Click VENT to vent the chamber, load the samples onto the stage and shut the chamber door immediately.

VENT

PUMP

HT

SNAPSHOT

LIVE VIEW

CAPTURE

FOCUS

   

   

WD

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AUTO BRIGHTNESS

& CONTRAST

IMAGE TILT CORRECTION

SURFACE
CROSS SECTION
DYNAMIC FOCUS
TILT CORRECTION

CENTRE STAGE

CENTRE FEATURE

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e beam view navigation photo

20µm

ion beam view CCD view

20µm

HT

SNAPSHOT

LIVE VIEW

CAPTURE

FOCUS

AUTO BRIGHTNESS & CONTRAST

BEAM SHIFT

DELETE PATTERN

hr min sec

REMAINING TIME

00 : 00 : 00
Pt Needle

PATTERN CONTROL

START

Loading resources

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The specimen chamber is maintained at high vacuum except during loading and unloading samples.

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The next step is to move the sample into the eucentric position. The eucentric height for this simulator is 7mm. Bring the sample to this position by adjusting the WD to 7mm.
Different instruments can have slightly different Eucentric Heights.

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  • What is Microscopy?
  • Why do microscopy?
  • Magnification
  • Magnification and measurement
  • Resolution
  • Depth of field
  • Electromagnetic Spectrum
  • Introduction to the Electromagnetic Spectrum
  • Wavelength, frequency and energy
  • Electromagnetic spectrum and microscopy
  • Interactions with Matter
  • Lenses and Aberrations
  • Lenses
  • Aberrations
  • Types of aberration
  • Overcoming aberrations
  • Calibrations
  • Nyquist Sampling
  • Detectors and Cameras
  • Digital Images
  • Introducing digital images
  • Images for Print in Journals and Posters
  • Images for Presentation
  • Colour enhancement
  • Image Ethics
  • Credits
  • What is SEM?
  • Background information
  • SEM Basics
  • Applications and uses of SEM
  • What can it do differently to a light microscope?
  • What can’t it do?
  • How does an SEM work?
  • Structure of an SEM
  • The electron gun
  • How the gun works
  • Electron sources
  • Filament saturation
  • The vacuum system
  • Vacuum system overview
  • Types of pumps
  • Vacuum requirements
  • Water chilling system
  • Structure of the column
  • The specimen chamber
  • Beam/specimen interactions
  • The image
  • How do I get a good image?
  • A basic guide to using an SEM
  • Specimen preparation
  • Accelerating voltage
  • Apertures
  • Spot size
  • Working distance
  • Contrast and brightness
  • Magnification and calibration
  • Scan rate and signal to noise
  • Image artefacts and trouble-shooting
  • Specialised SEM techniques
  • CL
  • ESEM
  • Cryo-SEM - Cold stage
  • FIB
  • EDS
  • EBSD
  • EBL
  • Backscatter
  • Credits
  • What is TEM?
  • Introduction to TEM
  • Key advantages
  • What the TEM can do
  • What the TEM can't do
  • How does a TEM work?
  • Overview of TEM workings
  • Instrument design
  • Resolution
  • Components of a TEM
  • Introducing TEM components
  • Vacuum system
  • Electron gun
  • Electron column
  • Electromagnetic lenses
  • Specimen/sample chamber
  • Image capture
  • Detectors
  • How images are formed
  • Image formation basics
  • Image types
  • Bright-field images
  • Dark-field images
  • Diffraction
  • How do I get a good image?
  • Instrument alignment
  • Getting started with instrument alignment
  • Condenser lens centre
  • Condenser lens stigmation
  • The eucentric position
  • Focus
  • Use of objective appertures
  • Final adjustment
  • Problems with lenses and alignments
  • Types of problems
  • Spherical aberration
  • Chromatic aberration
  • Astigmatism
  • Understanding instrument settings
  • Specimen preparation
  • Introduction to specimen preparation
  • Specimen holders
  • Organic (soft) samples
  • Getting started with organic samples
  • Ultramicrotomy
  • Immunolabelling
  • Staining
  • Cryo-fixation
  • Chemical fixation
  • Dehydration
  • Infiltration
  • Polymerisation
  • Grid mounting
  • Negative staining
  • Cryo-substitution
  • Low temperature polymerisation
