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Aghanoori MR, Burns KM, Subha M, Williams L, Hua M, Nobakht F, Krawec T, Yang G. Immunohistochemical analysis of the developing mouse cortex. Methods Cell Biol 2022; 170:31-46. [DOI: 10.1016/bs.mcb.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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2
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Guo J, Larabell CA. Soft X-ray tomography: virtual sculptures from cell cultures. Curr Opin Struct Biol 2019; 58:324-332. [PMID: 31495562 PMCID: PMC6791522 DOI: 10.1016/j.sbi.2019.06.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/24/2019] [Accepted: 06/27/2019] [Indexed: 12/20/2022]
Abstract
Cellular complexity is represented best in high-spatial resolution, three-dimensional (3D) reconstructions. Soft X-ray tomography (SXT) generates detailed volumetric reconstructions of cells preserved in a near-to-native, frozen-hydrated state. SXT is broadly applicable and can image specimens ranging from bacteria to large mammalian cells. As a reference, we summarize light and electron microscopic methods. We then present an overview of SXT and discuss its role in cellular imaging. We detail the methods used to image biological specimens and present recent highlights that illustrate the capabilities of the technique. We conclude by discussing correlative imaging, specifically the combination of SXT and fluorescence microscopy performed on the same specimen. This correlated approach combines the structural morphology of a cell with its physiological characteristics to build a deeply informative composite view.
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Affiliation(s)
- Jessica Guo
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Carolyn A Larabell
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA 94158, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
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Abstract
This chapter introduces to electronic cameras, discusses the various parameters considered for evaluating their performance, and describes some of the key features of different camera formats. The chapter also presents the basic understanding of functioning of the electronic cameras and how these properties can be exploited to optimize image quality under low-light conditions. Although there are many types of cameras available for microscopy, the most reliable type is the charge-coupled device (CCD) camera, which remains preferred for high-performance systems. If time resolution and frame rate are of no concern, slow-scan CCDs certainly offer the best available performance, both in terms of the signal-to-noise ratio and their spatial resolution. Slow-scan cameras are thus the first choice for experiments using fixed specimens such as measurements using immune fluorescence and fluorescence in situ hybridization. However, if video rate imaging is required, one need not evaluate slow-scan CCD cameras. A very basic video CCD may suffice if samples are heavily labeled or are not perturbed by high intensity illumination. When video rate imaging is required for very dim specimens, the electron multiplying CCD camera is probably the most appropriate at this technological stage. Intensified CCDs provide a unique tool for applications in which high-speed gating is required. The variable integration time video cameras are very attractive options if one needs to acquire images at video rate acquisition, as well as with longer integration times for less bright samples. This flexibility can facilitate many diverse applications with highly varied light levels.
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Daly SM, Leahy MJ. 'Go with the flow ': a review of methods and advancements in blood flow imaging. JOURNAL OF BIOPHOTONICS 2013; 6:217-55. [PMID: 22711377 DOI: 10.1002/jbio.201200071] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 05/22/2012] [Accepted: 05/23/2012] [Indexed: 05/25/2023]
Abstract
Physics has delivered extraordinary developments in almost every facet of modern life. From the humble thermometer and stethoscope to X-Ray, CT, MRI, ultrasound, PET and radiotherapy, our health has been transformed by these advances yielding both morphological and functional metrics. Recently high resolution label-free imaging of the microcirculation at clinically relevant depths has become available in the research domain. In this paper, we present a comprehensive review on current imaging techniques, state-of-the-art advancements and applications, and general perspectives on the prospects for these modalities in the clinical realm.
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Affiliation(s)
- Susan M Daly
- Biophotonics Research Facility, Department of Physics & Energy, University of Limerick, Ireland.
