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Tomography

Tomography is a non-invasive imaging technique that allows for the visualization and analysis of internal structures within a subject, such as the human body.
It works by taking a series of cross-sectional images, which are then combined to create a three-dimensional representation.
Tomography is widely used in medical diagnostics, scientific research, and industrial applications, enabling the detailed examination of tissues, organs, and other structures.
This powerful imaging modality enhances understanding, supports accurate diagnoses, and facilitates groundbreaking discoveries across a variety of fields.
Reserchers can leverge tomography to optimize their research and achive breakthroughing results.

Most cited protocols related to «Tomography»

1
Benchmarking Cryo-ET Template Matching
For the template matching benchmark, pre-aligned tilt series from EMPIAR-10045 were downloaded. The defocus was estimated, and full tomograms were reconstructed with a pixel size of 10 Å in Warp. The 80S ribosome map derived from these data in the original publication40 (link) and deposited under EMD-3228 was used as the template. Template matching was performed on the 10 Å/px tomograms with an angular sampling of 7.5 °, using a local 3D CTF. The same steps were performed using a binary missing wedge mask instead of the 3D CTF. The picked positions were screened manually to determine the false positive rate. Background statistics were calculated for the correlation volume trimmed to remove the vacuum region, and excluding 48 px windows around the peaks.
To benchmark CTF estimation and sub-tomogram export on EMPIAR-10045 data, the particles previously picked through template matching were exported together with their 3D CTF volumes at a pixel size of 5 Å. The sub-tomograms were then subjected to 3D refinement in RELION 3.0 without prior classification.
To benchmark CTF estimation and sub-tomogram export on HIV-1 particles, raw data from EMPIAR-10164 were downloaded. A subset of 5 tilt series previously used by the authors of NovaCTF41 (link) was selected. Movies were aligned in Warp using only global alignment with a temporal resolution of 5. Gold beads were picked manually and used to align the tilt series in IMOD62 (link). Full tomograms were reconstructed with a pixel size of 5 Å in Warp. Template matching was performed with the EMD-4015 map with an angular sampling of 7.5 ° and C6 symmetry. A custom script was used to remove particles not fitting into a regular hexagonal grid as described previously47 . The particles were exported together with their 3D CTF volumes at a pixel size of 1.35 Å. The sub-tomograms were then subjected to 3D refinement in RELION 3.0 without prior classification.
Tegunov D, & Cramer P. (2019). Real-time cryo–EM data pre-processing with Warp. Nature methods, 16(11), 1146-1152.
Publication 2019
Gold HIV-1 Ribosomes Tomography Vacuum
2
Evaluating Cryo-EM Data Correction Techniques

