02/2019] [Accepted: 01/12/2019] [Indexed: 12/25/2022]
Abstract
X-ray computed tomography is a strong tool that finds many applications both in medical applications and in the investigation of biological and nonbiological samples. In the clinics, X-ray tomography is widely used for diagnostic purposes whose three-dimensional imaging in high resolution helps physicians to obtain detailed image of investigated regions. Researchers in biological sciences and engineering use X-ray tomography because it is a nondestructive method to assess the structure of their samples. In both medical and biological applications, visualization of soft tissues and structures requires special treatment, in which special contrast agents are used. In this detailed report, molecule-based and nanoparticle-based contrast agents used in biological applications to enhance the image quality were compiled and reported. Special contrast agent applications and protocols to enhance the contrast for the biological applications and works to develop nanoparticle contrast agents to enhance the contrast for targeted drug delivery and general imaging applications were also assessed and listed.
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Affiliation(s)
- Mümin Mehmet Koç
- School of Engineering, University of Portsmouth, Portsmouth, United Kingdom.,Department of Physics, Kirklareli University, Kirklareli, Turkey
| | - Naim Aslan
- Department of Metallurgical and Materials Engineering, Munzur University, Tunceli, Turkey
| | - Alexander P Kao
- School of Engineering, University of Portsmouth, Portsmouth, United Kingdom
| | - Asa H Barber
- School of Engineering, London South Bank University, London, United Kingdom
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10
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A step towards valid detection and quantification of lung cancer volume in experimental mice with contrast agent-based X-ray microtomography. Sci Rep 2019; 9:1325. [PMID: 30718557 PMCID: PMC6362109 DOI: 10.1038/s41598-018-37394-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 11/30/2018] [Indexed: 12/18/2022] Open
Abstract
Tumor volume is a parameter used to evaluate the performance of new therapies in lung cancer research. Conventional methods that are used to estimate tumor size in mouse models fail to provide fast and reliable volumetric data for tumors grown non-subcutaneously. Here, we evaluated the use of iodine-staining combined with micro-computed tomography (micro-CT) to estimate the tumor volume of ex vivo tumor-burdened lungs. We obtained fast high spatial resolution three-dimensional information of the lungs, and we demonstrated that iodine-staining highlights tumors and unhealthy tissue. We processed iodine-stained lungs for histopathological analysis with routine hematoxylin and eosin (H&E) staining. We compared the traditional tumor burden estimation performed manually with H&E histological slices with a semi-automated method using micro-CT datasets. In mouse models that develop lung tumors with well precise boundaries, the method that we describe here enables to perform a quick estimation of tumorous tissue volume in micro-CT images. Our method overestimates the tumor burden in tumors surrounded by abnormal tissue, while traditional histopathological analysis underestimates tumor volume. We propose to embed micro-CT imaging to the traditional workflow of tumorous lung analyses in preclinical cancer research as a strategy to obtain a more accurate estimation of the total lung tumor burden.
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11
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3D vessel-wall virtual histology of whole-body perfused mice using a novel heavy element stain. Sci Rep 2019; 9:698. [PMID: 30679558 PMCID: PMC6345940 DOI: 10.1038/s41598-018-36905-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/23/2018] [Indexed: 01/17/2023] Open
Abstract
Virtual histology – utilizing high-resolution three-dimensional imaging – is becoming readily available. Micro-computed tomography (micro-CT) is widely available and is often coupled with x-ray attenuating histological stains that mark specific tissue components for 3D virtual histology. In this study we describe a new tri-element x-ray attenuating stain and perfusion protocol that provides micro-CT contrast of the entire vasculature of an intact mouse. The stain – derived from an established histology stain (Verhoeff’s) – is modified to enable perfusion through the vasculature; the attenuating elements of the stain are iodine, aluminum, and iron. After a 30-minute perfusion through the vasculature (10-minute flushing with detergent-containing saline followed by 15-minute perfusion with the stain and a final 5-minute saline flush), animals are scanned using micro-CT. We demonstrate that the new staining protocol enables sharp delineation of the vessel walls in three dimensions over the whole body; corresponding histological analysis verified that the CT stain is localized primarily in the endothelial cells and media of large arteries and the endothelium of smaller vessels, such as the coronaries. The rapid perfusion and scanning protocol ensured that all tissues are available for further analysis via higher resolution CT of smaller sections or traditional histological sectioning.
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