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Wendling O, Hentsch D, Jacobs H, Lemercier N, Taubert S, Pertuy F, Vonesch JL, Sorg T, Di Michele M, Le Cam L, Rosahl T, Carballo-Jane E, Liu M, Mu J, Mark M, Herault Y. High Resolution Episcopic Microscopy for Qualitative and Quantitative Data in Phenotyping Altered Embryos and Adult Mice Using the New "Histo3D" System. Biomedicines 2021; 9:767. [PMID: 34356832 PMCID: PMC8301480 DOI: 10.3390/biomedicines9070767] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 12/27/2022] Open
Abstract
3D imaging in animal models, during development or in adults, facilitates the identification of structural morphological changes that cannot be achieved with traditional 2D histological staining. Through the reconstruction of whole embryos or a region-of-interest, specific changes are better delimited and can be easily quantified. We focused here on high-resolution episcopic microscopy (HREM), and its potential for visualizing and quantifying the organ systems of normal and genetically altered embryos and adult organisms. Although the technique is based on episcopic images, these are of high resolution and are close to histological quality. The images reflect the tissue structure and densities revealed by histology, albeit in a grayscale color map. HREM technology permits researchers to take advantage of serial 2D aligned stacks of images to perform 3D reconstructions. Three-dimensional visualization allows for an appreciation of topology and morphology that is difficult to achieve with classical histological studies. The nature of the data lends itself to novel forms of computational analysis that permit the accurate quantitation and comparison of individual embryos in a manner that is impossible with histology. Here, we have developed a new HREM prototype consisting of the assembly of a Leica Biosystems Nanocut rotary microtome with optics and a camera. We describe some examples of applications in the prenatal and adult lifestage of the mouse to show the added value of HREM for phenotyping experimental cohorts to compare and quantify structure volumes. At prenatal stages, segmentations and 3D reconstructions allowed the quantification of neural tissue and ventricular system volumes of normal brains at E14.5 and E16.5 stages. 3D representations of normal cranial and peripheric nerves at E15.5 and of the normal urogenital system from stages E11.5 to E14.5 were also performed. We also present a methodology to quantify the volume of the atherosclerotic plaques of ApoEtm1Unc/tm1Unc mutant mice and illustrate a 3D reconstruction of knee ligaments in adult mice.
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Affiliation(s)
- Olivia Wendling
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (O.W.); (H.J.); (F.P.); (T.S.); (M.M.)
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (D.H.); (S.T.); (J.-L.V.)
| | - Didier Hentsch
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (D.H.); (S.T.); (J.-L.V.)
| | - Hugues Jacobs
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (O.W.); (H.J.); (F.P.); (T.S.); (M.M.)
| | | | - Serge Taubert
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (D.H.); (S.T.); (J.-L.V.)
| | - Fabien Pertuy
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (O.W.); (H.J.); (F.P.); (T.S.); (M.M.)
| | - Jean-Luc Vonesch
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (D.H.); (S.T.); (J.-L.V.)
| | - Tania Sorg
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (O.W.); (H.J.); (F.P.); (T.S.); (M.M.)
| | - Michela Di Michele
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Université Montpellier, 34298 Montpellier, France; (M.D.M.); (L.L.C.)
- Institut Régional du Cancer de Montpellier (ICM), Université Montpellier, 34298 Montpellier, France
| | - Laurent Le Cam
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Université Montpellier, 34298 Montpellier, France; (M.D.M.); (L.L.C.)
- Institut Régional du Cancer de Montpellier (ICM), Université Montpellier, 34298 Montpellier, France
| | - Thomas Rosahl
- Merck & Co. Inc., Kenilworth, NJ 07033, USA; (T.R.); (E.C.-J.); (M.L.); (J.M.)
| | - Ester Carballo-Jane
- Merck & Co. Inc., Kenilworth, NJ 07033, USA; (T.R.); (E.C.-J.); (M.L.); (J.M.)
| | - Mindy Liu
- Merck & Co. Inc., Kenilworth, NJ 07033, USA; (T.R.); (E.C.-J.); (M.L.); (J.M.)
| | - James Mu
- Merck & Co. Inc., Kenilworth, NJ 07033, USA; (T.R.); (E.C.-J.); (M.L.); (J.M.)
| | - Manuel Mark
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (O.W.); (H.J.); (F.P.); (T.S.); (M.M.)
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (D.H.); (S.T.); (J.-L.V.)
- Service de Biologie de la Reproduction, Hôpitaux Universitaires de Strasbourg (HUS), CEDEX, 67091 Strasbourg, France
| | - Yann Herault
- CNRS, INSERM, CELPHEDIA, PHENOMIN-Institut Clinique de la Souris (ICS), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (O.W.); (H.J.); (F.P.); (T.S.); (M.M.)
- CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, 1 Rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (D.H.); (S.T.); (J.-L.V.)
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2
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Horner NR, Venkataraman S, Armit C, Casero R, Brown JM, Wong MD, van Eede MC, Henkelman RM, Johnson S, Teboul L, Wells S, Brown SD, Westerberg H, Mallon AM. LAMA: automated image analysis for the developmental phenotyping of mouse embryos. Development 2021; 148:dev192955. [PMID: 33574040 PMCID: PMC8015254 DOI: 10.1242/dev.192955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/21/2020] [Indexed: 11/20/2022]
Abstract
Advanced 3D imaging modalities, such as micro-computed tomography (micro-CT), have been incorporated into the high-throughput embryo pipeline of the International Mouse Phenotyping Consortium (IMPC). This project generates large volumes of raw data that cannot be immediately exploited without significant resources of personnel and expertise. Thus, rapid automated annotation is crucial to ensure that 3D imaging data can be integrated with other multi-dimensional phenotyping data. We present an automated computational mouse embryo phenotyping pipeline that harnesses the large amount of wild-type control data available in the IMPC embryo pipeline in order to address issues of low mutant sample number as well as incomplete penetrance and variable expressivity. We also investigate the effect of developmental substage on automated phenotyping results. Designed primarily for developmental biologists, our software performs image pre-processing, registration, statistical analysis and segmentation of embryo images. We also present a novel anatomical E14.5 embryo atlas average and, using it with LAMA, show that we can uncover known and novel dysmorphology from two IMPC knockout lines.
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Affiliation(s)
- Neil R Horner
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - Shanmugasundaram Venkataraman
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Chris Armit
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh EH4 2XU, UK
- BGI Hong Kong, 26/F, Kings Wing Plaza 2, 1 On Kwan Street, Shek Mun, New Territories, Hong Kong
| | - Ramón Casero
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - James M Brown
- School of Computer Science, University of Lincoln, Lincoln LN6 7TS
| | - Michael D Wong
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada
| | - Matthijs C van Eede
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada
| | - R Mark Henkelman
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada
| | - Sara Johnson
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - Lydia Teboul
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - Sara Wells
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | - Steve D Brown
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
| | | | - Ann-Marie Mallon
- Medical Research Council Harwell Institute, Harwell OX11 0RD, UK
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3
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Ma D, Cardoso MJ, Zuluaga MA, Modat M, Powell NM, Wiseman FK, Cleary JO, Sinclair B, Harrison IF, Siow B, Popuri K, Lee S, Matsubara JA, Sarunic MV, Beg MF, Tybulewicz VLJ, Fisher EMC, Lythgoe MF, Ourselin S. Substantially thinner internal granular layer and reduced molecular layer surface in the cerebellar cortex of the Tc1 mouse model of down syndrome - a comprehensive morphometric analysis with active staining contrast-enhanced MRI. Neuroimage 2020; 223:117271. [PMID: 32835824 PMCID: PMC8417772 DOI: 10.1016/j.neuroimage.2020.117271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/03/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022] Open
Abstract
Down Syndrome is a chromosomal disorder that affects the development of cerebellar cortical lobules. Impaired neurogenesis in the cerebellum varies among different types of neuronal cells and neuronal layers. In this study, we developed an imaging analysis framework that utilizes gadolinium-enhanced ex vivo mouse brain MRI. We extracted the middle Purkinje layer of the mouse cerebellar cortex, enabling the estimation of the volume, thickness, and surface area of the entire cerebellar cortex, the internal granular layer, and the molecular layer in the Tc1 mouse model of Down Syndrome. The morphometric analysis of our method revealed that a larger proportion of the cerebellar thinning in this model of Down Syndrome resided in the inner granule cell layer, while a larger proportion of the surface area shrinkage was in the molecular layer.
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Affiliation(s)
- Da Ma
- Department of Medical Physics and Biomedical Engineering, University College London, United Kingdom; Centre for Advanced Biomedical Imaging, University College London, United Kingdom; School of Engineering Science, Simon Fraser University, Burnaby, Canada.
| | - Manuel J Cardoso
- Department of Medical Physics and Biomedical Engineering, University College London, United Kingdom; School of Biomedical Engineering & Imaging Sciences, King's College London, United Kingdom
| | - Maria A Zuluaga
- Department of Medical Physics and Biomedical Engineering, University College London, United Kingdom; Data Science Department, EURECOM, France
| | - Marc Modat
- Department of Medical Physics and Biomedical Engineering, University College London, United Kingdom; School of Biomedical Engineering & Imaging Sciences, King's College London, United Kingdom
| | - Nick M Powell
- Department of Medical Physics and Biomedical Engineering, University College London, United Kingdom; Centre for Advanced Biomedical Imaging, University College London, United Kingdom
| | - Frances K Wiseman
- UK Dementia Research Institute at University College London, UK London; Down Syndrome Consortium (LonDownS), London, United Kingdom
| | - Jon O Cleary
- Centre for Advanced Biomedical Imaging, University College London, United Kingdom; Department of Radiology, Guy´s and St Thomas' NHS Foundation Trust, United Kingdom; Melbourne Brain Centre Imaging Unit, Department of Medicine and Radiology, University of Melbourne, Melbourne, Australia
| | - Benjamin Sinclair
- Centre for Advanced Biomedical Imaging, University College London, United Kingdom
| | - Ian F Harrison
- Centre for Advanced Biomedical Imaging, University College London, United Kingdom
| | - Bernard Siow
- Centre for Advanced Biomedical Imaging, University College London, United Kingdom; The Francis Crick Institute, London, United Kingdom
| | - Karteek Popuri
- School of Engineering Science, Simon Fraser University, Burnaby, Canada
| | - Sieun Lee
- School of Engineering Science, Simon Fraser University, Burnaby, Canada
| | - Joanne A Matsubara
- Department of Ophthalmology & Visual Science, University of British Columbia, Vancouver, Canada
| | - Marinko V Sarunic
- School of Engineering Science, Simon Fraser University, Burnaby, Canada
| | - Mirza Faisal Beg
- School of Engineering Science, Simon Fraser University, Burnaby, Canada
| | - Victor L J Tybulewicz
- The Francis Crick Institute, London, United Kingdom; Department of Immunology and Inflammation, Imperial College, London, United Kingdom
| | | | - Mark F Lythgoe
- Centre for Advanced Biomedical Imaging, University College London, United Kingdom
| | - Sebastien Ourselin
- Department of Medical Physics and Biomedical Engineering, University College London, United Kingdom; School of Biomedical Engineering & Imaging Sciences, King's College London, United Kingdom
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4
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High-Resolution Episcopic Microscopy (HREM): Looking Back on 13 Years of Successful Generation of Digital Volume Data of Organic Material for 3D Visualisation and 3D Display. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9183826] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
High-resolution episcopic microscopy (HREM) is an imaging technique that permits the simple and rapid generation of three-dimensional (3D) digital volume data of histologically embedded and physically sectioned specimens. The data can be immediately used for high-detail 3D analysis of a broad variety of organic materials with all modern methods of 3D visualisation and display. Since its first description in 2006, HREM has been adopted as a method for exploring organic specimens in many fields of science, and it has recruited a slowly but steadily growing user community. This review aims to briefly introduce the basic principles of HREM data generation and to provide an overview of scientific publications that have been published in the last 13 years involving HREM imaging. The studies to which we refer describe technical details and specimen-specific protocols, and provide examples of the successful use of HREM in biological, biomedical and medical research. Finally, the limitations, potentials and anticipated further improvements are briefly outlined.