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Publication 2011
5'-deoxy-5'-phosphonomethyladenosine phosphate Axoneme Chlamydomonas reinhardtii Cone-Beam Computed Tomography DNA Replication Epistropheus Hypersensitivity Maritally Unattached Mental Orientation Microtubule-Associated Proteins Microtubules NADH Dehydrogenase Complex 1 Optimism Plant Embryos Radius Seizures Tomography Yarrowia lipolytica
3
Comprehensive Ophthalmological Assessment Protocol for Glaucoma
Each participant underwent a complete ophthalmological examination at baseline, which included relevant medical history, blood pressure measurement, best-corrected visual acuity, slitlamp biomicroscopy, gonioscopy, Goldmann applanation tonometry, central corneal thickness measurement, dilated funduscopy, stereoscopic ophthalmoscopy of the optic disc with a 78-diopter lens, and simultaneous stereoscopic disc photography. In addition to photography, the structure of the optic disc and nerve fiber layer was measured with a variety of imaging devices, including the Heidelberg Retina Tomograph (Heidelberg Engineering, Heidelberg, Germany), GDx (Carl Zeiss Meditec, Dublin, California), and optical coherence tomography (Stratus OCT; Carl Zeiss Meditec). Tests of visual function included SAP, short-wavelength automated perimetry, and frequency doubling technology perimetry. See Table 2 for details of the examinations and tests completed at each visit. We tracked all systemic and ocular procedures and medications and any concurrent conditions that might affect vision.
This examination protocol is repeated annually for patients with glaucoma, ocular hypertension, and suspected glaucoma, who receive treatment and glaucoma medications at no cost at the discretion of their glaucoma specialist. Transportation is provided when needed.
All color simultaneous stereophotographs were taken using a Nidek Stereo Camera Model 3-DX (Nidek Inc, Palo Alto, California) after maximal pupil dilation. All photograph evaluations were performed using a simultaneous stereoscopic viewer (Asahi Pentax Stereo Viewer II; Pentax, Tokyo, Japan) with a standard fluorescent light bulb. Certified photograph graders evaluated all photographs. To be certified, individuals were trained and then tested on separate standardized sets of stereophotographs depicting (1) glaucomatous and healthy eyes and (2) progressing and nonprogressing eyes. Recent evidence from the Ocular Hypertension Treatment Study (OHTS) and the European Glaucoma Prevention Study indicated that reproducibility of stereophotograph assessment is good when graders have been trained using this type of formal protocol.16 (link),17 (link)
Each photograph was graded by 2 independent graders according to a standard protocol using the standard photographs as reference. Each grader was masked to the participant’s identity, diagnostic status, study, race, and other results. In cases of disagreement, a third senior grader adjudicated. All photographs were graded for quality and evidence of glaucoma damage. To assess between-grader reproducibility, 80 randomly chosen stereophotographs graded by IDEA (Imaging Data Evaluation and Analysis) Center personnel were evaluated for consensus between 2 graders; 73 of 80 (91%) were assigned the same diagnostic classification of glaucoma or healthy both times. Among the same 80 photographs, IDEA Center graders agreed on a vertical cup-disc ratio within 0.2 mm 70 of 80 times (87%). Adjudication of baseline photos was required in 31% of African descent and 28% of European descent eyes.
Sample P.A., Girkin C.A., Zangwill L.M., Jain S., Racette L., Becerra L.M., Weinreb R.N., Medeiros F.A., Wilson M.R., De León-Ortega J., Tello C., Bowd C, & Liebmann J.M. (2009). The African Descent and Glaucoma Evaluation Study (ADAGES): Design and Baseline Data. Archives of ophthalmology, 127(9), 1136-1145.
Publication 2009
Administration, Ophthalmic Corneal Pachymetry Determination, Blood Pressure Diagnosis Europeans Examination Tables Eye Glaucoma Glaucoma, Suspect Gonioscopy High Blood Pressures Lens, Crystalline Light Medical Devices Medulla Oblongata Mydriasis Negroid Races Nerve Fibers Ocular Hypertension Ophthalmoscopy Optic Disk Patients Perimetry Pharmaceutical Preparations Retina Slit Lamp Examination Tomography Tomography, Optical Coherence Tonometry, Ocular Vision Vision Tests Visual Acuity
4
Continuous Deformation Modeling in Cryo-EM
Whereas the Warp model for a movie or tilt series describes the non-linear deformation of the entire particle ensemble and its environment, it is unclear whether this deformation gradient stays continuous throughout a single particle, i. e. if the protein structure is subject to the same compression and shearing as the ice around it. Many recent high-resolution maps were reconstructed using particles extracted from dose-weighted averages produced by MotionCor29 (link). The tool assumes the deformation gradient to be continuous in all parts of the image, and will thus deform images of particles and ice in the same way. This will be beneficial if the underlying physical model is indeed continuous. However, it also distorts the CTF locally without passing any knowledge of the distortion to downstream processing tools. In case of a strong local change in the motion direction, this will result in an artifact similar to lens astigmatism.
Warp assumes a continuous deformation field when exporting dose-weighted averages of whole 2D movies, i. e. each pixel will be shifted according to the grid interpolants at that exact position. This has the benefit of uniformly sharper images for visual inspection and particle picking. For particle and sub-tomogram extraction, however, the entire particle image will be shifted uniformly according to the grid interpolants at the particle’s center. This keeps the CTF true to its fitted analytical description, but makes the assumption that the protein is more rigid than the surrounding ice and thus deforms less due to BIM. For whole-tomogram reconstruction, a hybrid approach is pursued: the local volumes are produced using the same procedure as sub-tomogram extraction, but the combined volume is largely continuous depending on how small the local volumes were.
Dose weighting in Warp adds a B-factor of -4 Å2 per 1 e-/Å2 of dose, similar to a heuristic published previously7 . While a different heuristic is used in MotionCor29 (link) and Unblur7 , the accuracy of both approaches is of decreased significance as data-driven re-weighting is likely to be performed using an approach like the “particle polishing” in RELION 3.0.
Tegunov D, & Cramer P. (2019). Real-time cryo–EM data pre-processing with Warp. Nature methods, 16(11), 1146-1152.
Publication 2019
Complement Factor B Hybrids Lenticular Astigmatism Microtubule-Associated Proteins Muscle Rigidity PER1 protein, human Physical Examination Proteins Reconstructive Surgical Procedures Tomography
5
Automated Tomogram Alignment and Positioning

