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Kerstens A, Corthout N, Pavie B, Huang Z, Vernaillen F, Vande Velde G, Munck S. A Label-free Multicolor Optical Surface Tomography (ALMOST) imaging method for nontransparent 3D samples. BMC Biol 2019; 17:1. [PMID: 30616566 PMCID: PMC6323867 DOI: 10.1186/s12915-018-0614-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/26/2018] [Indexed: 12/22/2022] Open
Abstract
Background Current mesoscale 3D imaging techniques are limited to transparent or cleared samples or require the use of X-rays. This is a severe limitation for many research areas, as the 3D color surface morphology of opaque samples—for example, intact adult Drosophila, Xenopus embryos, and other non-transparent samples—cannot be assessed. We have developed “ALMOST,” a novel optical method for 3D surface imaging of reflective opaque objects utilizing an optical projection tomography device in combination with oblique illumination and optical filters. Results As well as demonstrating image formation, we provide background information and explain the reconstruction—and consequent rendering—using a standard filtered back projection algorithm and 3D software. We expanded our approach to fluorescence and multi-channel spectral imaging, validating our results with micro-computed tomography. Different biological and inorganic test samples were used to highlight the versatility of our approach. To further demonstrate the applicability of ALMOST, we explored the muscle-induced form change of the Drosophila larva, imaged adult Drosophila, dynamically visualized the closure of neural folds during neurulation of live Xenopus embryos, and showed the complementarity of our approach by comparison with transmitted light and fluorescence OPT imaging of a Xenopus tadpole. Conclusion Thus, our new modality for spectral/color, macro/mesoscopic 3D imaging can be applied to a variety of model organisms and enables the longitudinal surface dynamics during development to be revealed. Electronic supplementary material The online version of this article (10.1186/s12915-018-0614-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Axelle Kerstens
- VIB Bio Imaging Core, Herestraat 49, Box 602, 3000, Leuven, Belgium.,Research Group Molecular Neurobiology, Department of Neuroscience, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium.,VIB Center for Brain and Disease Research, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium
| | - Nikky Corthout
- VIB Bio Imaging Core, Herestraat 49, Box 602, 3000, Leuven, Belgium.,Research Group Molecular Neurobiology, Department of Neuroscience, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium.,VIB Center for Brain and Disease Research, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium
| | - Benjamin Pavie
- VIB Bio Imaging Core, Herestraat 49, Box 602, 3000, Leuven, Belgium.,Research Group Molecular Neurobiology, Department of Neuroscience, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium.,VIB Center for Brain and Disease Research, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium
| | - Zengjin Huang
- VIB Center for Brain and Disease Research, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium.,Neuronal Wiring Lab, Department of Neuroscience, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium
| | - Frank Vernaillen
- VIB BioInformatics Core, Rijvisschestraat 126 3R, 9052, Ghent, Belgium
| | - Greetje Vande Velde
- Department of Imaging and Pathology, KU Leuven - University of Leuven, Herestraat 49, Box 505, 3000, Leuven, Belgium
| | - Sebastian Munck
- VIB Bio Imaging Core, Herestraat 49, Box 602, 3000, Leuven, Belgium. .,Research Group Molecular Neurobiology, Department of Neuroscience, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium. .,VIB Center for Brain and Disease Research, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium.
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Feroze R, Shawky JH, von Dassow M, Davidson LA. Mechanics of blastopore closure during amphibian gastrulation. Dev Biol 2015; 398:57-67. [PMID: 25448691 PMCID: PMC4317491 DOI: 10.1016/j.ydbio.2014.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 11/04/2014] [Accepted: 11/11/2014] [Indexed: 11/16/2022]
Abstract
Blastopore closure in the amphibian embryo involves large scale tissue reorganization driven by physical forces. These forces are tuned to generate sustained blastopore closure throughout the course of gastrulation. We describe the mechanics of blastopore closure at multiple scales and in different regions around the blastopore by characterizing large scale tissue deformations, cell level shape change and subcellular F-actin organization and by measuring tissue force production and structural stiffness of the blastopore during gastrulation. We find that the embryo generates a ramping magnitude of force until it reaches a peak force on the order of 0.5μN. During this time course, the embryo also stiffens 1.5 fold. Strain rate mapping of the dorsal, ventral and lateral epithelial cells proximal to the blastopore reveals changing patterns of strain rate throughout closure. Cells dorsal to the blastopore, which are fated to become neural plate ectoderm, are polarized and have straight boundaries. In contrast, cells lateral and ventral to the blastopore are less polarized and have tortuous cell boundaries. The F-actin network is organized differently in each region with the highest percentage of alignment occurring in the lateral region. Interestingly F-actin was consistently oriented toward the blastopore lip in dorsal and lateral cells, but oriented parallel to the lip in ventral regions. Cell shape and F-actin alignment analyses reveal different local mechanical environments in regions around the blastopore, which was reflected by the strain rate maps.
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Affiliation(s)
- Rafey Feroze
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA; School of Medicine, University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joseph H Shawky
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michelangelo von Dassow
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA; Duke University Marine Lab, Beaufort, NC 28516, USA
| | - Lance A Davidson
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA; Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA.