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5
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Salmon ED, Shaw SL, Waters JC, Waterman-Storer CM, Maddox PS, Yeh E, Bloom K. A high-resolution multimode digital microscope system. Methods Cell Biol 2013; 114:179-210. [PMID: 23931508 DOI: 10.1016/b978-0-12-407761-4.00009-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This chapter describes the development of a high-resolution, multimode digital imaging system based on a wide-field epifluorescent and transmitted light microscope, and a cooled charge-coupled device (CCD) camera. The three main parts of this imaging system are Nikon FXA microscope, Hamamatsu C4880 cooled CCD camera, and MetaMorph digital imaging system. This chapter presents various design criteria for the instrument and describes the major features of the microscope components-the cooled CCD camera and the MetaMorph digital imaging system. The Nikon FXA upright microscope can produce high resolution images for both epifluorescent and transmitted light illumination without switching the objective or moving the specimen. The functional aspects of the microscope set-up can be considered in terms of the imaging optics, the epi-illumination optics, the transillumination optics, the focus control, and the vibration isolation table. This instrument is somewhat specialized for microtubule and mitosis studies, and it is also applicable to a variety of problems in cellular imaging, including tracking proteins fused to the green fluorescent protein in live cells. The instrument is also valuable for correlating the assembly dynamics of individual cytoplasmic microtubules (labeled by conjugating X-rhodamine to tubulin) with the dynamics of membranes of the endoplasmic reticulum (labeled with DiOC6) and the dynamics of the cell cortex (by differential interference contrast) in migrating vertebrate epithelial cells. This imaging system also plays an important role in the analysis of mitotic mutants in the powerful yeast genetic system Saccharomyces cerevisiae.
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Affiliation(s)
- Edward D Salmon
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
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6
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Advanced microscopy techniques to assess solid-state properties of inhalation medicines. Adv Drug Deliv Rev 2012; 64:369-82. [PMID: 22120022 DOI: 10.1016/j.addr.2011.11.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 11/07/2011] [Accepted: 11/11/2011] [Indexed: 11/22/2022]
Abstract
Efficient control and characterisation of the physico-chemical properties of active pharmaceutical ingredients (APIs) and excipients for orally inhaled drug products (OIDPs) are critical to successful product development. Control and reduction of risk require the introduction of a material science based approach to product development and the use of advanced analytical tools in understanding how the solid-state properties of the input materials influence structure and product functionality. The key issues to be addressed, at a microscopic scale, are understanding how the critical quality attributes of input materials influence surface, interfacial and particulate interactions within OIDPs. This review offers an in-depth discussion on the use of advanced microscopy techniques in characterising of the solid-state properties of particulate materials for OIDPs. The review covers the fundamental principles of the techniques, instrumentation types, data interpretation and specific applications in relation to the product development of OIDPs.
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Affiliation(s)
- Ivan Rasnik
- Physics Department, Emory University, Atlanta, Georgia 30322, USA
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Salmon ED, Shaw SL, Waters JC, Waterman-Storer CM, Maddox PS, Yeh E, Bloom K. A high-resolution multimode digital microscope system. Methods Cell Biol 2007; 81:187-218. [PMID: 17519169 DOI: 10.1016/s0091-679x(06)81011-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- E D Salmon
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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9
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Augustine-Rauch K. Alternative experimental approaches for interpreting skeletal findings in safety studies. ACTA ACUST UNITED AC 2007; 80:497-504. [DOI: 10.1002/bdrb.20132] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Collazo A, Bricaud O, Desai K. Use of confocal microscopy in comparative studies of vertebrate morphology. Methods Enzymol 2005; 395:521-43. [PMID: 15865982 DOI: 10.1016/s0076-6879(05)95027-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Laser scanning confocal microscopy provides a means to acquire and analyze images of complex morphological structures and to help place molecules or cells of interest in their proper morphological context. Confocal microscopy is a form of fluorescence microscopy that sharpens the images collected by visualizing the light from only one plane of focus. This allows for the collection of multiple focal planes in what is called a z-stack, which provides three-dimensional data. Five steps that any investigator using a confocal microscope should follow are described: (1) labeling and (2) mounting of specimens for viewing, (3) optimizing the image on the confocal, and (4) collecting and (5) analyzing of confocal image data. We describe three specific protocols incorporating these steps from our work on vertebrate inner ear development. The first two describe a collection of z-stacks in living, fluorescently labeled, and intact embryos. The second protocol is for time-lapse imaging of multiple focal planes at each time point. The third protocol describes confocal imaging of preserved material double labeled with antibodies and by retrograde labeling of neurons via axonal uptake. Finally, three alternative or complementary approaches to standard confocal microscopy are described and discussed.