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5
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Visualising the Cardiovascular System of Embryos of Biomedical Model Organisms with High Resolution Episcopic Microscopy (HREM). J Cardiovasc Dev Dis 2018; 5:jcdd5040058. [PMID: 30558275 PMCID: PMC6306920 DOI: 10.3390/jcdd5040058] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/09/2018] [Accepted: 12/11/2018] [Indexed: 12/17/2022] Open
Abstract
The article will briefly introduce the high-resolution episcopic microscopy (HREM) technique and will focus on its potential for researching cardiovascular development and remodelling in embryos of biomedical model organisms. It will demonstrate the capacity of HREM for analysing the cardiovascular system of normally developed and genetically or experimentally malformed zebrafish, frog, chick and mouse embryos in the context of the whole specimen and will exemplarily show the possibilities HREM offers for comprehensive visualisation of the vasculature of adult human skin. Finally, it will provide examples of the successful application of HREM for identifying cardiovascular malformations in genetically altered mouse embryos produced in the deciphering the mechanisms of developmental disorders (DMDD) program.
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6
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Harrison IF, Powell NM, Dexter DT. The histone deacetylase inhibitor nicotinamide exacerbates neurodegeneration in the lactacystin rat model of Parkinson's disease. J Neurochem 2018; 148:136-156. [PMID: 30269333 PMCID: PMC6487684 DOI: 10.1111/jnc.14599] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/14/2018] [Accepted: 09/21/2018] [Indexed: 01/03/2023]
Abstract
Histone hypoacetylation is associated with dopaminergic neurodegeneration in Parkinson's disease (PD), because of an imbalance in the activities of the enzymes responsible for histone (de)acetylation. Correction of this imbalance, with histone deacetylase (HDAC) inhibiting agents, could be neuroprotective. We therefore hypothesize that nicotinamide, being a selective inhibitor of HDAC class III as well as having modulatory effects on mitochondrial energy metabolism, would be neuroprotective in the lactacystin rat model of PD, which recapitulates the formation of neurotoxic accumulation of altered proteins within the substantia nigra to cause progressive dopaminergic cell death. Rats received nicotinamide for 28 days, starting 7 days after unilateral injection of the irreversible proteasome inhibitor, lactacystin, into the substantia nigra. Longitudinal motor behavioural testing and structural magnetic resonance imaging were used to track changes in this model of PD, and assessment of nigrostriatal integrity, histone acetylation and brain gene expression changes post-mortem used to quantify nicotinamide-induced neuroprotection. Counterintuitively, nicotinamide dose-dependently exacerbated neurodegeneration of dopaminergic neurons, behavioural deficits and structural brain changes in the lactacystin-lesioned rat. Nicotinamide treatment induced histone hyperacetylation and over-expression of numerous neurotrophic and anti-apoptotic factors in the brain, yet failed to result in neuroprotection, rather exacerbated dopaminergic pathology. These findings highlight the importance of inhibitor specificity within HDAC isoforms for therapeutic efficacy in PD, demonstrating the contrasting effects of HDAC class III inhibition upon cell survival in this animal model of the disease. OPEN SCIENCE BADGES: This article has received a badge for *Open Materials* because it provided all relevant information to reproduce the study in the manuscript. The complete Open Science Disclosure form for this article can be found at the end of the article. More information about the Open Practices badges can be found at https://cos.io/our-services/open-science-badges/.
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Affiliation(s)
- Ian F Harrison
- UCL Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, London, UK.,Parkinson's Disease Research Group, Division of Brain Sciences, Department of Medicine, Centre for Neuroinflammation and Neurodegeneration, Imperial College London, London, UK
| | - Nicholas M Powell
- UCL Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, London, UK.,Translational Imaging Group, Centre for Medical Image Computing, University College London, London, UK
| | - David T Dexter
- Parkinson's Disease Research Group, Division of Brain Sciences, Department of Medicine, Centre for Neuroinflammation and Neurodegeneration, Imperial College London, London, UK
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7
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Clayton EL, Mancuso R, Nielsen TT, Mizielinska S, Holmes H, Powell N, Norona F, Larsen JO, Milioto C, Wilson KM, Lythgoe MF, Ourselin S, Nielsen JE, Johannsen P, Holm I, Collinge J, Oliver PL, Gomez-Nicola D, Isaacs AM. Early microgliosis precedes neuronal loss and behavioural impairment in mice with a frontotemporal dementia-causing CHMP2B mutation. Hum Mol Genet 2017; 26:873-887. [PMID: 28093491 PMCID: PMC5409096 DOI: 10.1093/hmg/ddx003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/03/2017] [Indexed: 01/13/2023] Open
Abstract
Frontotemporal dementia (FTD)-causing mutations in the CHMP2B gene lead to the generation of mutant C-terminally truncated CHMP2B. We report that transgenic mice expressing endogenous levels of mutant CHMP2B developed late-onset brain volume loss associated with frank neuronal loss and FTD-like changes in social behaviour. These data are the first to show neurodegeneration in mice expressing mutant CHMP2B and indicate that our mouse model is able to recapitulate neurodegenerative changes observed in FTD. Neuroinflammation has been increasingly implicated in neurodegeneration, including FTD. Therefore, we investigated neuroinflammation in our CHMP2B mutant mice. We observed very early microglial proliferation that develops into a clear pro-inflammatory phenotype at late stages. Importantly, we also observed a similar inflammatory profile in CHMP2B patient frontal cortex. Aberrant microglial function has also been implicated in FTD caused by GRN, MAPT and C9orf72 mutations. The presence of early microglial changes in our CHMP2B mutant mice indicates neuroinflammation may be a contributing factor to the neurodegeneration observed in FTD.
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Affiliation(s)
- Emma L Clayton
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Renzo Mancuso
- Biological Sciences, University of Southampton, Southampton General Hospital, South Laboratory and Pathology Block, Tremona Road, Southampton SO166YD, UK
| | - Troels Tolstrup Nielsen
- Department of Neurology, Danish Dementia Research Centre, Rigshospitalet, University of Copenhagen, Denmark
| | - Sarah Mizielinska
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Holly Holmes
- Centre for Advanced Biomedical Imaging, Division of Medicine and Institute of Child Health, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Nicholas Powell
- Centre for Advanced Biomedical Imaging, Division of Medicine and Institute of Child Health, University College London, 72 Huntley Street, London WC1E 6DD, UK.,Faculty of Health and Medical Sciences, Department of Neuroscience and Pharmacology, Panum Institute, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Frances Norona
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Jytte Overgaard Larsen
- Translational Imaging Group, Centre for Medical Image Computing (CMIC), University College London, UK
| | - Carmelo Milioto
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Katherine M Wilson
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Mark F Lythgoe
- Centre for Advanced Biomedical Imaging, Division of Medicine and Institute of Child Health, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Sebastian Ourselin
- Faculty of Health and Medical Sciences, Department of Neuroscience and Pharmacology, Panum Institute, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Jörgen E Nielsen
- Department of Neurology, Danish Dementia Research Centre, Rigshospitalet, University of Copenhagen, Denmark.,Section of Neurogenetics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Peter Johannsen
- Department of Neurology, Danish Dementia Research Centre, Rigshospitalet, University of Copenhagen, Denmark
| | - Ida Holm
- Laboratory for Experimental Neuropathology, Department of Pathology, Randers Hospital, DK-8930 Randers NØ, Denmark.,Institute of Clinical Medicine, Aarhus University, DK-8000 Aarhus C, Denmark
| | - John Collinge
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.,MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | | | - Peter L Oliver
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
| | - Diego Gomez-Nicola
- Biological Sciences, University of Southampton, Southampton General Hospital, South Laboratory and Pathology Block, Tremona Road, Southampton SO166YD, UK
| | - Adrian M Isaacs
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
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8
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Wu YL, Lo CW. Diverse application of MRI for mouse phenotyping. Birth Defects Res 2017; 109:758-770. [PMID: 28544650 DOI: 10.1002/bdr2.1051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 04/15/2017] [Indexed: 02/01/2023]
Abstract
Small animal models, particularly mouse models, of human diseases are becoming an indispensable tool for biomedical research. Studies in animal models have provided important insights into the etiology of diseases and accelerated the development of therapeutic strategies. Detailed phenotypic characterization is essential, both for the development of such animal models and mechanistic studies into disease pathogenesis and testing the efficacy of experimental therapeutics. MRI is a versatile and noninvasive imaging modality with excellent penetration depth, tissue coverage, and soft tissue contrast. MRI, being a multi-modal imaging modality, together with proven imaging protocols and availability of good contrast agents, is ideally suited for phenotyping mutant mouse models. Here we describe the applications of MRI for phenotyping structural birth defects involving the brain, heart, and kidney in mice. The versatility of MRI and its ease of use are well suited to meet the rapidly increasing demands for mouse phenotyping in the coming age of functional genomics. Birth Defects Research 109:758-770, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Yijen L Wu
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,Rangos Research Center Animal Imaging Core, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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9
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Holmes HE, Powell NM, Ma D, Ismail O, Harrison IF, Wells JA, Colgan N, O'Callaghan JM, Johnson RA, Murray TK, Ahmed Z, Heggenes M, Fisher A, Cardoso MJ, Modat M, O'Neill MJ, Collins EC, Fisher EMC, Ourselin S, Lythgoe MF. Comparison of In Vivo and Ex Vivo MRI for the Detection of Structural Abnormalities in a Mouse Model of Tauopathy. Front Neuroinform 2017; 11:20. [PMID: 28408879 PMCID: PMC5374887 DOI: 10.3389/fninf.2017.00020] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/27/2017] [Indexed: 11/15/2022] Open
Abstract
With increasingly large numbers of mouse models of human disease dedicated to MRI studies, compromises between in vivo and ex vivo MRI must be fully understood in order to inform the choice of imaging methodology. We investigate the application of high resolution in vivo and ex vivo MRI, in combination with tensor-based morphometry (TBM), to uncover morphological differences in the rTg4510 mouse model of tauopathy. The rTg4510 mouse also offers a novel paradigm by which the overexpression of mutant tau can be regulated by the administration of doxycycline, providing us with a platform on which to investigate more subtle alterations in morphology with morphometry. Both in vivo and ex vivo MRI allowed the detection of widespread bilateral patterns of atrophy in the rTg4510 mouse brain relative to wild-type controls. Regions of volume loss aligned with neuronal loss and pathological tau accumulation demonstrated by immunohistochemistry. When we sought to investigate more subtle structural alterations in the rTg4510 mice relative to a subset of doxycycline-treated rTg4510 mice, ex vivo imaging enabled the detection of more regions of morphological brain changes. The disadvantages of ex vivo MRI may however mitigate this increase in sensitivity: we observed a 10% global shrinkage in brain volume of the post-mortem tissues due to formalin fixation, which was most notable in the cerebellum and olfactory bulbs. However, many central brain regions were not adversely affected by the fixation protocol, perhaps due to our “in-skull” preparation. The disparity between our TBM findings from in vivo and ex vivo MRI underlines the importance of appropriate study design, given the trade-off between these two imaging approaches. We support the utility of in vivo MRI for morphological phenotyping of mouse models of disease; however, for subtler phenotypes, ex vivo offers enhanced sensitivity to discrete morphological changes.