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Supatto W, McMahon A, Fraser SE, Stathopoulos A. Quantitative imaging of collective cell migration during Drosophila gastrulation: multiphoton microscopy and computational analysis. Nat Protoc 2009; 4:1397-412. [PMID: 19745822 DOI: 10.1038/nprot.2009.130] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes imaging and computational tools to collect and analyze live imaging data of embryonic cell migration. Our five-step protocol requires a few weeks to move through embryo preparation and four-dimensional (4D) live imaging using multi-photon microscopy, to 3D cell tracking using image processing, registration of tracking data and their quantitative analysis using computational tools. It uses commercially available equipment and requires expertise in microscopy and programming that is appropriate for a biology laboratory. Custom-made scripts are provided, as well as sample datasets to permit readers without experimental data to carry out the analysis. The protocol has offered new insights into the genetic control of cell migration during Drosophila gastrulation. With simple modifications, this systematic analysis could be applied to any developing system to define cell positions in accordance with the body plan, to decompose complex 3D movements and to quantify the collective nature of cell migration.
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Affiliation(s)
- Willy Supatto
- Division of Biology and Beckman Institute, California Institute of Technology, Pasadena, California, USA
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Metscher BD. MicroCT for developmental biology: a versatile tool for high-contrast 3D imaging at histological resolutions. Dev Dyn 2009; 238:632-40. [PMID: 19235724 DOI: 10.1002/dvdy.21857] [Citation(s) in RCA: 428] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Understanding developmental processes requires accurate visualization and parameterization of three-dimensional embryos. Tomographic imaging methods offer automatically aligned and calibrated volumetric images, but the usefulness of X-ray CT imaging for developmental biology has been limited by the low inherent contrast of embryonic tissues. Here, I demonstrate simple staining methods that allow high-contrast imaging of embryonic tissues at histological resolutions using a commercial microCT system. Quantitative comparisons of images of chick embryos treated with different contrast agents show that three very simple methods using inorganic iodine and phosphotungstic acid produce overall contrast and differential tissue contrast for X-ray imaging at least as high as that obtained with osmium. The stains can be used after any common fixation and after storage in aqueous or alcoholic media, and on a wide variety of species. These methods establish microCT imaging as a useful tool for comparative developmental studies, embryo phenotyping, and quantitative modeling of development.
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Affiliation(s)
- Brian D Metscher
- Department of Theoretical Biology, University of Vienna, Vienna, Austria.
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Louis DN. Molecular pathology of malignant gliomas. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2007; 2:277-305. [PMID: 18039109 DOI: 10.1146/annurev.pathol.2.010506.091930] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Malignant gliomas, the most common type of primary brain tumor, are a spectrum of tumors of varying differentiation and malignancy grades. These tumors may arise from neural stem cells and appear to contain tumor stem cells. Early genetic events differ between astrocytic and oligodendroglial tumors, but all tumors have an initially invasive phenotype, which complicates therapy. Progression-associated genetic alterations are common to different tumor types, targeting growth-promoting and cell cycle control pathways and resulting in focal hypoxia, necrosis, and angiogenesis. Knowledge of malignant glioma genetics has already impacted clinical management of these tumors, and researchers hope that further knowledge of the molecular pathology of malignant gliomas will result in novel therapies.
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Affiliation(s)
- David N Louis
- Molecular Pathology Unit, Department of Pathology and Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.
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Lee K, Avondo J, Morrison H, Blot L, Stark M, Sharpe J, Bangham A, Coen E. Visualizing plant development and gene expression in three dimensions using optical projection tomography. THE PLANT CELL 2006; 18:2145-56. [PMID: 16905654 PMCID: PMC1560903 DOI: 10.1105/tpc.106.043042] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2006] [Revised: 06/16/2006] [Accepted: 07/21/2006] [Indexed: 05/11/2023]
Abstract
A deeper understanding of the mechanisms that underlie plant growth and development requires quantitative data on three-dimensional (3D) morphology and gene activity at a variety of stages and scales. To address this, we have explored the use of optical projection tomography (OPT) as a method for capturing 3D data from plant specimens. We show that OPT can be conveniently applied to a wide variety of plant material at a range of scales, including seedlings, leaves, flowers, roots, seeds, embryos, and meristems. At the highest resolution, large individual cells can be seen in the context of the surrounding plant structure. For naturally semitransparent structures, such as roots, live 3D imaging using OPT is also possible. 3D domains of gene expression can be visualized using either marker genes, such as beta-glucuronidase, or more directly by whole-mount in situ hybridization. We also describe tools and software that allow the 3D data to be readily quantified and visualized interactively in different ways.
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Affiliation(s)
- Karen Lee
- Department of Cell and Developmental Biology, John Ines Centre, Norwich Research Park, Norwich, NR4 7UH United Kingdom
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Abstract
With the sequence of the mouse genome known, it is now possible to create or identify mutations in every gene to determine the molecules necessary for normal development. Consequently, there is a growing need for advanced phenotyping tools to best understand defects produced by altering gene function. Perhaps nothing is more satisfying than to directly observe a process in action; to disturb it and see for ourselves how the process changes before our very eyes. No doubt, this desire is what drove the invention of the very first microscopes and continues to this day to fuel progress in the field of biological imaging. Because mouse embryos are small and develop embedded within many tissue layers within the nurturing environment of the mother, directly observing the dynamic, micro- and nanoscopic events of early mammalian development has proven to be one of the greater challenges for imaging scientists. Here, I will review some of the imaging methods being used to study mouse development, highlighting the results obtained from imaging.
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Affiliation(s)
- Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.
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