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Publication 2016
Epistropheus Fiducial Markers IMod Reading Frames Tomography

Most recents protocols related to «Tomography»

1
Quantifying Presynaptic Density via PET Imaging
Participants in subcohort II will undergo PET neuroimaging with [11C]-UCB-J, which binds to the presynaptic vesicle glycoprotein 2A (SV2A). SV2A is ubiquitously and homogeneously located in synapses across the brain and allows for the determination of SV2A binding and presynaptic density in the brain [69 (link), 70 (link)]. However, due to the ubiquitous distribution of SV2A, there is no proper reference region in the brain, and we, therefore, measure the arterial input function. PET scanning is conducted using a High-Resolution Research Tomography (HRRT) PET scanner (CTI/Siemens, Knoxville, TN, USA). First a 6 min transmission scan, then an intravenous bolus of < 400 MBq of [11C]-UCB-J administered over 20 s followed by a 90-min dynamic acquisition (256 × 256 × 207 voxels; 1.22 × 1.22 × 1.22 mm).
Jensen K.H., Dam V.H., Ganz M., Fisher P.M., Ip C.T., Sankar A., Marstrand-Joergensen M.R., Ozenne B., Osler M., Penninx B.W., Pinborg L.H., Frokjaer V.G., Knudsen G.M, & Jørgensen M.B. (2023). Deep phenotyping towards precision psychiatry of first-episode depression — the Brain Drugs-Depression cohort. BMC Psychiatry, 23, 151.
Publication 2023
Arteries Brain Glycoproteins Radionuclide Imaging Synapses Tomography Transmission, Communicable Disease
2
Retrospective Study of Medullary Thyroid Carcinoma
The present retrospective study considered a consecutive series of adult patients referred to the Endocrine Unit of Careggi Hospital from February 2003 to February 2022, and who provided an informed consent. Inclusion criteria are: i) total thyroidectomy with a diagnosis of MTC on histology; ii) availability of histological, clinical and biochemical data; iii) absence of distant metastasis (M0) at diagnosis (by negative preoperative thoracic and abdomen computer tomography evaluation). Exclusion criteria are: i) absence of histological or biochemical information; ii) follow-up performed outside from the Endocrine Unit of Careggi Hospital; iii) presence of significant comorbidities (i.e. chronic renal failure) and/or ongoing medications interfering with CT assessments (i.e. pump proton inhibitors).
For each patient, we collected all clinical (gender, age at diagnosis, follow-up length), histological (including tumour size, multifocality, vascularization, number of metastatic lymph nodes at diagnosis), biochemical (CT and CEA measurements at diagnosis and during follow-up) and radiological information. In particular, neck ultrasound (US) results were available for 79% and 77% of cases at six months and one-year follow-up, respectively.
Biochemical tests have been performed in Careggi Hospital and CT measurement has been performed by chemiluminescence immunoassay LIAISON® XL (DiaSorin).
According to the results of the last available follow-up, each patient has been classified as complete response (CR) if: undetectable CT values (CT values below the lower reference limit of 0.1 pg/ml), normal CEA values and negative radiological assessment; persistent disease (PD) if: detectable serum CT and/or radiological evidence of diseases.
All histology has been classified according to the AJCC VIII edition (10 ). Germline and/or somatic assessment of RET mutations have been collected, when available (91% and 51%, respectively).
The present study was approved by the Local Ethics Committee (Comitato Etico Area Vasta Centro-CEAVC, Florence, Tuscany, Italy) and conducted in compliance with the Declaration of Helsinki principles.
Sparano C., Adornato V., Puccioni M., Zago E., Perigli G., Badii B., Santoro R., Maggi M, & Petrone L. (2023). Early calcitonin levels in medullary thyroid carcinoma: Prognostic role in patients without distant metastases at diagnosis. Frontiers in Oncology, 13, 1120799.
Publication 2023
Abdomen Adult Chemiluminescent Assays Chronic Kidney Diseases Diagnosis Diploid Cell Gender Germ Line inhibitors Mutation Neck Neoplasm Metastasis Neoplasms Nodes, Lymph Pathologic Neovascularization Patients Pharmaceutical Preparations Protons Regional Ethics Committees Serum System, Endocrine Thyroidectomy Tomography Ultrasonography X-Rays, Diagnostic
3