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Affiliation(s)
- Holly E Holmes
- Division of Medicine, UCL Centre for Advanced Biomedical Imaging, University College LondonLondon, UK
| | - Nick M Powell
- Division of Medicine, UCL Centre for Advanced Biomedical Imaging, University College LondonLondon, UK.,Centre for Medical Image Computing, University College LondonLondon, UK
| | - Da Ma
- Division of Medicine, UCL Centre for Advanced Biomedical Imaging, University College LondonLondon, UK.,Centre for Medical Image Computing, University College LondonLondon, UK
| | - Ozama Ismail
- Division of Medicine, UCL Centre for Advanced Biomedical Imaging, University College LondonLondon, UK
| | - Ian F Harrison
- Division of Medicine, UCL Centre for Advanced Biomedical Imaging, University College LondonLondon, UK
| | - Jack A Wells
- Division of Medicine, UCL Centre for Advanced Biomedical Imaging, University College LondonLondon, UK
| | - Niall Colgan
- Division of Medicine, UCL Centre for Advanced Biomedical Imaging, University College LondonLondon, UK
| | - James M O'Callaghan
- Division of Medicine, UCL Centre for Advanced Biomedical Imaging, University College LondonLondon, UK
| | - Ross A Johnson
- Tailored Therapeutics, Eli Lilly and Company, Lilly Corporate CenterIndianapolis, IN, USA
| | | | - Zeshan Ahmed
- Molecular Pathology, Eli Lilly & Co. LtdWindlesham, UK
| | | | - Alice Fisher
- Molecular Pathology, Eli Lilly & Co. LtdWindlesham, UK
| | - M Jorge Cardoso
- Centre for Medical Image Computing, University College LondonLondon, UK
| | - Marc Modat
- Centre for Medical Image Computing, University College LondonLondon, UK
| | | | - Emily C Collins
- Tailored Therapeutics, Eli Lilly and Company, Lilly Corporate CenterIndianapolis, IN, USA
| | - Elizabeth M C Fisher
- Department of Neurodegenerative Disease, Institute of Neurology, University College LondonLondon, UK
| | | | - Mark F Lythgoe
- Division of Medicine, UCL Centre for Advanced Biomedical Imaging, University College LondonLondon, UK
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10
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Hu J, Li P, Yin X, Wu T, Cao Y, Yang Z, Jiang L, Hu S, Lu H. Nondestructive imaging of the internal microstructure of vessels and nerve fibers in rat spinal cord using phase-contrast synchrotron radiation microtomography. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:482-489. [PMID: 28244444 DOI: 10.1107/s1600577517000121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 01/04/2017] [Indexed: 06/06/2023]
Abstract
The spinal cord is the primary neurological link between the brain and other parts of the body, but unlike those of the brain, advances in spinal cord imaging have been challenged by the more complicated and inhomogeneous anatomy of the spine. Fortunately with the advancement of high technology, phase-contrast synchrotron radiation microtomography has become widespread in scientific research because of its ability to generate high-quality and high-resolution images. In this study, this method has been employed for nondestructive imaging of the internal microstructure of rat spinal cord. Furthermore, digital virtual slices based on phase-contrast synchrotron radiation were compared with conventional histological sections. The three-dimensional internal microstructure of the intramedullary arteries and nerve fibers was vividly detected within the same spinal cord specimen without the application of a stain or contrast agent or sectioning. With the aid of image post-processing, an optimization of vessel and nerve fiber images was obtained. The findings indicated that phase-contrast synchrotron radiation microtomography is unique in the field of three-dimensional imaging and sets novel standards for pathophysiological investigations in various neurovascular diseases.
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Affiliation(s)
- Jianzhong Hu
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Ping Li
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Xianzhen Yin
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200135, People's Republic of China
| | - Tianding Wu
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Yong Cao
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Zhiming Yang
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Liyuan Jiang
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Shiping Hu
- Department of Spine Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Hongbin Lu
- Department of Sports Medicine, Research Centre of Sports Medicine, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
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11
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Powell NM, Modat M, Cardoso MJ, Ma D, Holmes HE, Yu Y, O’Callaghan J, Cleary JO, Sinclair B, Wiseman FK, Tybulewicz VLJ, Fisher EMC, Lythgoe MF, Ourselin S. Fully-Automated μMRI Morphometric Phenotyping of the Tc1 Mouse Model of Down Syndrome. PLoS One 2016; 11:e0162974. [PMID: 27658297 PMCID: PMC5033246 DOI: 10.1371/journal.pone.0162974] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/31/2016] [Indexed: 01/07/2023] Open
Abstract
We describe a fully automated pipeline for the morphometric phenotyping of mouse brains from μMRI data, and show its application to the Tc1 mouse model of Down syndrome, to identify new morphological phenotypes in the brain of this first transchromosomic animal carrying human chromosome 21. We incorporate an accessible approach for simultaneously scanning multiple ex vivo brains, requiring only a 3D-printed brain holder, and novel image processing steps for their separation and orientation. We employ clinically established multi-atlas techniques–superior to single-atlas methods–together with publicly-available atlas databases for automatic skull-stripping and tissue segmentation, providing high-quality, subject-specific tissue maps. We follow these steps with group-wise registration, structural parcellation and both Voxel- and Tensor-Based Morphometry–advantageous for their ability to highlight morphological differences without the laborious delineation of regions of interest. We show the application of freely available open-source software developed for clinical MRI analysis to mouse brain data: NiftySeg for segmentation and NiftyReg for registration, and discuss atlases and parameters suitable for the preclinical paradigm. We used this pipeline to compare 29 Tc1 brains with 26 wild-type littermate controls, imaged ex vivo at 9.4T. We show an unexpected increase in Tc1 total intracranial volume and, controlling for this, local volume and grey matter density reductions in the Tc1 brain compared to the wild-types, most prominently in the cerebellum, in agreement with human DS and previous histological findings.
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Affiliation(s)
- Nick M. Powell
- Translational Imaging Group, Centre for Medical Image Computing, University College London, 3rd Floor, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
- * E-mail:
| | - Marc Modat
- Translational Imaging Group, Centre for Medical Image Computing, University College London, 3rd Floor, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom
| | - M. Jorge Cardoso
- Translational Imaging Group, Centre for Medical Image Computing, University College London, 3rd Floor, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom
| | - Da Ma
- Translational Imaging Group, Centre for Medical Image Computing, University College London, 3rd Floor, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Holly E. Holmes
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Yichao Yu
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - James O’Callaghan
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Jon O. Cleary
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
- Melbourne Brain Centre Imaging Unit, Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Ben Sinclair
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Frances K. Wiseman
- Department of Neurodegenerative Disease, Institute of Neurology, University College, London WC1N 3BG, United Kingdom
| | - Victor L. J. Tybulewicz
- The Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, United Kingdom
- Imperial College, London W12 0NN, United Kingdom
| | - Elizabeth M. C. Fisher
- Department of Neurodegenerative Disease, Institute of Neurology, University College, London WC1N 3BG, United Kingdom
| | - Mark F. Lythgoe
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Sébastien Ourselin
- Translational Imaging Group, Centre for Medical Image Computing, University College London, 3rd Floor, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom
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12
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Verreet T, Rangarajan JR, Quintens R, Verslegers M, Lo AC, Govaerts K, Neefs M, Leysen L, Baatout S, Maes F, Himmelreich U, D'Hooge R, Moons L, Benotmane MA. Persistent Impact of In utero Irradiation on Mouse Brain Structure and Function Characterized by MR Imaging and Behavioral Analysis. Front Behav Neurosci 2016; 10:83. [PMID: 27199692 PMCID: PMC4854899 DOI: 10.3389/fnbeh.2016.00083] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 04/13/2016] [Indexed: 01/29/2023] Open
Abstract
Prenatal irradiation is known to perturb brain development. Epidemiological studies revealed that radiation exposure during weeks 8-15 of pregnancy was associated with an increased occurrence of mental disability and microcephaly. Such neurological deficits were reproduced in animal models, in which rodent behavioral testing is an often used tool to evaluate radiation-induced defective brain functionality. However, up to now, animal studies suggested a threshold dose of around 0.30 Gray (Gy) below which no behavioral alterations can be observed, while human studies hinted at late defects after exposure to doses as low as 0.10 Gy. Here, we acutely irradiated pregnant mice at embryonic day 11 with doses ranging from 0.10 to 1.00 Gy. A thorough investigation of the dose-response relationship of altered brain function and architecture following in utero irradiation was achieved using a behavioral test battery and volumetric 3D T2-weighted magnetic resonance imaging (MRI). We found dose-dependent changes in cage activity, social behavior, anxiety-related exploration, and spatio-cognitive performance. Although behavioral alterations in low-dose exposed animals were mild, we did unveil that both emotionality and higher cognitive abilities were affected in mice exposed to ≥0.10 Gy. Microcephaly was apparent from 0.33 Gy onwards and accompanied by deviations in regional brain volumes as compared to controls. Of note, total brain volume and the relative volume of the ventricles, frontal and posterior cerebral cortex, cerebellum, and striatum were most strongly correlated to altered behavioral parameters. Taken together, we present conclusive evidence for persistent low-dose effects after prenatal irradiation in mice and provide a better understanding of the correlation between their brain size and performance in behavioral tests.