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Affiliation(s)
- Andres Collazo
- Department of Cell and Molecular Biology, House Ear Institute, Los Angeles, California 90057, USA
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11
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Woodward JD, Maina JN. A 3D digital reconstruction of the components of the gas exchange tissue of the lung of the muscovy duck, Cairina moschata. J Anat 2005; 206:477-92. [PMID: 15857367 PMCID: PMC1571511 DOI: 10.1111/j.1469-7580.2005.00413.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2005] [Indexed: 11/28/2022] Open
Abstract
To elucidate the shape, size, and spatial arrangement and association of the terminal respiratory units of the avian lung, a three-dimensional (3D) computer-aided voxel reconstruction was generated from serial plastic sections of the lung of the adult muscovy duck, Cairina moschata. The air capillaries (ACs) are rather rotund structures that interconnect via short, narrow passageways, and the blood capillaries (BCs) comprise proliferative segments of rather uniform dimensions. The ACs and BCs anastomose profusely and closely intertwine with each other, forming a complex network. The two sets of respiratory units are, however, absolutely not mirror images of each other, as has been claimed by some investigators. Historically, the terms 'air capillaries' and 'blood capillaries' were derived from observations that the exchange tissue of the avian lung mainly consisted of a network of minuscule air- and vascular units. The entrenched notion that the ACs are straight (non-branching), blind-ending tubules that project outwards from the parabronchial lumen and that the BCs are direct tubules that run inwards parallel to and in contact with the ACs is overly simplistic, misleading and incorrect. The exact architectural properties of the respiratory units of the avian lung need to be documented and applied in formulating reliable physiological models. A few ostensibly isolated ACs were identified. The mechanism through which such units form and their functional significance, if any, are currently unclear.
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Affiliation(s)
- Jeremy D Woodward
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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12
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Molnar B, Berczi L, Diczhazy C, Tagscherer A, Varga SV, Szende B, Tulassay Z. Digital slide and virtual microscopy based routine and telepathology evaluation of routine gastrointestinal biopsy specimens. J Clin Pathol 2003; 56:433-8. [PMID: 12783970 PMCID: PMC1769977 DOI: 10.1136/jcp.56.6.433] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2003] [Indexed: 11/04/2022]
Abstract
AIMS To evaluate a recently developed digital slide and virtual microscope system, and to compare this method with optical microscopy on routine gastrointestinal biopsy specimens in both local and remote access modes. METHODS A fully computer controlled commercial microscope was used. The scanning program included object detection, autofocus, and image compression algorithms. The overall hard disk space for a gastric biopsy was between 30 and 50 MB and the scanning time was between 20 and 40 minutes. Haematoxylin and eosin stained routine gastric (61) and colon (42) biopsy specimens were selected, scanned, and evaluated by two specialists on an optical (OM) and virtual microscope (VM). RESULTS The overall concordance of VM and OM with the consensus diagnosis was 95.1% and 97%, respectively. Clinically important concordance was 96.1% and 98% for VM and OM, respectively. The two methods showed concordance in 92% of cases and clinically important concordance in 94.1% of cases. The reasons for discordance were image quality (one case), interpretation difference (three cases), and insufficient clinical information (three cases). Remote evaluation of the digital slides through the Internet has the advantages of the previously used static and dynamic telepathology methods. CONCLUSIONS Diagnostic concordance was found between OM and VM. The digital slide and the virtual microscope can be alternative techniques in the computerisation of the histology laboratory and in teleconsultation services after further evaluation of time and storage constraints.
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Affiliation(s)
- B Molnar
- Digital Microscopy Laboratory, Second Department of Medicine, Semmelweis University, Budapest, Hungary.
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13
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Femino AM, Fogarty K, Lifshitz LM, Carrington W, Singer RH. Visualization of single molecules of mRNA in situ. Methods Enzymol 2003; 361:245-304. [PMID: 12624916 DOI: 10.1016/s0076-6879(03)61015-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Andrea M Femino
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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14
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Merrett K, Cornelius RM, McClung WG, Unsworth LD, Sheardown H. Surface analysis methods for characterizing polymeric biomaterials. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2003; 13:593-621. [PMID: 12182547 DOI: 10.1163/156856202320269111] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Surface properties have an enormous effect on the success or failure of a biomaterial device, thus signifying the considerable importance of and the need for adequate characterization of the biomaterial surface. Microscopy techniques used in the analysis of biomaterial surfaces include scanning electron microscopy, transmission electron microscopy, atomic force microscopy, and confocal microscopy. Spectroscopic techniques include X-ray photoelectron spectroscopy, Fourier Transform infrared attenuated total reflection and secondary ion mass spectrometry. The measurement of contact angles, although one of the earlier techniques developed remains a very useful tool in the evaluation of surface hydrophobicity/hydrophilicity. This paper provides a brief, easy to understand synopsis of these and other techniques including emerging techniques, which are proving useful in the analysis of the surface properties of polymeric biomaterials. Cautionary statements have been made, numerous authors referenced and examples used to show the specific type of information that can be acquired from the different techniques used in the characterization of polymeric biomaterials surfaces.