Microfocus X-ray CT Analysis of Kidney Stones
We identified the crystal components in the kidney stones by using a microfocus X-ray CT system (inspeXio SMX-100CT Plus; Shimadzu). The measurement parameters were X-ray tube: 90 kV, 44 mA and voxel size: 0.005 mm/voxel. We measured a 2-mm-thick kidney stone sample and obtained a series of X-ray tomographic images. The main components of CaOx kidney stones, i.e., COM and COD, exhibit different amounts of X-ray absorption [26 (link)]. Approximate local phase identification was performed based on the differences in these absorption values. The amount of material can also affect X-ray absorption. Therefore, in the case of samples with crystals smaller than those that can be discriminated with an optical microscope (several micrometers or less), it is difficult to determine the ratio of COM/COD by microfocus X-ray CT system only. However, if crystal sizes are large enough to be distinguished with an optical microscope, the difference in density between COM and COD can be determined by the CT value. We thus carefully assessed the adequacy of this boundary condition by comparing it with the photographs obtained by the polarized-light microscopy. The samples used for the microfocus X-ray CT system and the samples used for the polarized-light microscopy observations were processed from the same kidney stone. The analysis procedure using the obtained X-ray tomographic images is shown in the S2 Fig.
Maruyama M., Sawada K.P., Tanaka Y., Okada A., Momma K., Nakamura M., Mori R., Furukawa Y., Sugiura Y., Tajiri R., Taguchi K., Hamamoto S., Ando R., Tsukamoto K., Takano K., Imanishi M., Yoshimura M., Yasui T, & Mori Y. (2023). Quantitative analysis of calcium oxalate monohydrate and dihydrate for elucidating the formation mechanism of calcium oxalate kidney stones. PLOS ONE, 18(3), e0282743.
Publication 2023
Kidney Calculi Light Microscopy Microscopy, Polarization Radiography Tomography Training Programs X-Ray Computed Tomography
4
Evaluating Solid Tumor Response Criteria
The responses to treatments were evaluated every 2 months or suspected disease
progression. Pelvic examination and plasma tumor markers were routinely
performed each time. Imaging tests including computed tomography (CT), positron
emission tomography-computed tomography (PET-CT), single-photon emission
computed tomography (SPECT), and magnetic resonance imaging (MRI) were used as
appropriate to determine the size of tumors. The Response Evaluation Criteria in
Solid Tumors (RECIST) version 1.1 was used to determine CR, PR, stable disease
(SD), or progressive disease (PD). During the nontreatment period, follow-up was
performed every 3 months until death or the patient was censored. Disease-free
survival (DFS) was defined as the period from the date of surgery to the
diagnosis of first recurrence/metastasis, and OS was defined as the period from
the beginning of treatment after first recurrence/metastasis to the death, with
patients alive at last follow-up censored on that date. PFS was defined as the
period from the treatment beginning after first recurrence/metastasis to the
second recurrence/metastasis or death, with patients censored if alive and with
no evidence of tumor recurrence/metastasis.
Qiu H., Su N., Yan S, & Li J. (2023). Real-world Efficacy Data on Anti-Angiogenic Drugs in Recurrent Small Cell Cervical Carcinoma: A Retrospective Study. Technology in Cancer Research & Treatment, 22, 15330338231160393.
Publication 2023
Neoplasm Metastasis Neoplasms Operative Surgical Procedures Patients Pelvic Examination Plasma Recurrence Tomography Tumor Markers X-Ray Computed Tomography
5
COVID-19 Medical Imaging Research Protocols
This study employed an a priori protocol. Two senior radiology professors (Dr. Liu and Dr. Zeng) jointly discussed and determined the topic and that the “sample of interest” were the studies published in the WoSCC pertaining to COVID-19 and medical imaging, and formulated the literature search words, which were reviewed by a literature search professional (Mrs. Zhao). Finally, two other co-authors (Dr. Zhang and Dr. Xu) were included in the publication in accordance with the predetermined inclusion and exclusion criteria (Fig. 1) and any discrepancy was resolved by discussion. The following search terms were used to gather relevant literature from the WoSCC:

