Talk:Computed Tomography

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Cite this page: Hill, M.A. (2021, July 23) Embryology Computed Tomography. Retrieved from



Design and Implementation of a Custom Built Optical Projection Tomography System

Wong MD, Dazai J, Walls JR, Gale NW, Henkelman RM (2013) Design and Implementation of a Custom Built Optical Projection Tomography System. PLoS ONE 8(9): e73491. doi:10.1371/journal.pone.0073491

Structural Stabilization of Tissue for Embryo Phenotyping Using Micro-CT with Iodine Staining

PLoS One. 2013 Dec 30;8(12):e84321. doi: 10.1371/journal.pone.0084321. eCollection 2013.

Wong MD1, Spring S2, Henkelman RM1. Author information


The International Mouse Phenotyping Consortium has been established to conduct large-scale phenotyping of the approximately 23,000 single-gene knockout mice generated by the International Knockout Mouse Consortium to investigate the role of each gene in the mouse genome. Of the generated mouse lines, 30% are predicted to be embryonic lethal, requiring the implementation of imaging techniques and analysis tools specific to late gestation mouse embryo phenotyping. A well-adopted technique combines the use of iodinated contrast solutions and micro-computed tomography imaging. This simple iodine immersion technique provides superior soft-tissue contrast enhancement, however, the hypertonic nature of iodine promotes dehydration causing moderate to severe tissue deformation. Here, we combine the stabilizing properties of a hydrogel mesh with the enhanced contrast properties of iodine. The protocol promotes cross linking of tissue through formaldehyde fixation and the linking of hydrogel monomers to biomolecules. As a result, the hydrogel supports tissue structure and preserves its conformation taking advantage of iodine-enhanced soft tissue contrast to produce high quality mouse embryo images with minimal tissue distortion. Hydrogel stabilization substantially reduces intersample anatomical variation of mature mouse embryos subjected to iodine preparation protocols. A 20% and 50% reduction in intersample variation of normalized brain and lung volume is achieved through hydrogel stabilization, as well as a 20% reduction in variation in overall embryo anatomy as measured through image registration methods. This increases the sensitivity of computer automated analysis to reveal significant anatomical differences between mutant and wild-type mice.

PMID 24386367

PMID 24255746

Concentration-dependent specimen shrinkage in iodine-enhanced microCT

J Anat. 2013 Aug;223(2):185-93. doi: 10.1111/joa.12068. Epub 2013 May 30.

Vickerton P, Jarvis J, Jeffery N. Source Department of Musculoskeletal Biology II, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK.


Iodine potassium iodide (I2 KI) solution can be employed as a contrast agent for the visualisation of soft tissue structures in micro-computed tomography studies. This technique provides high resolution images of soft tissue non-destructively but initial studies suggest that the stain can cause substantial specimen shrinkage. The degree of specimen shrinkage, and potential deformation, is an important consideration when using the data for morphological studies. Here we quantify the macroscopic volume changes in mouse skeletal muscle, cardiac muscle and cerebellum as a result of immersion in the common fixatives 10% phosphate-buffered formal saline, 70% ethanol and 3% glutaraldehyde, compared with I2 KI staining solution at concentrations of 2, 6, 10 and 20%. Immersion in the I2 KI solution resulted in dramatic changes of tissue volume, which were far larger than the shrinkage from formalin fixation alone. The degree of macroscopic change was most dependent upon the I2 KI concentration, with severe shrinkage of 70% seen in solutions of 20% I2 KI after 14 days' incubation. When using this technique care needs to be taken to use the lowest concentration that will give adequate contrast to minimise artefacts due to shrinkage. © 2013 Anatomical Society. KEYWORDS: iodine, iodine potassium iodide, microCT, shrinkage, stain

PMID 23721431

A coming of age: advanced imaging technologies for characterising the developing mouse

Trends Genet. 2013 Sep 12. pii: S0168-9525(13)00143-1. doi: 10.1016/j.tig.2013.08.004.

Norris FC, Wong MD, Greene ND, Scambler PJ, Weaver T, Weninger WJ, Mohun TJ, Henkelman RM, Lythgoe MF. Source University College London (UCL) Centre for Advanced Biomedical Imaging, Division of Medicine, UCL, London, UK; Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), UCL, London, UK.


The immense challenge of annotating the entire mouse genome has stimulated the development of cutting-edge imaging technologies in a drive for novel information. These techniques promise to improve understanding of the genes involved in embryo development, at least one third of which have been shown to be essential. Aligning advanced imaging technologies with biological needs will be fundamental to maximising the number of phenotypes discovered in the coming years. International efforts are underway to meet this challenge through an integrated and sophisticated approach to embryo phenotyping. We review rapid advances made in the imaging field over the past decade and provide a comprehensive examination of the relative merits of current and emerging techniques. The aim of this review is to provide a guide to state-of-the-art embryo imaging that will enable informed decisions as to which technology to use and fuel conversations between expert imaging laboratories, researchers, and core mouse production facilities. Copyright © 2013 Elsevier Ltd. All rights reserved. KEYWORDS: high-resolution episcopic microscopy, magnetic resonance imaging, micro X-ray computed tomography, mouse embryo, optical projection tomography, phenotyping

PMID 24035368


Quantitative in vivo imaging of embryonic development: opportunities and challenges

Differentiation. 2012 Jul;84(1):149-62. doi: 10.1016/j.diff.2012.05.003. Epub 2012 Jun 12.

Gregg CL, Butcher JT. Source Department of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA.