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Affiliation(s)
- K Merrett
- Department of Chemical Engineering, University of Ottawa, ON, Canada
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15
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Affiliation(s)
- Keith Berland
- Physics Department, Emory University, Atlanta, Georgia 30322, USA
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16
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Salmon ED, Shaw SL, Waters J, Waterman-Storer CM, Maddox PS, Yeh E, Bloom K. A high-resolution multimode digital microscope system. Methods Cell Biol 2003; 72:185-216. [PMID: 14719333 DOI: 10.1016/s0091-679x(03)72010-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- E D Salmon
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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17
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Two-photon excitation microscopy. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1076-5670(03)80016-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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18
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Lorén N, Langton M, Hermansson AM. Determination of temperature dependent structure evolution by fast-Fourier transform at late stage spinodal decomposition in bicontinuous biopolymer mixtures. J Chem Phys 2002. [DOI: 10.1063/1.1474583] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Machtynger J, Shotton DM. VANQUIS, a system for the interactive semantic content analysis and spatio-temporal query by content of videos. J Microsc 2002; 205:43-52. [PMID: 11856380 DOI: 10.1046/j.0022-2720.2001.00967.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Using the video metadata descriptors and data model defined in the accompanying paper (Shotton, D. M. et al. (2002) A metadata classification schema for semantic content analysis of videos. J. Microsc. 205, 33-42), we discuss how analysis of the content of scientific videos, and subsequent query by content of the resulting semantic metadata, can be enhanced by the use of an object-relational database. We illustrate this by describing VANQUIS, a Web-based prototype video analysis and query interface system for the interactive spatio-temporal analysis and subsequent query by content of videos. Using VANQUIS to generate standard SQL (structured query language) statements that address complex data types stored in an object-relational database, relationships between characters and events contained within and between videos can be identified, and the appropriate video segments containing these characters and events can be retrieved for viewing. We give examples of analysis and query implementation by using VANQUIS to analyse a biological microscopy video, and discuss the wider potential of this methodology for the analysis and query by content of videos containing more general subject matter.
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Affiliation(s)
- J Machtynger
- Institute of Cognitive Neuroscience, University College London, UK
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21
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Abstract
Confocal microscopy allows visualization of optical sections of material labeled with fluorescence or reflecting probes. By excluding light from planes above and below the plane of focus it is possible to obtain sharp images of objects deep within sections. Sections can be combined to construct three-dimensional images. This unit provides an overview and introduction to confocal microscopy.
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Abstract
This review article looks at the development of confocal imaging technology, with emphasis on its abilities to overcome some of the problems of imaging life processes, particularly in the intact organ or animal. A brief summary of three promising micro-imaging modalities is provided (which are microscopical analogues of conventional radiological techniques) with a bibliography for the interested reader to pursue.
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Affiliation(s)
- P J Tadrous
- Department of Histopathology, Imperial College School of Medicine, The Hammersmith Hospital, London W12 0NN, UK.
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23
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Zhang WH, Zhu SN, Lu SL, Huang YL, Zhao P. Three-dimensional image of hepatocellular carcinoma under confocal laser scanning microscope. World J Gastroenterol 2000; 6:344-347. [PMID: 11819594 PMCID: PMC4688748 DOI: 10.3748/wjg.v6.i3.344] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the application of confocal laser scanning microscopy (CLSM) in tumor pathology and three-dimensional (3-D) reconstruction by CLSM in pathologic specimens of hepatocellular carcinoma (HCC).
METHODS: The 30 μm thick sections were cut from the paraffin-embedded tissues of HCC, hyperplasia and normal liver, stained with DNA fluorescent probe YOYO-1 iodide and examined by CLSM to collect optical sections of nuclei and 3-D images reconstructed.
RESULTS: HCC displayed chaotic arrangement of carcinoma cell nuclei, marked pleomorphism, indented and irregular nuclear surface, and irregular and coarse chromatin texture.