Flow diagram of this study

TS = (“SARS-CoV-2” or “COVID-19” or “COVID 19” or “coronavirus disease 2019 virus” or “2019 novel coronavirus*” or “coronavirus, 2019 novel” or “novel coronavirus, 2019” or “SARS-CoV-2 Virus*” or “SARS-CoV-2 Virus*” or “Virus, SARS-CoV-2” or “2019-nCoV” or “COVID-19 Virus*” or “COVID 19 Virus*” or “Virus, COVID-19” or “SARS coronavirus 2” or “coronavirus 2, SARS”).
AND
TS = (“X-ray*” or “chest CT” or “chest radiology” or MRI or “magnetic resonance imaging” or “computed tomography” or “compute tomography” or “positron emission tomography” or “single-photon emission computed tomography” or “pet-ct” or “spect-ct” or “pet-mri” or “spect” or “SPECT/CT” or “PET/CT” or ultrasound or ultrasonography) from “DOP* = (2020–01-01/2020–01-31)” to “DOP = (2022–06-01/2022–06-30).”
Initially, 7767 articles were retrieved. Figure 1 illustrates the research steps in this study. Only “articles” and “review articles” were included. We had no language restrictions. The time span was 30 months, from 1 January 2020 to 30 June 2022. After retrieving the studies, publications based solely on COVID-19 themes or medical image themes were excluded, leaving a final sample of 4444 studies. Detailed inclusion and exclusion criteria are provided in Fig. 1. All data were downloaded directly from the database; therefore, no ethical statement or approval was required.
Wen R., Zhang M., Xu R., Gao Y., Liu L., Chen H., Wang X., Zhu W., Lin H., Liu C, & Zeng X. (2023). COVID-19 imaging, where do we go from here? Bibliometric analysis of medical imaging in COVID-19. European Radiology, 33(5), 3133-3143.
Publication 2023
Chest Coronavirus COVID 19 Positron-Emission Tomography Radiography Radiography, Thoracic SARS-CoV-2 Scan, CT PET Severe Acute Respiratory Syndrome Single Photon Emission Computed Tomography Computed Tomography Tomography Tomography, Emission-Computed, Single-Photon Ultrasonography Virus X-Ray Computed Tomography

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More about "Tomography"

Tomography is a powerful non-invasive imaging technique that allows for the visualization and analysis of internal structures within a subject, such as the human body.
This innovative technology works by taking a series of cross-sectional images, which are then combined to create a comprehensive three-dimensional representation.
Tomography is widely utilized in various fields, including medical diagnostics, scientific research, and industrial applications, enabling the detailed examination of tissues, organs, and other structures.
The use of tomography in research and diagnostics has been significantly enhanced by advancements in imaging technologies.
Researchers can leverage a variety of specialized equipment, such as the MATLAB software, Pentacam and Pentacam HR systems, Titan Krios electron microscopes, High Resolution Research Tomographs, K2 Summit direct electron detectors, and Vitrobot Mark IV plunge freezers, to optimize their investigations and achieve groundbreaking results.
Tomographic imaging encompasses several key subtopics, including computed tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), and ultrasound (US).
These modalities, often referred to by their abbreviations, offer distinct advantages and are utilized in different contexts to suit the specific needs of researchers and clinicians.
The power of tomography lies in its ability to enhance understanding, support accurate diagnoses, and facilitate discoveries across a variety of fields.
Researchers can leverage sophisticated software tools, such as Amira and NRecon, to visualize, analyze, and interpret the wealth of data generated by tomographic imaging systems, including the Skyscan 1172 micro-CT scanner.
By harnessing the insights and capabilities of tomography, researchers can optimize their investigations, streamline their workflows, and unlock groundbreaking advancements that have the potential to transform our understanding of the world around us.