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Affiliation(s)
- Tine Verreet
- Laboratory of Molecular and Cellular Biology, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK•CEN)Mol, Belgium; Laboratory of Neural Circuit Development and Regeneration, Animal Physiology and Neurobiology Section, Department of Biology, Faculty of Science, Katholieke Universiteit LeuvenLeuven, Belgium
| | - Janaki Raman Rangarajan
- Faculty of Medicine, Molecular Small Animal Imaging Center, Katholieke Universiteit LeuvenLeuven, Belgium; Department of Electrical Engineering (ESAT/PSI), Katholieke Universiteit Leuven and Medical Image Research Center, University Hospital LeuvenLeuven, Belgium
| | - Roel Quintens
- Laboratory of Molecular and Cellular Biology, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
| | - Mieke Verslegers
- Laboratory of Molecular and Cellular Biology, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
| | - Adrian C Lo
- Laboratory of Biological Psychology, Faculty of Psychology and Educational Sciences, Katholieke Universiteit Leuven Leuven, Belgium
| | - Kristof Govaerts
- Biomedical MRI Unit, Department of Imaging and Pathology, Faculty of Medicine, Katholieke Universiteit Leuven Leuven, Belgium
| | - Mieke Neefs
- Laboratory of Molecular and Cellular Biology, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
| | - Liselotte Leysen
- Laboratory of Molecular and Cellular Biology, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
| | - Sarah Baatout
- Laboratory of Molecular and Cellular Biology, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
| | - Frederik Maes
- Department of Electrical Engineering (ESAT/PSI), Katholieke Universiteit Leuven and Medical Image Research Center, University Hospital Leuven Leuven, Belgium
| | - Uwe Himmelreich
- Faculty of Medicine, Molecular Small Animal Imaging Center, Katholieke Universiteit LeuvenLeuven, Belgium; Biomedical MRI Unit, Department of Imaging and Pathology, Faculty of Medicine, Katholieke Universiteit LeuvenLeuven, Belgium
| | - Rudi D'Hooge
- Laboratory of Biological Psychology, Faculty of Psychology and Educational Sciences, Katholieke Universiteit Leuven Leuven, Belgium
| | - Lieve Moons
- Laboratory of Neural Circuit Development and Regeneration, Animal Physiology and Neurobiology Section, Department of Biology, Faculty of Science, Katholieke Universiteit Leuven Leuven, Belgium
| | - Mohammed A Benotmane
- Laboratory of Molecular and Cellular Biology, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK•CEN) Mol, Belgium
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13
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Xie Z, Liang X, Guo L, Kitamoto A, Tamura M, Shiroishi T, Gillies D. Automatic classification framework for ventricular septal defects: a pilot study on high-throughput mouse embryo cardiac phenotyping. J Med Imaging (Bellingham) 2015; 2:041003. [PMID: 26835488 DOI: 10.1117/1.jmi.2.4.041003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/30/2015] [Indexed: 12/30/2022] Open
Abstract
Intensive international efforts are underway toward phenotyping the entire mouse genome by modifying all its [Formula: see text] genes one-by-one for comparative studies. A workload of this scale has triggered numerous studies harnessing image informatics for the identification of morphological defects. However, existing work in this line primarily rests on abnormality detection via structural volumetrics between wild-type and gene-modified mice, which generally fails when the pathology involves no severe volume changes, such as ventricular septal defects (VSDs) in the heart. Furthermore, in embryo cardiac phenotyping, the lack of relevant work in embryonic heart segmentation, the limited availability of public atlases, and the general requirement of manual labor for the actual phenotype classification after abnormality detection, along with other limitations, have collectively restricted existing practices from meeting the high-throughput demands. This study proposes, to the best of our knowledge, the first fully automatic VSD classification framework in mouse embryo imaging. Our approach leverages a combination of atlas-based segmentation and snake evolution techniques to derive the segmentation of heart ventricles, where VSD classification is achieved by checking whether the left and right ventricles border or overlap with each other. A pilot study has validated our approach at a proof-of-concept level and achieved a classification accuracy of 100% through a series of empirical experiments on a database of 15 images.
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Affiliation(s)
- Zhongliu Xie
- Imperial College London, Department of Computing, South Kensington Campus, London SW7 2AZ, United Kingdom; National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan
| | - Xi Liang
- National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan; University of Melbourne, Department of Computer Science and Software Engineering, Parkville Campus, Melbourne VIC 3010, Australia
| | - Liucheng Guo
- Imperial College London , Department of Electrical and Electronic Engineering, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Asanobu Kitamoto
- National Institute of Informatics , 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan
| | - Masaru Tamura
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan; RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Toshihiko Shiroishi
- National Institute of Genetics , 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Duncan Gillies
- Imperial College London , Department of Computing, South Kensington Campus, London SW7 2AZ, United Kingdom
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14
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Labrousse M, Micard E, Tonnelet R, Cendre R, Delmas V, Naidich T, Braun M. Embryo Form Project: An original technique for the three-dimensional reconstruction of human embryo morphology. Reprod Toxicol 2015. [PMID: 26219247 DOI: 10.1016/j.reprotox.2015.07.076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Our current knowledge on the developmental stages of human embryogenesis has derived from limited numbers of classical studies. Computer technology now permits accurate 3D reconstruction of embryo morphology from serial histological sections. We present a successful technique that uses either fresh or preserved serial histological sections to generate highly detailed 3D image reconstructions of very small human embryos. We present the data we obtained from the reconstruction in virtual space of previously sectioned 15 and 22.5mm embryos. Their morphologies were studied using a DICOM viewer which permitted the analysis of any specific structure in any required orientation. To our knowledge, this is the first time human embryos have been reconstructed in this way. We believe that this reconstruction technique could improve our knowledge on embryo morphogenesis, especially if coupled to the study of genes involved in embryonic development. It may also prove to be a useful pedagogical tool.
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Affiliation(s)
- M Labrousse
- Department of Anatomy, Faculty of Medicine and University Hospital, Université de Reims Champagne-Ardenne, France.
| | - E Micard
- INSERM CIT801, CIC-IT, CHU Nancy, France
| | - R Tonnelet
- IADI, INSERM U947, Université de Lorraine, Nancy, France
| | - R Cendre
- INSERM CIT801, CIC-IT, CHU Nancy, France
| | - V Delmas
- URDIA EA4465, Saints-Pères Faculty of Medicine, Université Paris Descartes, Paris, France
| | - T Naidich
- Department of Radiology, Mount Sinai School of Medicine, New York University, New York, NY, United States
| | - M Braun
- Department of Anatomy, Faculty of Medicine and University Hospital, Université de Lorraine, Nancy, France
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15
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Weninger WJ, Geyer SH, Martineau A, Galli A, Adams DJ, Wilson R, Mohun TJ. Phenotyping structural abnormalities in mouse embryos using high-resolution episcopic microscopy. Dis Model Mech 2015; 7:1143-52. [PMID: 25256713 PMCID: PMC4174525 DOI: 10.1242/dmm.016337] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The arrival of simple and reliable methods for 3D imaging of mouse embryos has opened the possibility of analysing normal and abnormal development in a far more systematic and comprehensive manner than has hitherto been possible. This will not only help to extend our understanding of normal tissue and organ development but, by applying the same approach to embryos from genetically modified mouse lines, such imaging studies could also transform our knowledge of gene function in embryogenesis and the aetiology of developmental disorders. The International Mouse Phenotyping Consortium is coordinating efforts to phenotype single gene knockouts covering the entire mouse genome, including characterising developmental defects for those knockout lines that prove to be embryonic lethal. Here, we present a pilot study of 34 such lines, utilising high-resolution episcopic microscopy (HREM) for comprehensive 2D and 3D imaging of homozygous null embryos and their wild-type littermates. We present a simple phenotyping protocol that has been developed to take advantage of the high-resolution images obtained by HREM and that can be used to score tissue and organ abnormalities in a reliable manner. Using this approach with embryos at embryonic day 14.5, we show the wide range of structural abnormalities that are likely to be detected in such studies and the variability in phenotypes between sibling homozygous null embryos.
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Affiliation(s)
- Wolfgang J Weninger
- Centre for Anatomy and Cell Biology & MIC, Medical University of Vienna, 1090 Wien, Austria.
| | - Stefan H Geyer
- Centre for Anatomy and Cell Biology & MIC, Medical University of Vienna, 1090 Wien, Austria
| | | | | | - David J Adams
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Robert Wilson
- MRC National Institute for Medical Research, London NW7 1AA, UK
| | - Timothy J Mohun
- MRC National Institute for Medical Research, London NW7 1AA, UK
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16
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Foxley S, Domowicz M, Karczmar GS, Schwartz N. 3D high spectral and spatial resolution imaging of ex vivo mouse brain. Med Phys 2015; 42:1463-72. [PMID: 25735299 PMCID: PMC5148176 DOI: 10.1118/1.4908203] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Widely used MRI methods show brain morphology both in vivo and ex vivo at very high resolution. Many of these methods (e.g., T2*-weighted imaging, phase-sensitive imaging, or susceptibility-weighted imaging) are sensitive to local magnetic susceptibility gradients produced by subtle variations in tissue composition. However, the spectral resolution of commonly used methods is limited to maintain reasonable run-time combined with very high spatial resolution. Here, the authors report on data acquisition at increased spectral resolution, with 3-dimensional high spectral and spatial resolution MRI, in order to analyze subtle variations in water proton resonance frequency and lineshape that reflect local anatomy. The resulting information compliments previous studies based on T2* and resonance frequency. METHODS The proton free induction decay was sampled at high resolution and Fourier transformed to produce a high-resolution water spectrum for each image voxel in a 3D volume. Data were acquired using a multigradient echo pulse sequence (i.e., echo-planar spectroscopic imaging) with a spatial resolution of 50 × 50 × 70 μm(3) and spectral resolution of 3.5 Hz. Data were analyzed in the spectral domain, and images were produced from the various Fourier components of the water resonance. This allowed precise measurement of local variations in water resonance frequency and lineshape, at the expense of significantly increased run time (16-24 h). RESULTS High contrast T2*-weighted images were produced from the peak of the water resonance (peak height image), revealing a high degree of anatomical detail, specifically in the hippocampus and cerebellum. In images produced from Fourier components of the water resonance at -7.0 Hz from the peak, the contrast between deep white matter tracts and the surrounding tissue is the reverse of the contrast in water peak height images. This indicates the presence of a shoulder in the water resonance that is not present at +7.0 Hz and may be specific to white matter anatomy. Moreover, a frequency shift of 6.76 ± 0.55 Hz was measured between the molecular and granular layers of the cerebellum. This shift is demonstrated in corresponding spectra; water peaks from voxels in the molecular and granular layers are consistently 2 bins apart (7.0 Hz, as dictated by the spectral resolution) from one another. CONCLUSIONS High spectral and spatial resolution MR imaging has the potential to accurately measure the changes in the water resonance in small voxels. This information can guide optimization and interpretation of more commonly used, more rapid imaging methods that depend on image contrast produced by local susceptibility gradients. In addition, with improved sampling methods, high spectral and spatial resolution data could be acquired in reasonable run times, and used for in vivo scans to increase sensitivity to variations in local susceptibility.