CONCLUSION: The serial optical tomograms of CLSM can be used to create 3-D reconstruction of cancer cell nuclei. Such 3-D impressions might be helpful or even essential in making an accurate diagnosis.
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Kricka LJ, Stanley PE. Assays using digital fluorescence: 1985-1998. LUMINESCENCE 1999; 14:271-9. [PMID: 10512992 DOI: 10.1002/(sici)1522-7243(199909/10)14:5<271::aid-bio549>3.0.co;2-o] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Luminescence continues to provide comprehensive literature surveys which will be published in most issues. These are a continuation of the literature surveys begun in 1986 in the Journal of Bioluminescence and Chemiluminescence which, up until 1998, encompassed more than 6000 references cited by year or specialized topic. With this newly named journal these searches are expanding to reflect the journal's wider scope. In future we will cover all fundamental and applied aspects of biological and chemical luminescence and include not only bioluminescence and chemiluminescence but also fluorescence, time resolved fluorescence, electrochemiluminescence, phosphorescence, sonoluminescence, lyoluminescence and triboluminescence. The compilers would be pleased to receive any comments from the readership. Contact by e-mail: L.J. Kricka: larry_kricka@path1a.med.upenn.edu or P.E. Stanley: Stanley@LUMIWEB.COM Copyright 1999 John Wiley & Sons, Ltd.
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Boudier T, Shotton DM. Video on the Internet: An introduction to the digital encoding, compression, and transmission of moving image data. J Struct Biol 1999; 125:133-55. [PMID: 10222270 DOI: 10.1006/jsbi.1999.4097] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this paper, we seek to provide an introduction to the fast-moving field of digital video on the Internet, from the viewpoint of the biological microscopist who might wish to store or access videos, for instance in image databases such as the BioImage Database (http://www.bioimage.org). We describe and evaluate the principal methods used for encoding and compressing moving image data for digital storage and transmission over the Internet, which involve compromises between compression efficiency and retention of image fidelity, and describe the existing alternate software technologies for downloading or streaming compressed digitized videos using a Web browser. We report the results of experiments on video microscopy recordings and three-dimensional confocal animations of biological specimens to evaluate the compression efficiencies of the principal video compression-decompression algorithms (codecs) and to document the artefacts associated with each of them. Because MPEG-1 gives very high compression while yet retaining reasonable image quality, these studies lead us to recommend that video databases should store both a high-resolution original version of each video, ideally either uncompressed or losslessly compressed, and a separate edited and highly compressed MPEG-1 preview version that can be rapidly downloaded for interactive viewing by the database user.
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Affiliation(s)
- T Boudier
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, United Kingdom.
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26
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Shotton DM, Attaran A. Variant antigenic peptide promotes cytotoxic T lymphocyte adhesion to target cells without cytotoxicity. Proc Natl Acad Sci U S A 1998; 95:15571-6. [PMID: 9861010 PMCID: PMC28084 DOI: 10.1073/pnas.95.26.15571] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/1998] [Indexed: 11/18/2022] Open
Abstract
Timelapse video microscopy has been used to record the motility and dynamic interactions between an H-2Db-restricted murine cytotoxic T lymphocyte clone (F5) and Db-transfected L929 mouse fibroblasts (LDb) presenting normal or variant antigenic peptides from human influenza nucleoprotein. F5 cells will kill LDb target cells presenting specific antigen (peptide NP68: ASNENMDAM) after "browsing" their surfaces for between 8 min and many hours. Cell death is characterized by abrupt cellular rounding followed by zeiosis (vigorous "boiling" of the cytoplasm and blebbing of the plasma membrane) for 10-20 min, with subsequent cessation of all activity. Departure of cytotoxic T lymphocytes from unkilled target cells is rare, whereas serial killing is sometimes observed. In the absence of antigenic peptide, cytotoxic T lymphocytes browse target cells for much shorter periods, and readily leave to encounter other targets, while never causing target cell death. Two variant antigenic peptides, differing in nonamer position 7 or 8, also act as antigens, albeit with lower efficiency. A third variant peptide NP34 (ASNENMETM), which differs from NP68 in both positions and yet still binds Db, does not stimulate F5 cytotoxicity. Nevertheless, timelapse video analysis shows that NP34 leads to a significant modification of cell behavior, by up-regulating F5-LDb adhesive interactions. These data extend recent studies showing that partial agonists may elicit a subset of the T cell responses associated with full antigen stimulation, by demonstrating that TCR interaction with variant peptide antigens can trigger target cell adhesion and surface exploration without activating the signaling pathway that results in cytotoxicity.