  • Freezing methods
  • Cryo-ultramicrotomy
  • Cryo-transfer
  • Freeze-etch
  • Replica
  • Inorganic (hard) samples
  • Sample prep flow chart
  • Powders
  • Preparing from the bulk
  • Dimpling
  • Mechanical polishing
  • Electro-polishing
  • Ion beam thinning
  • Focussed ion beam milling
  • Artifacts
  • Specialised TEM techniques
  • Cryo - TEM
  • Introduction to Cryo
  • Why Cryo TEM?
  • The freezing process
  • Diffraction
  • Introduction to diffraction
  • Image appearance
  • The diffracted beam
  • Tilting
  • Camera length
  • Kikuchi patterns
  • Selected area diffraction (SAD)
  • Ring patterns
  • Convergent beam electron diffraction (CBED)
  • Dark-field imaging
  • High resolution imaging
  • What is high resolution imaging?
  • Scanning TEM (STEM)
  • Bright field STEM
  • Beam–sample interactions
  • Use of ronchigrams in STEM
  • STEM detectors
  • High-angle-annular dark-field (HAADF)
  • Energy dispersive spectroscopy (EDS)
  • Introduction to EDS
  • Quantification of EDS data
  • Electron energy loss spectroscopy (EELS)
  • Credits
  • Introduction
  • Basics
  • What makes an objective good?
  • Aberrations
  • Light microscopy
  • The complete microscope
  • Koehler illumination
  • The light path and microscope
  • Performing Koehler illumination
  • Transmitted Light Imaging
  • What is Brightfield imaging?
  • Microscope components for transmitted light imaging
  • Light Path for BF microscopy
  • Types of transmitted light imaging
  • The five techniques
  • Bright field
  • Dark field microscopy
  • Phase contrast
  • Differential interference contrast imaging (DIC or Nomarski imaging)
  • Polarised light microscopy
  • Reflected light imaging
  • Fluorescence microscopy
  • What is Fluorescence imaging?
  • The light path and microscope parts
  • Confocal microscopy
  • What is Confocal imaging?
  • A practical confocal microscope
  • Components of the confocal microscope
  • Laser
  • Filters
  • Photomultiplier tubes (PMTs)
  • Practical image acquisition
  • Adjustments
  • The eternal triangle
  • What is important?
  • The Confocal Pinhole
  • Scanning and resolution
  • How scanning works
  • Scan areas and relationship to pixels and resolution
  • Zoom
  • Detection parameters
  • Laser power
  • Adjusting the Image and Detector Controls
  • Averaging
  • Sequential and simultaneous imaging
  • Using multiple dyes
  • Fluorescence Spectra
  • Fluorescence Spectral Overlap
  • Simultaneous Imaging
  • Sequential Imaging
  • Collecting Z stacks
  • What is a Z-stack?
  • Optical Section Thickness
  • Nyquist Sampling for Z stacks
  • Under and Over Sampling in Z Stacks
  • Projections
  • Image rotations
  • Axial resolution and Optical section thickness
  • Super-Resolution Microscopy
  • The power of Super-Resolution
  • Criteria for optical resolution
  • Advantages of higher resolved images
  • STED/RESOLFT techniques
  • Overview to STED/RESOLFT
  • STED
  • Introduction to STED
  • The Photo-physical Principle
  • Resolution in STED microscopy
  • RESOLFT
  • Single molecule localisation techniques
  • One point at a time
  • PALM
  • dSTORM / GSDIM
  • STORM
  • PAINT and DNA PAINT
  • 3D-SMLM
  • Sample preparation for Super-Resolution Microscopy
  • General Considerations
  • Sample preparation
  • Sample fixation
  • Properties of labels
  • Live-cell Imaging
  • Labeling via affinity probes
  • Sample preparation for STED microscopy
  • Fluorophores and strategies for fixed samples
  • Live-cell STED Imaging
  • Sample preparation for PALM
  • Fluorophores and their properties
  • Sample preparation for dSTORM
  • Fluorophores and strategies for fixed samples
  • Super-Resolution Image Acquisition
  • STED
  • The optical path of a STED microscope
  • STED Imaging
  • SMLM
  • The optical path of a SMLM microscope
  • Imaging strategies for dSTORM
  • Blinking fluorophores
  • Laser power
  • Buffer
  • UV Light
  • Exposure time
  • Image reconstruction from SMLM data
  • Credits
  • What is Cryo-EM?
  • Introduction to cryo techniques
  • Why cryo?
  • Which cryo technique to use