Animal models are critically important for a mechanistic understanding of embryonic morphogenesis. For decades, visualizing these rapid and complex multidimensional events has relied on projection images and thin section reconstructions. While much insight has been gained, fixed tissue specimens offer limited information on dynamic processes that are essential for tissue assembly and organ patterning. Quantitative imaging is required to unlock the important basic science and clinically relevant secrets that remain hidden. Recent advances in live imaging technology have enabled quantitative longitudinal analysis of embryonic morphogenesis at multiple length and time scales. Four different imaging modalities are currently being used to monitor embryonic morphogenesis: optical, ultrasound, magnetic resonance imaging (MRI), and micro-computed tomography (micro-CT). Each has its advantages and limitations with respect to spatial resolution, depth of field, scanning speed, and tissue contrast. In addition, new processing tools have been developed to enhance live imaging capabilities. In this review, we analyze each type of imaging source and its use in quantitative study of embryonic morphogenesis in small animal models. We describe the physics behind their function, identify some examples in which the modality has revealed new quantitative insights, and then conclude with a discussion of new research directions with live imaging. Copyright © 2012 International Society of Differentiation. Published by Elsevier B.V. All rights reserved.

PMID 22695188


Rapid Three-Dimensional Phenotyping of Cardiovascular Development in Mouse Embryos by Micro-CT with Iodine Staining

Degenhardt K, Wright AC, Horng D, Padmanabhan A, Epstein JA. Circ Cardiovasc Imaging. 2010 Feb 27. PMID: 20190279


MicroCT for comparative morphology: simple staining methods allow high-contrast 3D imaging of diverse non-mineralized animal tissues

BMC Physiol. 2009 Jun 22;9:11.

Metscher BD.

Department of Theoretical Biology, Gerd Müller, University of Vienna, Althanstrasse 14, 1090 Austria. Abstract BACKGROUND: Comparative, functional, and developmental studies of animal morphology require accurate visualization of three-dimensional structures, but few widely applicable methods exist for non-destructive whole-volume imaging of animal tissues. Quantitative studies in particular require accurately aligned and calibrated volume images of animal structures. X-ray microtomography (microCT) has the potential to produce quantitative 3D images of small biological samples, but its widespread use for non-mineralized tissues has been limited by the low x-ray contrast of soft tissues. Although osmium staining and a few other techniques have been used for contrast enhancement, generally useful methods for microCT imaging for comparative morphology are still lacking.

RESULTS: Several very simple and versatile staining methods are presented for microCT imaging of animal soft tissues, along with advice on tissue fixation and sample preparation. The stains, based on inorganic iodine and phosphotungstic acid, are easier to handle and much less toxic than osmium, and they produce high-contrast x-ray images of a wide variety of soft tissues. The breadth of possible applications is illustrated with a few microCT images of model and non-model animals, including volume and section images of vertebrates, embryos, insects, and other invertebrates. Each image dataset contains x-ray absorbance values for every point in the imaged volume, and objects as small as individual muscle fibers and single blood cells can be resolved in their original locations and orientations within the sample.

CONCLUSION: With very simple contrast staining, microCT imaging can produce quantitative, high-resolution, high-contrast volume images of animal soft tissues, without destroying the specimens and with possibilities of combining with other preparation and imaging methods. Such images are expected to be useful in comparative, developmental, functional, and quantitative studies of morphology.

PMID 19545439


Guidelines for computed tomography and magnetic resonance imaging use during pregnancy and lactation

Obstet Gynecol. 2008 Aug;112(2 Pt 1):333-40.

Chen MM, Coakley FV, Kaimal A, Laros RK Jr.

Department of Radiology, University of California, San Francisco, School of Medicine, San Francisco, California, USA. Abstract There has been a substantial increase in the use of computed tomography (CT) and magnetic resonance imaging (MRI) in pregnancy and lactation. Among some physicians and patients, however, there are misperceptions regarding risks, safety, and appropriate use of these modalities in pregnancy. We have developed a set of evidence-based guidelines for the use of CT, MRI, and contrast media during pregnancy for selected indications including suspected acute appendicitis, pulmonary embolism, renal colic, trauma, and cephalopelvic disproportion. Ultrasonography is the initial modality of choice for suspected appendicitis, but if the ultrasound examination is negative, MRI or CT can be obtained. Computed tomography should be the initial diagnostic imaging modality for suspected pulmonary embolism. Ultrasonography should be the initial study of choice for suspected renal colic. Ultrasonography can be the initial imaging evaluation for trauma, but CT should be performed if serious injury is suspected. Pelvimetry now is used rarely for suspected cephalopelvic disproportion, but when required, low-dose CT pelvimetry can be performed with minimal risk. Although iodinated contrast seems safe to use in pregnancy, intravenous gadolinium is contraindicated and should be used only when absolutely essential. It seems to be safe to continue breast-feeding immediately after receiving iodinated contrast or gadolinium. Although teratogenesis is not a major concern after exposure to prenatal diagnostic radiation, carcinogenesis is a potential risk. When used appropriately, CT and MRI can be valuable tools in imaging pregnant and lactating women; risks and benefits always should be considered and discussed with patients.

PMID 18669732

From Wiki

Computed Tomography (CT) imaging works through X-rays that are emitted from a focused radiation source that is rotated around the test subject placed in the middle of the CT scanner.[1] The X-ray is attenuated at different rates depending on the density of tissue it is passing through, and is then picked up by sensors on the opposite end of the CT scanner from the emission source. In contrast to traditional 2D X-ray, since the emission source in a CT scanner is rotated around the animal, a series of 2D images can then be combined into 3D structures by the computer.

Optical coherence tomography (OCT) is an optical signal acquisition and processing method. It captures micrometer-resolution, three-dimensional images from within optical scattering media (e.g., biological tissue). Optical coherence tomography is an interferometric technique, typically employing near-infrared light.