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Affiliation(s)
| | - Miriam Domowicz
- Department of Pediatrics, University of Chicago, Chicago, Illinois 60637
| | | | - Nancy Schwartz
- Department of Pediatrics, Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
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17
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Norris FC, Siow BM, Cleary JO, Wells JA, De Castro SC, Ordidge RJ, Greene ND, Copp AJ, Scambler PJ, Alexander DC, Lythgoe MF. Diffusion microscopic MRI of the mouse embryo: Protocol and practical implementation in the splotch mouse model. Magn Reson Med 2015; 73:731-9. [PMID: 24634098 PMCID: PMC4737188 DOI: 10.1002/mrm.25145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 01/01/2014] [Accepted: 01/03/2014] [Indexed: 12/13/2022]
Abstract
PURPOSE Advanced methodologies for visualizing novel tissue contrast are essential for phenotyping the ever-increasing number of mutant mouse embryos being generated. Although diffusion microscopic MRI (μMRI) has been used to phenotype embryos, widespread routine use is limited by extended scanning times, and there is no established experimental procedure ensuring optimal data acquisition. METHODS We developed two protocols for designing experimental procedures for diffusion μMRI of mouse embryos, which take into account the effect of embryo preparation and pulse sequence parameters on resulting data. We applied our protocols to an investigation of the splotch mouse model as an example implementation. RESULTS The protocols provide DTI data in 24 min per direction at 75 μm isotropic using a three-dimensional fast spin-echo sequence, enabling preliminary imaging in 3 h (6 directions plus one unweighted measurement), or detailed imaging in 9 h (42 directions plus six unweighted measurements). Application to the splotch model enabled assessment of spinal cord pathology. CONCLUSION We present guidelines for designing diffusion μMRI experiments, which may be adapted for different studies and research facilities. As they are suitable for routine use and may be readily implemented, we hope they will be adopted by the phenotyping community.
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Affiliation(s)
- Francesca C. Norris
- UCL Centre for Advanced Biomedical Imaging, Division of MedicineUniversity College LondonLondonUnited Kingdom
- Centre for Mathematics and Physics in the Life Sciences and EXperimental Biology (CoMPLEX)University College LondonLondonUnited Kingdom
| | - Bernard M. Siow
- UCL Centre for Advanced Biomedical Imaging, Division of MedicineUniversity College LondonLondonUnited Kingdom
- Centre for Medical Image Computing, Departments of Medical Physics and Bioengineering and Computer ScienceUniversity College LondonUnited Kingdom
| | - Jon O. Cleary
- UCL Centre for Advanced Biomedical Imaging, Division of MedicineUniversity College LondonLondonUnited Kingdom
- Department of Anatomy and NeuroscienceUniversity of MelbourneAustralia
| | - Jack A. Wells
- UCL Centre for Advanced Biomedical Imaging, Division of MedicineUniversity College LondonLondonUnited Kingdom
| | - Sandra C.P. De Castro
- Neural Development Unit, UCL Institute of Child HealthUniversity College LondonLondonUnited Kingdom
| | - Roger J. Ordidge
- Department of Anatomy and NeuroscienceUniversity of MelbourneAustralia
| | - Nicholas D.E. Greene
- Neural Development Unit, UCL Institute of Child HealthUniversity College LondonLondonUnited Kingdom
| | - Andrew J. Copp
- Neural Development Unit, UCL Institute of Child HealthUniversity College LondonLondonUnited Kingdom
| | - Peter J. Scambler
- Molecular Medicine Unit, UCL Institute of Child HealthUniversity College LondonLondonUnited Kingdom
| | - Daniel. C. Alexander
- Centre for Medical Image Computing, Departments of Medical Physics and Bioengineering and Computer ScienceUniversity College LondonUnited Kingdom
| | - Mark F. Lythgoe
- UCL Centre for Advanced Biomedical Imaging, Division of MedicineUniversity College LondonLondonUnited Kingdom
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18
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Phenotyping the central nervous system of the embryonic mouse by magnetic resonance microscopy. Neuroimage 2014; 97:95-106. [PMID: 24769183 DOI: 10.1016/j.neuroimage.2014.04.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 04/07/2014] [Accepted: 04/13/2014] [Indexed: 11/20/2022] Open
Abstract
Genetic mouse models of neurodevelopmental disorders are being massively generated, but technologies for their high-throughput phenotyping are missing. The potential of high-resolution magnetic resonance imaging (MRI) for structural phenotyping has been demonstrated before. However, application to the embryonic mouse central nervous system has been limited by the insufficient anatomical detail. Here we present a method that combines staining of live embryos with a contrast agent together with MR microscopy after fixation, to provide unprecedented anatomical detail at relevant embryonic stages. By using this method we have phenotyped the embryonic forebrain of Robo1/2(-/-) double mutant mice enabling us to identify most of the well-known anatomical defects in these mutants, as well as novel more subtle alterations. We thus demonstrate the potential of this methodology for a fast and reliable screening of subtle structural abnormalities in the developing mouse brain, as those associated to defects in disease-susceptibility genes of neurologic and psychiatric relevance.
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19
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Wong MD, Maezawa Y, Lerch JP, Henkelman RM. Automated pipeline for anatomical phenotyping of mouse embryos using micro-CT. Development 2014; 141:2533-41. [PMID: 24850858 DOI: 10.1242/dev.107722] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The International Mouse Phenotyping Consortium (IMPC) plans to phenotype 20,000 single-gene knockout mice to gain an insight into gene function. Approximately 30% of these knockout mouse lines will be embryonic or perinatal lethal. The IMPC has selected three-dimensional (3D) imaging to phenotype these mouse lines at relevant stages of embryonic development in an attempt to discover the cause of lethality using detailed anatomical information. Rate of throughput is paramount as IMPC production centers have been given the ambitious task of completing this phenotyping project by 2021. Sifting through the wealth of data within high-resolution 3D mouse embryo data sets by trained human experts is infeasible at this scale. Here, we present a phenotyping pipeline that identifies statistically significant anatomical differences in the knockout, in comparison with the wild type, through a computer-automated image registration algorithm. This phenotyping pipeline consists of three analyses (intensity, deformation, and atlas based) that can detect missing anatomical structures and differences in volume of whole organs as well as on the voxel level. This phenotyping pipeline was applied to micro-CT images of two perinatal lethal mouse lines: a hypomorphic mutation of the Tcf21 gene (Tcf21-hypo) and a knockout of the Satb2 gene. With the proposed pipeline we were able to identify the majority of morphological phenotypes previously published for both the Tcf21-hypo and Satb2 mutant mouse embryos in addition to novel phenotypes. This phenotyping pipeline is an unbiased, automated method that highlights only those structural abnormalities that survive statistical scrutiny and illustrates them in a straightforward fashion.
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Affiliation(s)
- Michael D Wong
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada
| | - Yoshiro Maezawa
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Jason P Lerch
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - R Mark Henkelman
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario M5T 3H7, Canada Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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O’Callaghan J, Wells J, Richardson S, Holmes H, Yu Y, Walker-Samuel S, Siow B, Lythgoe MF. Is your system calibrated? MRI gradient system calibration for pre-clinical, high-resolution imaging. PLoS One 2014; 9:e96568. [PMID: 24804737 PMCID: PMC4013024 DOI: 10.1371/journal.pone.0096568] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 04/08/2014] [Indexed: 11/27/2022] Open
Abstract
High-field, pre-clinical MRI systems are widely used to characterise tissue structure and volume in small animals, using high resolution imaging. Both applications rely heavily on the consistent, accurate calibration of imaging gradients, yet such calibrations are typically only performed during maintenance sessions by equipment manufacturers, and potentially with acceptance limits that are inadequate for phenotyping. To overcome this difficulty, we present a protocol for gradient calibration quality assurance testing, based on a 3D-printed, open source, structural phantom that can be customised to the dimensions of individual scanners and RF coils. In trials on a 9.4 T system, the gradient scaling errors were reduced by an order of magnitude, and displacements of greater than 100 µm, caused by gradient non-linearity, were corrected using a post-processing technique. The step-by-step protocol can be integrated into routine pre-clinical MRI quality assurance to measure and correct for these errors. We suggest that this type of quality assurance is essential for robust pre-clinical MRI experiments that rely on accurate imaging gradients, including small animal phenotyping and diffusion MR.
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Affiliation(s)
- James O’Callaghan
- UCL Centre for Advanced Biomedical Imaging, Division of Medicine, London, United Kingdom
| | - Jack Wells
- UCL Centre for Advanced Biomedical Imaging, Division of Medicine, London, United Kingdom
| | - Simon Richardson
- UCL Centre for Advanced Biomedical Imaging, Division of Medicine, London, United Kingdom
- UCL Centre for Medical Image Computing, London, United Kingdom
| | - Holly Holmes
- UCL Centre for Advanced Biomedical Imaging, Division of Medicine, London, United Kingdom
| | - Yichao Yu
- UCL Centre for Advanced Biomedical Imaging, Division of Medicine, London, United Kingdom
| | - Simon Walker-Samuel
- UCL Centre for Advanced Biomedical Imaging, Division of Medicine, London, United Kingdom
| | - Bernard Siow
- UCL Centre for Advanced Biomedical Imaging, Division of Medicine, London, United Kingdom
- UCL Centre for Medical Image Computing, London, United Kingdom
| | - Mark F. Lythgoe
- UCL Centre for Advanced Biomedical Imaging, Division of Medicine, London, United Kingdom
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21
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Zani A, Cananzi M, Fascetti-Leon F, Lauriti G, Smith VV, Bollini S, Ghionzoli M, D'Arrigo A, Pozzobon M, Piccoli M, Hicks A, Wells J, Siow B, Sebire NJ, Bishop C, Leon A, Atala A, Lythgoe MF, Pierro A, Eaton S, De Coppi P. Amniotic fluid stem cells improve survival and enhance repair of damaged intestine in necrotising enterocolitis via a COX-2 dependent mechanism. Gut 2014; 63:300-9. [PMID: 23525603 DOI: 10.1136/gutjnl-2012-303735] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Necrotising enterocolitis (NEC) remains one of the primary causes of morbidity and mortality in neonates and alternative strategies are needed. Stem cells have become a therapeutic option for other intestinal diseases, which share some features with NEC. We tested the hypothesis that amniotic fluid stem (AFS) cells exerted a beneficial effect in a neonatal rat model of NEC. DESIGN Rats intraperitoneally injected with AFS cells and their controls (bone marrow mesenchymal stem cells, myoblast) were analysed for survival, behaviour, bowel imaging (MRI scan), histology, bowel absorption and motility, immunofluorescence for AFS cell detection, degree of gut inflammation (myeloperoxidase and malondialdehyde), and enterocyte apoptosis and proliferation. RESULTS AFS cells integrated in the bowel wall and improved rat survival and clinical conditions, decreased NEC incidence and macroscopic gut damage, improved intestinal function, decreased bowel inflammation, increased enterocyte proliferation and reduced apoptosis. The beneficial effect was achieved via modulation of stromal cells expressing cyclooxygenase 2 in the lamina propria, as shown by survival studies using selective and non-selective cyclooxygenase 2 inhibitors. Interestingly, AFS cells differentially expressed genes of the Wnt/β-catenin pathway, which regulate intestinal epithelial stem cell function and cell migration and growth factors known to maintain gut epithelial integrity and reduce mucosal injury. CONCLUSIONS We demonstrated here for the first time that AFS cells injected in an established model of NEC improve survival, clinical status, gut structure and function. Understanding the mechanism of this effect may help us to develop new cellular or pharmacological therapies for infants with NEC.
