scholarly journals Quantifying distortions in two-photon remote focussing microscope images using a volumetric calibration specimen

2014 ◽  
Vol 5 ◽  
Author(s):  
Alexander D. Corbett ◽  
Rebecca A. B. Burton ◽  
Gil Bub ◽  
Patrick S. Salter ◽  
Simon Tuohy ◽  
...  
Keyword(s):  
Two Photon ◽  
Microscope Images ◽  
Calibration Specimen

Automatic quantification of mitochondrial fragmentation from two-photon microscope images of mouse brain tissue

2015 ◽  
Vol 260 (3) ◽  
pp. 338-351 ◽  
Author(s):  
E. LIHAVAINEN ◽  
M. KISLIN ◽  
D. TOPTUNOV ◽  
L. KHIROUG ◽  
A.S. RIBEIRO
Keyword(s):  
Brain Tissue ◽  
Mouse Brain ◽  
Mitochondrial Fragmentation ◽  
Automatic Quantification ◽  
Two Photon ◽  
Microscope Images

Electron Microscope Observations of Magnetic and Electric Effects

1970 ◽  
Vol 28 ◽  
pp. 430-431
Author(s):  
John Silcox
Keyword(s):  
Electron Microscope ◽  
Electric Fields ◽  
Magnetic Image ◽  
Magnetic Effects ◽  
Ferromagnetic Films ◽  
Diffraction Contrast ◽  
Microscope Images ◽  
Electric Effects ◽  
Image Detail

Several aspects of magnetic and electric effects in electron microscope images are of interest and will be discussed here. Clearly electrons are deflected by magnetic and electric fields and can give rise to image detail. We will review situations in ferromagnetic films in which magnetic image effects are the predominant ones, others in which the magnetic effects give rise to rather subtle changes in diffraction contrast, cases of contrast at specimen edges due to leakage fields in both ferromagnets and superconductors and some effects due to electric fields in insulators.

Interlayer mixing in GaAs/AlxGa1-xAs heterostructures as a result of Se+ ion implantation

1988 ◽  
Vol 46 ◽  
pp. 908-909
Author(s):  
E.G. Bithell ◽  
W.M. Stobbs
Keyword(s):  
Ion Implantation ◽  
Diffusion Coefficients ◽  
Dark Field ◽  
Atomic Mass ◽  
Composition Profile ◽  
Semiconductor Heterostructures ◽  
Transmission Electron ◽  
Microscope Images ◽  
Damage Process ◽  
Electron Energy Loss

It is well known that the microstructural consequences of the ion implantation of semiconductor heterostructures can be severe: amorphisation of the damaged region is possible, and layer intermixing can result both from the original damage process and from the enhancement of the diffusion coefficients for the constituents of the original composition profile. A very large number of variables are involved (the atomic mass of the target, the mass and energy of the implant species, the flux and the total dose, the substrate temperature etc.) so that experimental data are needed despite the existence of relatively well developed models for the implantation process. A major difficulty is that conventional techniques (e.g. electron energy loss spectroscopy) have inadequate resolution for the quantification of any changes in the composition profile of fine scale multilayers. However we have demonstrated that the measurement of 002 dark field intensities in transmission electron microscope images of GaAs / AlxGa1_xAs heterostructures can allow the measurement of the local Al / Ga ratio.

Simulation of three Dimensional Defect Images in Transmission Electron Microscopy

1976 ◽  
Vol 34 ◽  
pp. 470-471
Author(s):  
W. D. Cooper ◽  
C. S. Hartley ◽  
J. J. Hren
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Three Dimensional ◽  
Crystalline Lattice ◽  
Continuum Models ◽  
Thin Foils ◽  
Transmission Electron ◽  
Microscope Images ◽  
General Computer Program ◽  
General Computer

Interpretation of electron microscope images of crystalline lattice defects can be greatly aided by computer simulation of theoretical contrast from continuum models of such defects in thin foils. Several computer programs exist at the present time, but none are sufficiently general to permit their use as an aid in the identification of the range of defect types encountered in electron microscopy. This paper presents progress in the development of a more general computer program for this purpose which eliminates a number of restrictions contained in other programs. In particular, the program permits a variety of foil geometries and defect types to be simulated.The conventional approximation of non-interacting columns is employed for evaluation of the two-beam dynamical scattering equations by a piecewise solution of the Howie-Whelan equations.

