Foundations of Confocal Scanned Imaging in Light Microscopy -- Fundamental Limits in Confocal Microscopy -- Special Optical Elements -- Points, Pixels, and Gray Levels: Digitizing Image Data -- Laser Sources for Confocal Microscopy -- Non-Laser Light Sources for Three-Dimensional Microscopy -- Objective Lenses for Confocal Microscopy -- The Contrast Formation in Optical Microscopy -- The Intermediate Optical System of Laser-Scanning Confocal Microscopes -- Disk-Scanning Confocal Microscopy -- Measuring the Real Point Spread Function of High Numerical Aperture Microscope Objective Lenses -- Photon Detectors for Confocal Microscopy -- Structured Illumination Methods -- Visualization Systems for Multi-Dimensional Microscopy Images -- Automated Three-Dimensional Image Analysis Methods for Confocal Microscopy -- Fluorophores for Confocal Microscopy: Photophysics and Photochemistry -- Practical Considerations in the Selection and Application of Fluorescent Probes -- Guiding Principles of Specimen Preservation for Confocal Fluorescence Microscopy -- Confocal Microscopy of Living Cells -- Aberrations in Confocal and Multi-Photon Fluorescence Microscopy Induced by Refractive Index Mismatch -- Interaction of Light with Botanical Specimens -- Signal-to-Noise Ratio in Confocal Microscopes -- Comparison of Widefield/Deconvolution and Confocal Microscopy for Three-Dimensional Imaging -- Blind Deconvolution -- Image Enhancement by Deconvolution -- Fiber-Optics in Scanning Optical Microscopy -- Fluorescence Lifetime Imaging in Scanning Microscopy -- Multi-Photon Molecular Excitation in Laser-Scanning Microscopy -- Multifocal Multi-Photon Microscopy -- 4Pi Microscopy -- Nanoscale Resolution with Focused Light: Stimulated Emission Depletion and Other Reversible Saturable Optical Fluorescence Transitions Microscopy Concepts -- Mass Storage, Display, and Hard Copy -- Coherent Anti-Stokes Raman Scattering Microscopy -- Related Methods for Three-Dimensional Imaging -- Tutorial on Practical Confocal Microscopy and Use of the Confocal Test Specimen -- Practical Confocal Microscopy -- Selective Plane Illumination Microscopy -- Cell Damage During Multi-Photon Microscopy -- Photobleaching -- Nonlinear (Harmonic Generation) Optical Microscopy -- Imaging Brain Slices -- Fluorescent Ion Measurement -- Confocal and Multi-Photon Imaging of Living Embryos -- Imaging Plant Cells -- Practical Fluorescence Resonance Energy Transfer or Molecular Nanobioscopy of Living Cells -- Automated Confocal Imaging and High-Content Screening for Cytomics -- Automated Interpretation of Subcellular Location Patterns from Three-Dimensional Confocal Microscopy -- Display and Presentation Software -- When Light Microscope Resolution Is Not Enough:Correlational Light Microscopy and Electron Microscopy -- Databases for Two- and Three-Dimensional Microscopical Images in Biology -- Confocal Microscopy of Biofilms — Spatiotemporal Approaches -- Bibliography of Confocal Microscopy.

Handbook of biological confocal microscopy

http://xrm.phys.northwestern.edu/research/pdf_papers/2004/egerton_micron_2004.pdf

Radiation damage in the TEM and SEM.

Beams of electrons and ions are now fairly routinely focused to dimensions in the nanometer range. Since the beams can be used to locally alter material at the point where they are incident on a surface, they represent direct nanofabrication tools. The authors will focus here on direct fabrication rather than lithography, which is indirect in that it uses the intermediary of resist. In the case of both ions and electrons, material addition or removal can be achieved using precursor gases. In addition ions can also alter material by sputtering (milling), by damage, or by implantation. Many material removal and deposition processes employing precursor gases have been developed for numerous practical applications, such as mask repair, circuit restructuring and repair, and sample sectioning. The authors will also discuss structures that are made for research purposes or for demonstration of the processing capabilities. In many cases the minimum dimensions at which these processes can be realized are considerably larger than the beam diameters. The atomic level mechanisms responsible for the precursor gas activation have not been studied in detail in many cases. The authors will review the state of the art and level of understanding of direct ion and electron beam fabrication and point out some of the unsolved problems.