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Affiliation(s)
- Augusto Zani
- Surgery Unit, University College London Institute of Child Health, , London, UK
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22
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Ma D, Cardoso MJ, Modat M, Powell N, Wells J, Holmes H, Wiseman F, Tybulewicz V, Fisher E, Lythgoe MF, Ourselin S. Automatic structural parcellation of mouse brain MRI using multi-atlas label fusion. PLoS One 2014; 9:e86576. [PMID: 24475148 PMCID: PMC3903537 DOI: 10.1371/journal.pone.0086576] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 12/13/2013] [Indexed: 11/23/2022] Open
Abstract
Multi-atlas segmentation propagation has evolved quickly in recent years, becoming a state-of-the-art methodology for automatic parcellation of structural images. However, few studies have applied these methods to preclinical research. In this study, we present a fully automatic framework for mouse brain MRI structural parcellation using multi-atlas segmentation propagation. The framework adopts the similarity and truth estimation for propagated segmentations (STEPS) algorithm, which utilises a locally normalised cross correlation similarity metric for atlas selection and an extended simultaneous truth and performance level estimation (STAPLE) framework for multi-label fusion. The segmentation accuracy of the multi-atlas framework was evaluated using publicly available mouse brain atlas databases with pre-segmented manually labelled anatomical structures as the gold standard, and optimised parameters were obtained for the STEPS algorithm in the label fusion to achieve the best segmentation accuracy. We showed that our multi-atlas framework resulted in significantly higher segmentation accuracy compared to single-atlas based segmentation, as well as to the original STAPLE framework.
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Affiliation(s)
- Da Ma
- Centre for Medical Imaging Computing, University College London, London, England, United Kingdom
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, London, England, United Kingdom
| | - Manuel J. Cardoso
- Centre for Medical Imaging Computing, University College London, London, England, United Kingdom
| | - Marc Modat
- Centre for Medical Imaging Computing, University College London, London, England, United Kingdom
| | - Nick Powell
- Centre for Medical Imaging Computing, University College London, London, England, United Kingdom
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, London, England, United Kingdom
| | - Jack Wells
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, London, England, United Kingdom
| | - Holly Holmes
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, London, England, United Kingdom
| | - Frances Wiseman
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, England, United Kingdom
| | - Victor Tybulewicz
- Division of Immune Cell Biology, MRC National Institute for Medical Research, London, England, United Kingdom
| | - Elizabeth Fisher
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, England, United Kingdom
| | - Mark F. Lythgoe
- Centre for Advanced Biomedical Imaging, Division of Medicine, University College London, London, England, United Kingdom
| | - Sébastien Ourselin
- Centre for Medical Imaging Computing, University College London, London, England, United Kingdom
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23
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Wong MD, Spring S, Henkelman RM. Structural stabilization of tissue for embryo phenotyping using micro-CT with iodine staining. PLoS One 2013; 8:e84321. [PMID: 24386367 PMCID: PMC3875560 DOI: 10.1371/journal.pone.0084321] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 11/21/2013] [Indexed: 12/01/2022] Open
Abstract
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.
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Affiliation(s)
- Michael D. Wong
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
| | - Shoshana Spring
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - R. Mark Henkelman
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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24
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Richardson L, Venkataraman S, Stevenson P, Yang Y, Moss J, Graham L, Burton N, Hill B, Rao J, Baldock RA, Armit C. EMAGE mouse embryo spatial gene expression database: 2014 update. Nucleic Acids Res 2013; 42:D835-44. [PMID: 24265223 PMCID: PMC3965061 DOI: 10.1093/nar/gkt1155] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
EMAGE (http://www.emouseatlas.org/emage/) is a freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression. EMAGE is unique in providing both text-based descriptions of gene expression plus spatial maps of gene expression patterns. This mapping allows spatial queries to be accomplished alongside more traditional text-based queries. Here, we describe our recent progress in spatial mapping and data integration. EMAGE has developed a method of spatially mapping 3D embryo images captured using optical projection tomography, and through the use of an IIP3D viewer allows users to view arbitrary sections of raw and mapped 3D image data in the context of a web browser. EMAGE now includes enhancer data, and we have spatially mapped images from a comprehensive screen of transgenic reporter mice that detail the expression of mouse non-coding genomic DNA fragments with enhancer activity. We have integrated the eMouseAtlas anatomical atlas and the EMAGE database so that a user of the atlas can query the EMAGE database easily. In addition, we have extended the atlas framework to enable EMAGE to spatially cross-index EMBRYS whole mount in situ hybridization data. We additionally report on recent developments to the EMAGE web interface, including new query and analysis capabilities.
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Affiliation(s)
- Lorna Richardson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital EH4 2XU, UK
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25
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Norris FC, Wong MD, Greene NDE, Scambler PJ, Weaver T, Weninger WJ, Mohun TJ, Henkelman RM, Lythgoe MF. A coming of age: advanced imaging technologies for characterising the developing mouse. Trends Genet 2013; 29:700-11. [PMID: 24035368 DOI: 10.1016/j.tig.2013.08.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/17/2013] [Accepted: 08/12/2013] [Indexed: 12/21/2022]
Abstract
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.
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Affiliation(s)
- Francesca C Norris
- 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
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26
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Adams D, Baldock R, Bhattacharya S, Copp AJ, Dickinson M, Greene NDE, Henkelman M, Justice M, Mohun T, Murray SA, Pauws E, Raess M, Rossant J, Weaver T, West D. Bloomsbury report on mouse embryo phenotyping: recommendations from the IMPC workshop on embryonic lethal screening. Dis Model Mech 2013; 6:571-9. [PMID: 23519032 PMCID: PMC3634642 DOI: 10.1242/dmm.011833] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Identifying genes that are important for embryo development is a crucial first step towards understanding their many functions in driving the ordered growth, differentiation and organogenesis of embryos. It can also shed light on the origins of developmental disease and congenital abnormalities. Current international efforts to examine gene function in the mouse provide a unique opportunity to pinpoint genes that are involved in embryogenesis, owing to the emergence of embryonic lethal knockout mutants. Through internationally coordinated efforts, the International Knockout Mouse Consortium (IKMC) has generated a public resource of mouse knockout strains and, in April 2012, the International Mouse Phenotyping Consortium (IMPC), supported by the EU InfraCoMP programme, convened a workshop to discuss developing a phenotyping pipeline for the investigation of embryonic lethal knockout lines. This workshop brought together over 100 scientists, from 13 countries, who are working in the academic and commercial research sectors, including experts and opinion leaders in the fields of embryology, animal imaging, data capture, quality control and annotation, high-throughput mouse production, phenotyping, and reporter gene analysis. This article summarises the outcome of the workshop, including (1) the vital scientific importance of phenotyping embryonic lethal mouse strains for basic and translational research; (2) a common framework to harmonise international efforts within this context; (3) the types of phenotyping that are likely to be most appropriate for systematic use, with a focus on 3D embryo imaging; (4) the importance of centralising data in a standardised form to facilitate data mining; and (5) the development of online tools to allow open access to and dissemination of the phenotyping data.
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Affiliation(s)
- David Adams
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | | | | | - Andrew J. Copp
- UCL Institute of Child Health, Gower Street, London, WC1E 6BT, UK
| | | | | | | | | | - Timothy Mohun
- MRC National Institute for Medical Research, London, NW7 1AA, UK
| | | | - Erwin Pauws
- UCL Institute of Child Health, Gower Street, London, WC1E 6BT, UK
| | - Michael Raess
- Helmholtz Zentrum Munich and Infrafrontier, Ingolstädter Landstraße 1 85764 Neuherberg, Munich, Germany
| | | | - Tom Weaver
- MRC Harwell, Harwell Science and Innovation Campus, Oxford, OX11 0RD, UK
| | - David West
- CHORI, 5700 Martin Luther King Jr Way, Oakland, CA 94609, USA
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27
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Anderson GA, Wong MD, Yang J, Henkelman RM. 3D imaging, registration, and analysis of the early mouse embryonic vasculature. Dev Dyn 2013; 242:527-38. [DOI: 10.1002/dvdy.23947] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/07/2013] [Accepted: 02/07/2013] [Indexed: 11/06/2022] Open
Affiliation(s)
| | | | - Jian Yang
- Mouse Imaging Centre; The Hospital For Sick Children; Toronto; Canada
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28
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Parasoglou P, Berrios-Otero CA, Nieman BJ, Turnbull DH. High-resolution MRI of early-stage mouse embryos. NMR IN BIOMEDICINE 2013; 26:224-31. [PMID: 22915475 PMCID: PMC3524402 DOI: 10.1002/nbm.2843] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/19/2012] [Accepted: 07/19/2012] [Indexed: 05/08/2023]
Abstract
Both the availability of methods to manipulate genes and the completion of the mouse genome sequence have led to the generation of thousands of genetically modified mouse lines that provide a new platform for the study of mammalian development and developmental diseases. Phenotyping of mouse embryos has traditionally been performed on fixed embryos by the use of ex vivo histological, optical and high-resolution MRI techniques. Although potentially powerful, longitudinal imaging of individual animals is difficult or impossible with conventional optical methods because of the inaccessibility of mouse embryos inside the maternal uterus. To address this problem, we present a method of imaging the mouse embryo from stages as early as embryonic day (E)10.5, close to the onset of organogenesis in most physiological systems. This method uses a self-gated MRI protocol, combined with image registration, to obtain whole-embryo high-resolution (100 µm isotropic) three-dimensional images. Using this approach, we demonstrate high contrast in the cerebral vasculature, limbs, spine and central nervous system without the use of contrast agents. These results indicate the potential of MRI for the longitudinal imaging of developing mouse embryos in utero and for future applications in analyzing mutant mouse phenotypes.