Improved 3-D reconstruction using stereo computer graphics and multiple tilt EM images

1995 ◽  
Vol 53 ◽  
pp. 630-631
Author(s):  
Lee D. Peachey ◽  
Lou Fodor ◽  
John C. Haselgrove ◽  
Stanley M. Dunn ◽  
Junqing Huang
Keyword(s):  
Computer Graphics ◽  
High Performance ◽  
Transverse Section ◽  
Three Dimensional ◽  
Stereo Pair ◽  
3D Reconstructions ◽  
Video Cameras ◽  
Biological Objects ◽  
Microscope Images ◽  
High Performance Computer

Stereo pairs of electron microscope images provide valuable visual impressions of the three-dimensional nature of specimens, including biological objects. Beyond this one seeks quantitatively accurate models and measurements of the three dimensional positions and sizes of structures in the specimen. In our laboratory, we have sought to combine high resolution video cameras with high performance computer graphics systems to improve both the ease of building 3D reconstructions and the accuracy of 3D measurements, by using multiple tilt images of the same specimen tilted over a wider range of angles than can be viewed stereoscopically. Ultimately we also wish to automate the reconstruction and measurement process, and have initiated work in that direction.Figure 1 is a stereo pair of 400 kV images from a 1 micrometer thick transverse section of frog skeletal muscle stained with the Golgi stain. This stain selectively increases the density of the transverse tubular network in these muscle cells, and it is this network that we reconstruct in this example.

Two-photon excitation microscopy in cellular biophysics

1995 ◽  
Vol 53 ◽  
pp. 62-63
Author(s):  
David W. Piston ◽  
Brian D. Bennett ◽  
Robert G. Summers
Keyword(s):  
Confocal Microscopy ◽  
Laser Beam ◽  
Duty Cycle ◽  
Excited Electronic State ◽  
Input Power ◽  
Two Photon ◽  
Simultaneous Absorption ◽  
Photon Excitation ◽  
Very High ◽  
Two Photon Excitation

Two-photon excitation microscopy (TPEM) provides attractive advantages over confocal microscopy for three-dimensionally resolved fluorescence imaging and photochemistry. Two-photon excitation arises from the simultaneous absorption of two photons in a single quantitized event whose probability is proportional to the square of the instantaneous intensity. For example, two red photons can cause the transition to an excited electronic state normally reached by absorption in the ultraviolet. In practice, two-photon excitation is made possible by the very high local instantaneous intensity provided by a combination of diffraction-limited focusing of a single laser beam in the microscope and the temporal concentration of 100 femtosecond pulses generated by a mode-locked laser. Resultant peak excitation intensities are 106 times greater than the CW intensities used in confocal microscopy, but the pulse duty cycle of 10-5 maintains the average input power on the order of 10 mW, only slightly greater than the power normally used in confocal microscopy.

Distortion in lattice-resolution scanned-probe microscope images

1993 ◽  
Vol 51 ◽  
pp. 522-523
Author(s):  
L. Fei
Keyword(s):  
Film Studies ◽  
Lattice Structure ◽  
Substrate Material ◽  
Repulsive Force ◽  
Instrument Calibration ◽  
Microscope Images ◽  
Probe Microscope ◽  
Electron Microscopes ◽  
Diffraction Patterns ◽  
Lattice Resolution

Scanned probe microscopes (SPM) have been widely used for studying the structure of a variety material surfaces and thin films. Interpretation of SPM images, however, remains a debatable subject at best. Unlike electron microscopes (EMs) where diffraction patterns and images regularly provide data on lattice spacings and angles within 1-2% and ∽1° accuracy, our experience indicates that lattice distances and angles in raw SPM images can be off by as much as 10% and ∽6°, respectively. Because SPM images can be affected by processes like the coupling between fast and slow scan direction, hysteresis of piezoelectric scanner, thermal drift, anisotropic tip and sample interaction, etc., the causes for such a large discrepancy maybe complex even though manufacturers suggest that the correction can be done through only instrument calibration.We show here that scanning repulsive force microscope (SFM or AFM) images of freshly cleaved mica, a substrate material used for thin film studies as well as for SFM instrument calibration, are distorted compared with the lattice structure expected for mica.