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Affiliation(s)
- D M Shotton
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom.
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27
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Chaves I, Zomerdijk J, Dirks-Mulder A, Dirks RW, Raap AK, Borst P. Subnuclear localization of the active variant surface glycoprotein gene expression site in Trypanosoma brucei. Proc Natl Acad Sci U S A 1998; 95:12328-33. [PMID: 9770486 PMCID: PMC22831 DOI: 10.1073/pnas.95.21.12328] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Trypanosoma brucei, transcription by RNA polymerase II and 5' capping of messenger RNA are uncoupled: a capped spliced leader is trans spliced to every RNA. This decoupling makes it possible to have protein-coding gene transcription driven by RNA polymerase I. Indeed, indirect evidence suggests that the genes for the major surface glycoproteins, variant surface glycoproteins (VSGs) in bloodstream-form trypanosomes, are transcribed by RNA polymerase I. In a single trypanosome, only one VSG expression site is maximally transcribed at any one time, and it has been speculated that transcription takes place at a unique site within the nucleus, perhaps in the nucleolus. We tested this by using fluorescence in situ hybridization. With probes that cover about 50 kb of the active 221 expression site, we detected nuclear transcripts of this site in a single fluorescent spot, which did not colocalize with the nucleolus. Analysis of marker gene-tagged active expression site DNA by fluorescent DNA in situ hybridization confirmed the absence of association with the nucleolus. Even an active expression site in which the promoter had been replaced by an rDNA promoter did not colocalize with the nulceolus. As expected, marker genes inserted in the rDNA array predominantly colocalize with the nucleolus, whereas the tubulin gene arrays do not. We conclude that transcription of the active VSG expression site does not take place in the nucleolus.
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Affiliation(s)
- I Chaves
- Division of Molecular Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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28
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Abstract
Recent advances in optical imaging have dramatically expanded the capabilities of the light microscope and its usefulness in microbiology research. Some of these advances include improved fluorescent probes, better cameras, new techniques such as confocal and deconvolution microscopy, and the use of computers in imaging and image analysis. These new technologies have now been applied to microbiological problems with resounding success.
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Affiliation(s)
- D C Fung
- Department of Biochemistry, Beckman Center, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
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Affiliation(s)
- K Berland
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill 27599, USA
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31
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Barak LS, Ferguson SS, Zhang J, Martenson C, Meyer T, Caron MG. Internal trafficking and surface mobility of a functionally intact beta2-adrenergic receptor-green fluorescent protein conjugate. Mol Pharmacol 1997; 51:177-84. [PMID: 9203621 DOI: 10.1124/mol.51.2.177] [Citation(s) in RCA: 176] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The beta2-adrenergic receptor (beta2AR) is prototypic of the large family of G protein-coupled receptors (GPCRs) whose desensitization and resensitization are regulated by intracellular kinases, arrestin proteins, phosphatases, and ill-defined components of the cellular endocytic machinery. The study of beta2AR signal transduction and behavior in living cells is technically difficult because of the relatively low cellular expression of the receptor and a lack of useful biological reagents. Availability of a functional beta2AR tagged with the highly sensitive Green Fluorescent Protein (GFP) could allow measurements of the various properties of the beta2AR. We demonstrate that a fully functional beta2AR/GFP can be engineered. In mammalian cells, beta2AR/S65T/GFP demonstrates strong, diffuse plasma membrane fluorescence when observed with 480 nm excitation. The fluorescent receptor binds agonist and antagonist, stimulates adenylyl cyclase, undergoes phosphorylation, and is internalized in a manner indistinguishable from wild-type receptor. We then show that its internal trafficking and surface mobility can be determined by measuring only the endogenous fluorescence of the conjugate. beta2AR/S65T/GFP was found to be localized on endosomal membranes in living cells within minutes of agonist treatment, and within 15 min it is observed in more complicated structures formed from fusion of multiple endosomes. Finally, its free diffusion (diffusion coefficient, 4.0-12 x 10(-9) cm2/sec) was assessed on living cells using photobleaching recovery measurements. This approach and the fidelity of the biochemical properties of the beta2AR/S65T/GFP demonstrate that real-time optical measurements of beta2AR (as well as other GPCR) interactions and dynamics on living cells are feasible.