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Affiliation(s)
- Prodromos Parasoglou
- Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York, USA
- Department of Radiology, New York University School of Medicine, New York, New York, USA
| | - Cesar A Berrios-Otero
- Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York, USA
- Department of Radiology, New York University School of Medicine, New York, New York, USA
| | - Brian J Nieman
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Daniel H Turnbull
- Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York, USA
- Department of Radiology, New York University School of Medicine, New York, New York, USA
- Correspondence to: Daniel H. Turnbull, PhD, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, NY 10016,
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29
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Frangi AF, Hose DR, Hunter PJ, Ayache N, Brooks D. Special issue on medical imaging and image computing in computational physiology. IEEE TRANSACTIONS ON MEDICAL IMAGING 2013; 32:1-7. [PMID: 23409282 DOI: 10.1109/tmi.2012.2234320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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30
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Hikishima K, Sawada K, Murayama A, Komaki Y, Kawai K, Sato N, Inoue T, Itoh T, Momoshima S, Iriki A, Okano H, Sasaki E, Okano H. Atlas of the developing brain of the marmoset monkey constructed using magnetic resonance histology. Neuroscience 2013; 230:102-13. [DOI: 10.1016/j.neuroscience.2012.09.053] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 08/29/2012] [Accepted: 09/22/2012] [Indexed: 10/27/2022]
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31
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Roy S, Liang X, Kitamoto A, Tamura M, Shiroishi T, Brown MS. Phenotype detection in morphological mutant mice using deformation features. MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION : MICCAI ... INTERNATIONAL CONFERENCE ON MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION 2013; 16:437-444. [PMID: 24505791 DOI: 10.1007/978-3-642-40760-4_55] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Large-scale global efforts are underway to knockout each of the approximately 25,000 mouse genes and interpret their roles in shaping the mammalian embryo. Given the tremendous amount of data generated by imaging mutated prenatal mice, high-throughput image analysis systems are inevitable to characterize mammalian development and diseases. Current state-of-the-art computational systems offer only differential volumetric analysis of pre-defined anatomical structures between various gene-knockout mice strains. For subtle anatomical phenotypes, embryo phenotyping still relies on the laborious histological techniques that are clearly unsuitable in such big data environment. This paper presents a system that automatically detects known phenotypes and assists in discovering novel phenotypes in muCT images of mutant mice. Deformation features obtained from non-linear registration of mutant embryo to a normal consensus average image are extracted and analyzed to compute phenotypic and candidate phenotypic areas. The presented system is evaluated using C57BL/10 embryo images. All cases of ventricular septum defect and polydactyly, well-known to be present in this strain, are successfully detected. The system predicts potential phenotypic areas in the liver that are under active histological evaluation for possible phenotype of this mouse line.
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Affiliation(s)
- Sharmili Roy
- School of Computing, National University of Singapore.
| | - Xi Liang
- National ICT Australia (NICTA), Australia
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32
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Norris FC, Betts-Henderson J, Wells JA, Cleary JO, Siow BM, Walker-Samuel S, McCue K, Salomoni P, Scambler PJ, Lythgoe MF. Enhanced tissue differentiation in the developing mouse brain using magnetic resonance micro-histology. Magn Reson Med 2012; 70:1380-8. [DOI: 10.1002/mrm.24573] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 10/29/2012] [Accepted: 10/30/2012] [Indexed: 12/15/2022]
Affiliation(s)
- Francesca C. Norris
- Department of Medicine and UCL Institute of Child Health; Centre for Advanced Biomedical Imaging; University College London; UK
- Centre for Mathematics and Physics in the Life Sciences and EXperimental Biology (CoMPLEX); University College London; UK
| | | | - Jack A. Wells
- Department of Medicine and UCL Institute of Child Health; Centre for Advanced Biomedical Imaging; University College London; UK
| | - Jon O. Cleary
- Department of Medicine and UCL Institute of Child Health; Centre for Advanced Biomedical Imaging; University College London; UK
- Department of Medical Physics and Bioengineering; University College London; UK
| | - Bernard M. Siow
- Department of Medicine and UCL Institute of Child Health; Centre for Advanced Biomedical Imaging; University College London; UK
- Departments of Medical Physics and Bioengineering and Computer Science; Centre for Medical Image Computing; University College London; UK
| | - Simon Walker-Samuel
- Department of Medicine and UCL Institute of Child Health; Centre for Advanced Biomedical Imaging; University College London; UK
| | - Karen McCue
- Molecular Medicine Unit; UCL Institute of Child Health; University College London; UK
| | - Paolo Salomoni
- Samantha Dickson Brain Cancer Unit; UCL Cancer Institute; London UK
| | - Peter J. Scambler
- Molecular Medicine Unit; UCL Institute of Child Health; University College London; UK
| | - Mark F. Lythgoe
- Department of Medicine and UCL Institute of Child Health; Centre for Advanced Biomedical Imaging; University College London; UK
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33
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Wong MD, Dorr AE, Walls JR, Lerch JP, Henkelman RM. A novel 3D mouse embryo atlas based on micro-CT. Development 2012; 139:3248-56. [PMID: 22872090 DOI: 10.1242/dev.082016] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The goal of the International Mouse Phenotyping Consortium (IMPC) is to phenotype targeted knockout mouse strains throughout the whole mouse genome (23,000 genes) by 2021. A significant percentage of the generated mice will be embryonic lethal; therefore, phenotyping methods tuned to the mouse embryo are needed. Methods that are robust, quantitative, automated and high-throughput are attractive owing to the numbers of mice involved. Three-dimensional (3D) imaging is a useful method for characterizing morphological phenotypes. However, tools to automatically quantify morphological information of mouse embryos from 3D imaging have not been fully developed. We present a representative mouse embryo average 3D atlas comprising micro-CT images of 35 individual C57BL/6J mouse embryos at 15.5 days post-coitum. The 35 micro-CT images were registered into a consensus average image with our automated image registration software and 48 anatomical structures were segmented manually. We report the mean and variation in volumes for each of the 48 segmented structures. Mouse organ volumes vary by 2.6-4.2% on a linear scale when normalized to whole body volume. A power analysis of the volume data reports that a 9-14% volume difference can be detected between two classes of mice with sample sizes of eight. This resource will be crucial in establishing baseline anatomical phenotypic measurements for the assessment of mutant mouse phenotypes, as any future mutant embryo image can be registered to the atlas and subsequent organ volumes calculated automatically.
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Affiliation(s)
- Michael D Wong
- Department of Medical Biophysics, University of Toronto, and Hospital for Sick Children, Toronto, ON M5G 2M9, Canada.
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Laufer J, Norris F, Cleary J, Zhang E, Treeby B, Cox B, Johnson P, Scambler P, Lythgoe M, Beard P. In vivo photoacoustic imaging of mouse embryos. JOURNAL OF BIOMEDICAL OPTICS 2012; 17:061220. [PMID: 22734750 DOI: 10.1117/1.jbo.17.6.061220] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The ability to noninvasively image embryonic vascular anatomy in mouse models is an important requirement for characterizing the development of the normal cardiovascular system and malformations in the heart and vascular supply. Photoacoustic imaging, which can provide high resolution non invasive images of the vasculature based upon optical absorption by endogenous hemoglobin, is well suited to this application. In this study, photoacoustic images of mouse embryos were obtained ex vivo and in vivo. The images show intricate details of the embryonic vascular system to depths of up to 10 mm, which allowed whole embryos to be imaged in situ. To achieve this, an all-optical photoacoustic scanner and a novel time reversal image reconstruction algorithm, which provide deep tissue imaging capability while maintaining high spatial resolution and contrast were employed. This technology may find application as an imaging tool for preclinical embryo studies in developmental biology as well as more generally in preclinical and clinical medicine for studying pathologies characterized by changes in the vasculature.
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Affiliation(s)
- Jan Laufer
- University College London, Department of Medical Physics and Bioengineering, Gower Street, London WC1E 6BT, United Kingdom
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Norris FC, Modat M, Cleary JO, Price AN, McCue K, Scambler PJ, Ourselin S, Lythgoe MF. Segmentation propagation using a 3D embryo atlas for high-throughput MRI phenotyping: comparison and validation with manual segmentation. Magn Reson Med 2012; 69:877-83. [PMID: 22556102 DOI: 10.1002/mrm.24306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 02/29/2012] [Accepted: 03/29/2012] [Indexed: 11/09/2022]
Abstract
Effective methods for high-throughput screening and morphometric analysis are crucial for phenotyping the increasing number of mouse mutants that are being generated. Automated segmentation propagation for embryo phenotyping is an emerging application that enables noninvasive and rapid quantification of substructure volumetric data for morphometric analysis. We present a study to assess and validate the accuracy of brain and kidney volumes generated via segmentation propagation in an ex vivo mouse embryo MRI atlas comprising three different groups against the current "gold standard"--manual segmentation. Morphometric assessment showed good agreement between automatically and manually segmented volumes, demonstrating that it is possible to assess volumes for phenotyping a population of embryos using segmentation propagation with the same variation as manual segmentation. As part of this study, we have made our average atlas and segmented volumes freely available to the community for use in mouse embryo phenotyping studies. These MRI datasets and automated methods of analyses will be essential for meeting the challenge of high-throughput, automated embryo phenotyping.
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Affiliation(s)
- Francesca C Norris
- Centre for Advanced Biomedical Imaging, Department of Medicine and UCL Institute of Child Health, University College London, London, United Kingdom.
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Berquist RM, Gledhill KM, Peterson MW, Doan AH, Baxter GT, Yopak KE, Kang N, Walker HJ, Hastings PA, Frank LR. The Digital Fish Library: using MRI to digitize, database, and document the morphological diversity of fish. PLoS One 2012; 7:e34499. [PMID: 22493695 PMCID: PMC3321017 DOI: 10.1371/journal.pone.0034499] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 03/02/2012] [Indexed: 01/01/2023] Open
Abstract
Museum fish collections possess a wealth of anatomical and morphological data that are essential for documenting and understanding biodiversity. Obtaining access to specimens for research, however, is not always practical and frequently conflicts with the need to maintain the physical integrity of specimens and the collection as a whole. Non-invasive three-dimensional (3D) digital imaging therefore serves a critical role in facilitating the digitization of these specimens for anatomical and morphological analysis as well as facilitating an efficient method for online storage and sharing of this imaging data. Here we describe the development of the Digital Fish Library (DFL, http://www.digitalfishlibrary.org), an online digital archive of high-resolution, high-contrast, magnetic resonance imaging (MRI) scans of the soft tissue anatomy of an array of fishes preserved in the Marine Vertebrate Collection of Scripps Institution of Oceanography. We have imaged and uploaded MRI data for over 300 marine and freshwater species, developed a data archival and retrieval system with a web-based image analysis and visualization tool, and integrated these into the public DFL website to disseminate data and associated metadata freely over the web. We show that MRI is a rapid and powerful method for accurately depicting the in-situ soft-tissue anatomy of preserved fishes in sufficient detail for large-scale comparative digital morphology. However these 3D volumetric data require a sophisticated computational and archival infrastructure in order to be broadly accessible to researchers and educators.