  • Challenges of cryo
  • Principles of freezing
  • Properties of water
  • Freezing of water
  • Types of freezing
  • Plunge freezing
  • High pressure freezing
  • Other freezing techniques
  • Cryo-TEM
  • Introducing cryo-TEM
  • The cryo TEM
  • The microscope
  • Electron energy filters
  • Phase plates
  • Electron detectors
  • Imaging in a cryo-TEM
  • How images are formed
  • Fourier Transformation
  • Why do Fourier transforms
  • What is a Fourier Transform?
  • Fourier transforms in cryo-TEM image processing
  • The power spectrum
  • Why do we even need to look at the power spectrum?
  • Contrast transfer function
  • Single particle analysis
  • Introducing Single Particle Analysis
  • Biochemical preparation and stabilisation
  • Specimen screening by negative staining
  • Vitrification
  • Optimisation of orientation and distribution
  • Specimen screening by cryo
  • Data acquisition
  • Motion correction
  • Dose weighting
  • Averaging
  • Particle picking
  • 2D classification
  • 3D reconstruction
  • Validation
  • Sub-tomogram averaging
  • Cryo-tomography (cryo-ET)
  • Introducing cryo-electron tomography
  • The TEM for cryo-ET
  • Phase plates
  • Sample preparation
  • Data acquisition
  • Tomogram reconstruction
  • Tomogram interpretation
  • Sub-tomogram averaging
  • Introducing sub-tomogram averaging
  • Particle picking
  • Sub-tomogram averaging and alignment
  • Sub-tomogram classification
  • Model refinement and validation
  • Electron crystallography
  • Diffraction-based Cryo-EM Techniques
  • 2D crystallography
  • Introducing Micro-ED
  • The sample for Micro-ED
  • Sample preparation for Micro-ED
  • The TEM for Micro-ED
  • Sample screening for Micro-ED
  • Data collection – Micro-ED
  • Data analysis – Micro-ED
  • Cryo-SEM
  • Introducing cryo-SEM
  • Cryo-SEM design
  • Sample preparation – Freezing & cryo-transfer
  • Sample preparation – Fracturing and cryo-planing
  • Sample preparation – Sublimation
  • Sample preparation – Coating
  • Cryo-SEM operation
  • Cryo-SEM microanalysis
  • Cryo-SEM artefacts
  • Cryo-FIB
  • Introducing cryo-FIB
  • TEM lamella production by cryo-FIB
  • Cryo-FIB-SEM Volume Imaging
  • Cryo-ultramicrotomy
  • Credits
  • Introduction to XRD
  • XRD basics
  • Interesting facts
  • Nobel prizes for research with X-rays
  • Background information
  • X-rays Overview
  • Properties of X-rays
  • Production of X-rays
  • The geometry of crystals
  • Crystal structure
  • Miller Indices
  • Principles of diffraction
  • Wave structure
  • Interaction of X-rays with matter
  • Diffraction of X-rays by a crystal
  • Penetration depth
  • Diffraction measurements
  • XRD in practice
  • Anatomy of an X-ray diffractometer
  • Anatomy of an X-ray diffractometer - Intro
  • Source
  • Primary optics
  • Sample holder & stage
  • Secondary optics
  • Sample preparation
  • Types of samples
  • What is good data?
  • The importance of specimen height
  • Safety
  • Analysis of data
  • What the data tells you
  • Phase identification
  • Quantitative powder diffraction
  • Quantitative analysis
  • Factors affecting peak intensity
  • Factors affecting peak intensity - Intro
  • Structure Factor
  • Multiplicity factor
  • Lorentz polarisation factors
  • Temperature Factor
  • Summation of factors effecting peak intensity
  • Factors effecting peak width
  • Rietveld Refinement
  • What is Rietveld refinement?
  • Summary of analysis cues
  • Specialist techniques using XRD
  • Texture
  • What is texture?
  • Displaying texture
  • Measuring texture with X-rays
  • Normalisations
  • Residual stress
  • Glancing Angle XRD
  • Glancing angle XRD
  • Credits
  • Introduction
  • Welcome
  • What is microanalysis?
  • Background information
  • What is energy dispersive spectroscopy?
  • Outputs from EDS analysis
  • X-ray generation
  • Generation of X-rays in the electron microscope
  • Bremsstrahlung X-ray generation
  • Kramer's law
  • Characteristic X-rays
  • Characteristic X-ray generation
  • Nomenclature
  • The X-ray spectrum
  • Moseley's law
  • X-ray intensity