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Affiliation(s)
- L S Barak
- Howard Hughes Medical Institute Laboratories, Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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Abstract
RNA in situ hybridization is a useful method for localizing specific mRNAs and studying the spatial and temporal organization of RNA transcription, processing and transport in cells. In this review, I describe methods of RNA in situ hybridization for tissue sections and cell preparations. Special emphasis is placed on the application of non-radioactive-labeled probes for multiparameter cell analysis. In addition, a summary of RNA in situ hybridization studies on RNA transport in the cytoplasm as well as in the nucleus of cells is given.
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Affiliation(s)
- R W Dirks
- Department of Cytochemistry and Cytometry, Sylvius Laboratories, Leiden University, Netherlands
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Trendelenburg MF, Zatsepina OV, Waschek T, Schlegel W, Tröster H, Rudolph D, Schmahl G, Spring H. Multiparameter microscopic analysis of nucleolar structure and ribosomal gene transcription. Histochem Cell Biol 1996; 106:167-92. [PMID: 8877378 DOI: 10.1007/bf02484399] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A survey of novel microscopic approaches for structural and functional analysis of subnucleolar compartments will be presented. Research on nucleolar structure and function concentrates predominantly on two distinct types of nucleoli: (1) nucleoli present during the interphase of the cell cycle in somatic tissue culture cells and (2) nucleoli present in meiotic cells, e.g. oocytes of amphibians. These nucleoli are found during meiotic prophase of oogenesis and are functional during several months of the diplotene stage of oogenesis. A further characteristic is the fact that these nucleoli are extrachromosomal, since they originate by selective ribosomal DNA (rDNA) amplification during the early pachytene stage of oogenesis. Miller-type chromatin spread preparations using transcriptionally active nucleoli, to a major part, contributed to our understanding of the structural organization of polymerase I directed pre-rRNA transcription. Although the structural organization of the template-associated pre-rRNA transcript is known in some detail from chromatin spreads, relatively little is known about structural aspects of pre-rRNA processing. In order to investigate this intriguing question in more detail, we have developed a computer-based densitometry analysis of both template-associated and template-dissociated pre-rRNA transcripts in order to follow the structural modification of pre-rRNA transcripts during processing. Another line of experiments is devoted to the in situ structure of actively transcribing genes in the nucleolus. In order to bridge the gap between light microscopy and electron microscopy we started video-enhanced light microscopical analysis of actively transcribing genes. Although the dimensions of individual spread genes are critical for detection by optical microscopy, we succeeded in obtaining the first series of images of transcribing genes in their "native' hydrated state. An additional promising type of microscopy is transmission X-ray microscopy. Recent progress in instrumentation as well as in sample preparation has allowed us to obtain the first images of density distribution within intact, fully hydrated nucleoli using amplitude-contrast and/or phase-contrast X-ray microscopy of non-contrasted, fully hydrated nucleoli at different states of transcriptional activity. Whereas the above mentioned investigations using video microscopy and X-ray microscopy are predominantly applicable to the analysis of amplified nucleoli in amphibian oocytes, which are characterized by an extremely high transcription rate of 80-90% of rDNA genes per individual nucleolus, structural analysis of the in situ arrangement of actively transcribing genes in somatic nucleoli as present in the interphase nucleus is far more difficult to perform, mainly due to the much lower number of simultaneously transcribed active genes per individual nucleolus. Visualization of actively transcribed gene clusters is approached by an integrated experimental assay using video microscopy, confocal laser scan microscopy, and antibodies against specific nucleolar proteins.