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Affiliation(s)
- Rachel M. Berquist
- Center for Scientific Computation in Imaging, University of California San Diego, La Jolla, California, United States of America
| | - Kristen M. Gledhill
- Center for Scientific Computation in Imaging, University of California San Diego, La Jolla, California, United States of America
| | - Matthew W. Peterson
- Center for Scientific Computation in Imaging, University of California San Diego, La Jolla, California, United States of America
| | - Allyson H. Doan
- Center for Scientific Computation in Imaging, University of California San Diego, La Jolla, California, United States of America
| | - Gregory T. Baxter
- Center for Scientific Computation in Imaging, University of California San Diego, La Jolla, California, United States of America
| | - Kara E. Yopak
- Center for Scientific Computation in Imaging, University of California San Diego, La Jolla, California, United States of America
| | - Ning Kang
- Center for Scientific Computation in Imaging, University of California San Diego, La Jolla, California, United States of America
| | - H. J. Walker
- Marine Vertebrate Collection and Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Philip A. Hastings
- Marine Vertebrate Collection and Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Lawrence R. Frank
- Center for Scientific Computation in Imaging, University of California San Diego, La Jolla, California, United States of America
- Center for Functional Magnetic Resonance Imaging, University of California San Diego, La Jolla, California, United States of America
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Abstract
A phase-contrast X-ray microtomography system using the Talbot imaging has been built at the SPring-8 synchrotron radiation facility. This system has much higher density resolution than absorption-based X-ray microtomography. The tomographic sections of formalin-fixed mouse fetuses obtained with this method clearly depict various organs without any staining at a pixel resolution of up to 5 µm. Since this technique allows us to obtain three-dimensional structural information without sectioning, it will be particularly useful to examine anomalies that take place during development. It can be also used to quantitatively measure volume and mass of organs during development.
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Affiliation(s)
- Masato Hoshino
- Japan Synchrotron Radiation Research Institute , SPring-8, 1-1-1 Kouto, Sayo, Hyogo 679-5198 , Japan
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Baldock RA, Burger A. Biomedical atlases: systematics, informatics and analysis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 736:655-77. [PMID: 22161358 DOI: 10.1007/978-1-4419-7210-1_39] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Biomedical imaging is ubiquitous in the Life Sciences. Technology advances, and the resulting multitude of imaging modalities, have led to a sharp rise in the quantity and quality of such images. In addition, computational models are increasingly used to study biological processes involving spatio-temporal changes from the cell to the organism level, e.g., the development of an embryo or the growth of a tumour, and models and images are extensively described in natural language, for example, in research publications and patient records. Together this leads to a major spatio-temporal data and model integration challenge. Biomedical atlases have emerged as a key technology in solving this integration problem. Such atlases typically include an image-based (2D and/or 3D) component as well as a conceptual representation (ontologies) of the organisms involved. In this chapter, we review the notion of atlases in the biomedical domain, how they can be created, how they provide an index to spatio-temporal experimental data, issues of atlas data integration and their use for the analysis of large volumes of biomedical data.
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Affiliation(s)
- Richard A Baldock
- MRC Human Genetics Unit, MRC Institute of Genetic and Molecular Medicine, Western General Hospital, Edinburgh EH4 2XU, UK.
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Ward JM, Elmore SA, Foley JF. Pathology methods for the evaluation of embryonic and perinatal developmental defects and lethality in genetically engineered mice. Vet Pathol 2011; 49:71-84. [PMID: 22146849 DOI: 10.1177/0300985811429811] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The normal embryonic development of organs and other tissues in mice and all species is preprogrammed by genes. Inactivation of a gene involved in any stage of normal embryonic development can have severe consequences leading to embryonic or postnatal developmental defects and lethality. Pathology methods are reviewed for evaluating normal and abnormal placenta and embryo, especially after E12.5. These methods include pathology protocols for necropsy and histopathology in addition to references that will provide additional knowledge for embryo assessment including histology atlases and advanced embryo imaging techniques.
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Affiliation(s)
- J M Ward
- Global VetPathology, Montgomery Village, MD 20886, USA.
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Powell KA, Wilson D. 3-dimensional imaging modalities for phenotyping genetically engineered mice. Vet Pathol 2011; 49:106-15. [PMID: 22146851 DOI: 10.1177/0300985811429814] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A variety of 3-dimensional (3D) digital imaging modalities are available for whole-body assessment of genetically engineered mice: magnetic resonance microscopy (MRM), X-ray microcomputed tomography (microCT), optical projection tomography (OPT), episcopic and cryoimaging, and ultrasound biomicroscopy (UBM). Embryo and adult mouse phenotyping can be accomplished at microscopy or near microscopy spatial resolutions using these modalities. MRM and microCT are particularly well-suited for evaluating structural information at the organ level, whereas episcopic and OPT imaging provide structural and functional information from molecular fluorescence imaging at the cellular level. UBM can be used to monitor embryonic development longitudinally in utero. Specimens are not significantly altered during preparation, and structures can be viewed in their native orientations. Technologies for rapid automated data acquisition and high-throughput phenotyping have been developed and continually improve as this exciting field evolves.
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Affiliation(s)
- K A Powell
- Small Animal Imaging Shared Resource, The James Comprehensive Cancer Center Department of Biomedical Informatics, Ohio State University, Columbus, Ohio, USA.
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Caplan J, Niethammer M, Taylor RM, Czymmek KJ. The power of correlative microscopy: multi-modal, multi-scale, multi-dimensional. Curr Opin Struct Biol 2011; 21:686-93. [PMID: 21782417 DOI: 10.1016/j.sbi.2011.06.010] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 06/22/2011] [Indexed: 11/24/2022]
Abstract
Correlative microscopy is a sophisticated approach that combines the capabilities of typically separate, but powerful microscopy platforms: often including, but not limited, to conventional light, confocal and super-resolution microscopy, atomic force microscopy, transmission and scanning electron microscopy, magnetic resonance imaging and micro/nano CT (computed tomography). When targeting rare or specific events within large populations or tissues, correlative microscopy is increasingly being recognized as the method of choice. Furthermore, this multi-modal assimilation of technologies provides complementary and often unique information, such as internal and external spatial, structural, biochemical and biophysical details from the same targeted sample. The development of a continuous stream of cutting-edge applications, probes, preparation methodologies, hardware and software developments will enable realization of the full potential of correlative microscopy.
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Affiliation(s)
- Jeffrey Caplan
- Delaware Biotechnology Institute Bio-Imaging Center, University of Delaware, Newark, DE 19711, United States
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Cleary JO, Wiseman FK, Norris FC, Price AN, Choy M, Tybulewicz VL, Ordidge RJ, Brandner S, Fisher EM, Lythgoe MF. Structural correlates of active-staining following magnetic resonance microscopy in the mouse brain. Neuroimage 2011; 56:974-83. [PMID: 21310249 PMCID: PMC3590453 DOI: 10.1016/j.neuroimage.2011.01.082] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 12/14/2010] [Accepted: 01/31/2011] [Indexed: 12/01/2022] Open
Abstract
Extensive worldwide efforts are underway to produce knockout mice for each of the ~25,000 mouse genes, which may give new insights into the underlying pathophysiology of neurological disease. Microscopic magnetic resonance imaging (μMRI) is a key method for non-invasive morphological phenotyping, capable of producing high-resolution 3D images of ex-vivo brains, after fixation with an MR contrast agent. These agents have been suggested to act as active-stains, enhancing structures not normally visible on MRI. In this study, we investigated the structural correlates of the MRI agent Gd-DTPA, together with the optimal preparation and scan parameters for contrast-enhanced gradient-echo imaging of the mouse brain. We observed that in-situ preparation was preferential to ex-situ due to the degree of extraction damage. In-situ brains scanned with optimised parameters, enabled images with a high signal-to-noise-ratio (SNR ~30) and comprehensive anatomical delineation. Direct correlation of the MR brain structures to histology, detailed fine histoarchitecture in the cortex, cerebellum, olfactory bulb and hippocampus. Neurofilament staining demonstrated that regions of negative MR contrast strongly correlated to myelinated white-matter structures, whilst structures of more positive MR contrast corresponded to areas with high grey matter content. We were able to identify many sub-regions, particularly within the hippocampus, such as the unmyelinated mossy fibres (stratum lucidum) and their region of synapse in the stratum pyramidale, together with the granular layer of the dentate gyrus, an area of densely packed cell bodies, which was clearly visible as a region of hyperintensity. This suggests that cellular structure influences the site-specific distribution of the MR contrast agent, resulting in local variations in T(2)*, which leads to enhanced tissue discrimination. Our findings provide insights not only into the cellular distribution and mechanism of MR active-staining, but also allow for three dimensional analysis, which enables interpretation of magnetic resonance microscopy brain data and highlights cellular structure for investigation of disease processes in development and disease.
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Key Words
- mri, magnetic resonance imaging
- cns, central nervous system
- gd-dtpa, gadolinium-diethylene-triamine-pentaacetic acid
- snr, signal-to-noise ratio
- cnr, contrast-to-noise ratio
- fov, field of view
- nsa, number of signal averages
- te, echo time
- tr, repetition time
- fa, flip angle
- magnetic resonance microscopy
- mouse brain phenotyping
- active staining
- mouse brain histology
- immunohistochemistry
- myelin
- grey matter
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Affiliation(s)
- Jon O. Cleary
- Centre for Advanced Biomedical Imaging, Department of Medicine and Institute of Child Health, University College London, 72 Huntley Street, London, WC1E 6DD, UK
- Department of Medical Physics and Bioengineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - Frances K. Wiseman
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, Queen Square, London, WC1N 3BG, UK
| | - Francesca C. Norris
- Centre for Advanced Biomedical Imaging, Department of Medicine and Institute of Child Health, University College London, 72 Huntley Street, London, WC1E 6DD, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, Gower Street, London, WC1E 6BT, UK
| | - Anthony N. Price
- Centre for Advanced Biomedical Imaging, Department of Medicine and Institute of Child Health, University College London, 72 Huntley Street, London, WC1E 6DD, UK
| | - ManKin Choy
- Centre for Advanced Biomedical Imaging, Department of Medicine and Institute of Child Health, University College London, 72 Huntley Street, London, WC1E 6DD, UK
| | - Victor L.J. Tybulewicz
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Roger J. Ordidge
- Department of Medical Physics and Bioengineering, University College London, Gower Street, London, WC1E 6BT, UK
- Wellcome Trust Advanced MRI Group, University College London, 8–11 Queen Square, Queen Square, London, WC1N 3BG, UK
| | - Sebastian Brandner
- Division of Neuropathology and Department of Neurodegenerative Disease, Institute of Neurology, University College London, Queen Square, London, WC1N 3BG, UK
| | - Elizabeth M.C. Fisher
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, Queen Square, London, WC1N 3BG, UK
| | - Mark F. Lythgoe
- Centre for Advanced Biomedical Imaging, Department of Medicine and Institute of Child Health, University College London, 72 Huntley Street, London, WC1E 6DD, UK
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