Three-Dimensional Subcellular Organization of Hepatocytes in Intact Liver: Simultaneous Visualization of Cytoskeletal and Membrane Markers by Confocal Microscopy

1996 ◽  
Vol 54 ◽  
pp. 288-289
Author(s):  
Greg V. Martin ◽  
Ann L. Hubbard
Keyword(s):  
Three Dimensional ◽  
Integral Membrane Proteins ◽  
Polarized Secretion ◽  
Microscope Images ◽  
Computer Aided ◽  
Intracellular Organelles ◽  
Cytoskeletal Elements ◽  
Simultaneous Visualization

The microtubule (MT) cytoskeleton is necessary for many of the polarized functions of hepatocytes. Among the functions dependent on the MT-based cytoskeleton are polarized secretion of proteins, delivery of endocytosed material to lysosomes, and transcytosis of integral plasma membrane (PM) proteins. Although microtubules have been shown to be crucial to the establishment and maintenance of functional and structural polarization in the hepatocyte, little is known about the architecture of the hepatocyte MT cytoskeleton in vivo, particularly with regard to its relationship to PM domains and membranous organelles. Using an in situ extraction technique that preserves both microtubules and cellular membranes, we have developed a protocol for immunofluorescent co-localization of cytoskeletal elements and integral membrane proteins within 20 µm cryosections of fixed rat liver. Computer-aided 3D reconstruction of multi-spectral confocal microscope images was used to visualize the spatial relationships among the MT cytoskeleton, PM domains and intracellular organelles.

Two-photon excitation fluorescence microscopy in living systems

1993 ◽  
Vol 51 ◽  
pp. 154-155 ◽  
Author(s):  
David W. Piston
Keyword(s):  
Confocal Microscopy ◽  
Fluorescence Microscopy ◽  
Singlet State ◽  
Excited Electronic State ◽  
Input Power ◽  
Two Photon ◽  
Simultaneous Absorption ◽  
Photon Excitation ◽  
Very High ◽  
Two Photon Excitation

Two-photon excitation fluorescence microscopy provides attractive advantages over confocal microscopy for three-dimensionally resolved fluorescence imaging. Two-photon excitation arises from the simultaneous absorption of two photons in a single quantitized event whose probability is proportional to the square of the instantaneous intensity. For example, two red photons can cause the transition to an excited electronic state normally reached by absorption in the ultraviolet. In our fluorescence experiments, the final excited state is the same singlet state that is populated during a conventional fluorescence experiment. Thus, the fluorophore exhibits the same emission properties (e.g. wavelength shifts, environmental sensitivity) used in typical biological microscopy studies. In practice, two-photon excitation is made possible by the very high local instantaneous intensity provided by a combination of diffraction-limited focusing of a single laser beam in the microscope and the temporal concentration of 100 femtosecond pulses generated by a mode-locked laser. Resultant peak excitation intensities are 106 times greater than the CW intensities used in confocal microscopy, but the pulse duty cycle of 10−5 maintains the average input power on the order of 10 mW, only slightly greater than the power normally used in confocal microscopy.

Routine Digital Processing of Microscope Images

1990 ◽  
Vol 48 (1) ◽  
pp. 550-551
Author(s):  
E. Wisse ◽  
A. Geerts ◽  
R.B. De Zanger
Keyword(s):  
Operating System ◽  
Digital Processing ◽  
Hard Disks ◽  
The Sun ◽  
Tape Drive ◽  
High Definition ◽  
Fluorescent Microscope ◽  
Microscope Images ◽  
Helical Scan ◽  
Ethernet Connection

The slowscan and TV signal of the Philips SEM 505 and the signal of a TV camera attached to a Leitz fluorescent microscope, were digitized by the data acquisition processor of a Masscomp 5520S computer, which is based on a 16.7 MHz 68020 CPU with 10 Mb RAM memory, a graphics processor with two frame buffers for images with 8 bit / 256 grey values, a high definition (HD) monitor (910 × 1150), two hard disks (70 and 663 Mb) and a 60 Mb tape drive. The system is equipped with Imaging Technology video digitizing boards: analog I/O, an ALU, and two memory mapped frame buffers for TV images of the IP 512 series. The Masscomp computer has an ethernet connection to other computers, such as a Vax PDP 11/785, and a Sun 368i with a 327 Mb hard disk and a SCSI interface to an Exabyte 2.3 Gb helical scan tape drive. The operating system for these computers is based on different versions of Unix, such as RTU 4.1 (including NFS) on the acquisition computer, bsd 4.3 for the Vax, and Sun OS 4.0.1 for the Sun (with NFS).

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