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Affiliation(s)
- Peter M. Cooke
- McCrone Research Institute Inc., Chicago, Illinois 60616
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Oberholzer M, Ostreicher M, Christen H, Brühlmann M. Methods in quantitative image analysis. Histochem Cell Biol 1996; 105:333-55. [PMID: 8781988 DOI: 10.1007/bf01463655] [Citation(s) in RCA: 119] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The main steps of image analysis are image capturing, image storage (compression), correcting imaging defects (e.g. non-uniform illumination, electronic-noise, glare effect), image enhancement, segmentation of objects in the image and image measurements. Digitisation is made by a camera. The most modern types include a frame-grabber, converting the analog-to-digital signal into digital (numerical) information. The numerical information consists of the grey values describing the brightness of every point within the image, named a pixel. The information is stored in bits. Eight bits are summarised in one byte. Therefore, grey values can have a value between 0 and 256 (2(8)). The human eye seems to be quite content with a display of 5-bit images (corresponding to 64 different grey values). In a digitised image, the pixel grey values can vary within regions that are uniform in the original scene: the image is noisy. The noise is mainly manifested in the background of the image. For an optimal discrimination between different objects or features in an image, uniformity of illumination in the whole image is required. These defects can be minimised by shading correction [subtraction of a background (white) image from the original image, pixel per pixel, or division of the original image by the background image]. The brightness of an image represented by its grey values can be analysed for every single pixel or for a group of pixels. The most frequently used pixel-based image descriptors are optical density, integrated optical density, the histogram of the grey values, mean grey value and entropy. The distribution of the grey values existing within an image is one of the most important characteristics of the image. However, the histogram gives no information about the texture of the image. The simplest way to improve the contrast of an image is to expand the brightness scale by spreading the histogram out to the full available range. Rules for transforming the grey value histogram of an existing image (input image) into a new grey value histogram (output image) are most quickly handled by a look-up table (LUT). The histogram of an image can be influenced by gain, offset and gamma of the camera. Gain defines the voltage range, offset defines the reference voltage and gamma the slope of the regression line between the light intensity and the voltage of the camera. A very important descriptor of neighbourhood relations in an image is the co-occurrence matrix. The distance between the pixels (original pixel and its neighbouring pixel) can influence the various parameters calculated from the co-occurrence matrix. The main goals of image enhancement are elimination of surface roughness in an image (smoothing), correction of defects (e.g. noise), extraction of edges, identification of points, strengthening texture elements and improving contrast. In enhancement, two types of operations can be distinguished: pixel-based (point operations) and neighbourhood-based (matrix operations). The most important pixel-based operations are linear stretching of grey values, application of pre-stored LUTs and histogram equalisation. The neighbourhood-based operations work with so-called filters. These are organising elements with an original or initial point in their centre. Filters can be used to accentuate or to suppress specific structures within the image. Filters can work either in the spatial or in the frequency domain. The method used for analysing alterations of grey value intensities in the frequency domain is the Hartley transform. Filter operations in the spatial domain can be based on averaging or ranking the grey values occurring in the organising element. The most important filters, which are usually applied, are the Gaussian filter and the Laplace filter (both averaging filters), and the median filter, the top hat filter and the range operator (all ranking filters). Segmentation of objects is traditionally based on threshold grey values. (AB
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Affiliation(s)
- M Oberholzer
- Department of Pathology of the University of Basel, Switzerland
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Halbhuber KJ, Scheven C, Jirikowski G, Feuerstein H, Ott U. Reflectance enzyme histochemistry (REH): visualization of cerium-based and DAB primary reaction products of phosphatases and oxidases in cryostat sections by confocal laser scanning microscopy. Histochem Cell Biol 1996; 105:239-49. [PMID: 8681042 DOI: 10.1007/bf01462297] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In the present study the reflectance mode of confocal laser scanning microscopy was adapted to detect and to assess semiquantitatively cerium-based primary reaction products of oxidases [Ce(IV) perhydroxide] and phosphatases [Ce(III) hydroxyphosphate converted into Ce(IV) perhydroxyphosphate] as well as of the 3,3'-diaminobenzidine (DAB)-based primary reaction product of cytochrome c oxidase in cryostat sections. Confocal laser scanning microscopy offers a unique way of making visible histochemical reaction products which are weakly absorbant but sufficiently reflective. It was easily possible to record simultaneously the reflectance signals at the wavelength of the exciting laser (preferentially 488 nm) and the autofluorescence signals ( > 580 nm in our set-up) of glutaraldehyde-fixed tissue. The results of an imbibition study of cerium-containing model precipitates indicate that the cerium, generally, should be oxidized prior to observation because the index of refraction of Ce(IV) compounds is considerably higher than that of the corresponding Ce(III) compounds. An attempt at comparative numerical assessment of reflection intensities from reflectant parts in morphologically similar sections is presented. The proposed technique may open new possibilities in enzyme- and immunohistochemistry.
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Affiliation(s)
- K J Halbhuber
- Institute of Anatomy II, Friedrich Schiller University Jena, Germany
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