/pdf/gas-assisted-focused-electron-beam-and-ion-beam-processing-2wl9i66zrn.pdf

Gas-assisted focused electron beam and ion beam processing and fabrication

This paper surveys experimental results concerned with secondary electron emission of surfaces bombarded by primary electrons with respect to scanning electron microscopy. The energy distribution, the angular distribution, and the yield of secondary electrons from metals and insulators are reviewed as well as the escape depth of the secondary electrons and the contribution of the backscattered electrons to the secondary electron yield. The different detectors for secondary electrons in the scanning electron microscope are described. The contrast mechanisms in the scanning electron microscope, material, topography, voltage, magnetic, and crystallographic orientation contrast based on secondary electron emission, as well as the lateral resolution, depending among other things on the spatial distribution of the emitted secondary electrons, are discussed.

Secondary electron emission in the scanning electron microscope

In a scanning electron microscope (SEM) an electron beam sets up an omni-directional source of scattered electrons within a specimen. Diffraction of these electrons will occur simultaneously on all lattice planes in the sample and the backscattered electrons (BSE), which escape from the specimen, will form a diffraction pattern that can be imaged on a phosphor screen. This is the basis of electron backscatter diffraction (EBSD). Similar diffraction effects cause individual grains of different orientations to give different total BSE. SEM images that exploit this effect will show orientation contrast (OC). EBSD and OC imaging are SEM-based crystallographic tools. EBSD enables measurement of the crystallographic orientation of individual rock-forming minerals as small as 1 mu m, and the calculation of misorientation axes and angles between any two data points. OC images enable mapping of all misorientation boundaries in a specimen and thus provide a location map for EBSD analyses. EBSD coupled to OC imaging in the SEM enables complete specimen microtextures and mesotextures to be determined. EBSD and OC imaging can be applied to any mineral at a range of scales and enable us to expand the microstructural approach, so successful in studies of quartz rocks, for example, to the full range of rock-forming minerals. Automated EBSD analysis of rocks remains problematic, although continuing technical developments are enabling progress in this area. EBSD and OC are important new tools for petrologists and petrographers. Present and future applications of EBSD and OC imaging include phase identification, studying deformation mechanisms, constraining dislocation slip systems, empirical quantification of microstructures, studying metamorphic processes, studying magmatic processes, and constraining geochemical microsampling. In all these cases, quantitative crystallographic orientation data enable more rigorous testing of models to explain observed microstructures.

/pdf/the-application-of-electron-backscatter-diffraction-and-4zs27kbzgg.pdf

The application of electron backscatter diffraction and orientation contrast imaging in the SEM to textural problems in rocks

Measuring the backscattering coefficient and secondary electron yield inside a scanning electron microscope

Measurements of the electron range R, and the backscattering coefficient η and the secondary electron yield δ at normal and tilted incidence for different elements show characteristic differences for electron energies in the range of 0.5 to 5 keV, compared with energies larger than 5 keV. The backscattering coefficient does not increase monotonically with increasing atomic number; for example, the secondary electron yield shows a lesser increase with increasing tilt angle. This can be confirmed in back-scattered electron (BSE) and secondary electron (SE) micrographs of test specimens.

The results are in rather good agreement with Monte Carlo simulations using elastic Mott cross-sections and a continuous-slowing-down model with a Rao Sahib-Wittry approach for the stopping power at low electron energies. Therefore, this method can be used to calculate quantities of BSE and SE emission, which need a larger experimental effort. Calculations of the angular distribution of BSEs show an increasing intensity with increasing atomic number at high takeoff angles than expected from a cosine law that describes the angular characteristics at high electron energies. When simulating the energy distribution of BSEs, the continuous-slowing-down model should be substituted by using an electron energy-loss spectrum (EELS) that considers plasmon losses and inner-shell ionizations individually (single-scattering-function model). The EELS can be approached via the theory for aluminium or from EELS spectra recorded in a transmission electron microscope for other elements.

Measurements of electron range Rα En of 1 to 10 keV electrons are obtained from transmission experiments with thin films of known mass thickness. In agreement with other authors the exponent n is lower than at higher electron energies.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/sca.4950150102

Electron-specimen interactions in low-voltage scanning electron microscopy

Operation modes of electron spectroscopic imaging and electron energy-loss spectroscopy in a transmission electron microscope

Calculation and tabulation of mott cross‐sections for large‐angle electron scattering

Solutions of the stationary and time-dependent equations of diffusion are presented for contamination when scanning a rectangular area in the scanning electron microscope (SEM). A method is described to record the thickness of the contamination layer by the signal of secondary or backscattered electrons and to measure the influence of electron current density, beam energy, and specimen cooling on the contamination rate.

Ludwig Reimer

Papers

Measuring the backscattering coefficient and secondary electron yield inside a scanning electron microscope

Electron-specimen interactions in low-voltage scanning electron microscopy

Operation modes of electron spectroscopic imaging and electron energy-loss spectroscopy in a transmission electron microscope

Calculation and tabulation of mott cross‐sections for large‐angle electron scattering

Contamination in a scanning electron microscope and the influence of specimen cooling