  • Intensity basics
  • Fluorescence yield
  • X-ray absorption
  • X-ray detection
  • X-ray detection by EDS
  • The detector
  • The pulse processor
  • The multi-channel analyser or display
  • Care and calibration
  • EDS spectral resolution
  • EDS spectral artefacts
  • Qualitative EDS
  • Qualitative EDS X-ray microanalysis using SEM and TEM
  • X-ray peak identification
  • Quantitative EDS
  • Quantitative EDS - overview
  • Limitations of quantitative analysis
  • Standardized quantitative analysis
  • Spectral processing
  • Concentration calculation
  • Accuracy of EDS
  • Accuracy, precision and detection limits
  • Random and systematic errors
  • X-ray mapping
  • Mapping information
  • Parameters for X-ray mapping
  • Artefacts in X-ray mapping
  • Credits
  • What is APT?
  • Background Information
  • Overview
  • Applications of APT
  • What can APT do differently?
  • What can't APT do?
  • A brief history of APT
  • How does APT work?
  • Intro to the technique
  • The principle of APT
  • Two flight path options
  • Position of atoms within the sample
  • Atomic position in the sample
  • Chemical identification
  • 3D data visualisation
  • Laser-assisted APT
  • Spatial resolution of APT
  • Mass resolution of APT
  • Essential parts of an Atom Probe
  • The vacuum system
  • Handling and transferring samples
  • The local electrode
  • Ion detection
  • The voltage control system
  • The Laser system
  • The cryogenic system
  • The control system
  • How do I get good APT data?
  • Specimen preparation
  • Specimen requirements
  • Two main techniques
  • Electropolishing
  • Focused Ion Beam (FIB)
  • Sample insertion in the atom probe
  • Mounting the sample
  • Inserting the sample in the atom probe
  • Specimen coarse alignment
  • Collecting data
  • Data quality
  • Experimental parameters
  • Voltage mode acquisition
  • Laser mode acquisition
  • End of data acquisition
  • Data processing and reconstruction
  • Data processing steps
  • Selection of ion sequence range
  • Selection of region of interest (ROI)
  • Time of flight corrections
  • Mass calibration
  • Ranged-ion assignment
  • Reconstruction
  • Key reconstruction parameters
  • How do I analyse APT data
  • Mass spectral analysis
  • Concentration space analysis
  • Grid voxelisation
  • Interfaces
  • Proxigram analysis
  • Solute analysis / Clustering
  • Spatial distribution maps
  • Specialised APT techniques
  • Field Ion Microscopy
  • Correlative SEM / APT
  • Cryogenic transfer capabilities
  • Credits
  • What is FIB?
  • FIB overview
  • Common applications of FIB
  • Ion sources
  • Ion–Solid Interactions
  • Introduction to ion solid interactions
  • How many ions?
  • Interaction Overview
  • Dislocation/Displacements
  • Ion Implantation
  • Secondary Electrons
  • Secondary Ions, Backscattered Ions and Phonons
  • Energy loss
  • Collision Cascade
  • Sputtering
  • Sputtering Overview
  • Sputtering Yield
  • How does a FIB-SEM work?
  • Overview
  • Components of FIB
  • Introduction to components
  • Vacuum system and Chamber
  • SEM and FIB columns
  • Imaging and Analytical Detectors
  • Sample Stage
  • Gas Injectors
  • Manipulators
  • Geometry
  • Concepts
  • Stage Tilt
  • Beam Geometry
  • Imaging Artefacts
  • Eucentric Height
  • Coincidence Point
  • Applications
  • Ion Beam Imaging
  • Image Formation
  • Charging
  • Channeling Contrast
  • Destructive Imaging
  • Milling
  • Patterning Mechanism
  • Patterning Parameters
  • Patterning Parameters
  • Acceleration Voltage
  • Aperture/Beam current
  • Passes/Dwell time
  • Overlap/Pitch
  • Scan Direction
  • Beam Alignments
  • Artefacts
  • Introduction to Artefacts
  • Curtaining
  • Redeposition
  • Implantation
  • Phase Transformations
  • Amorphization
  • Interface Mixing
  • Heat damage
  • Channeling
  • Deposition
  • Cross-sectioning
  • Introduction to cross-sectioning
  • Tips and Tricks
  • TEM-lamella preparation
  • Intro to TEM-lamella preparation
  • Process Steps
  • Deposition of protective layer
  • Prepare Lamella via cross-sectioning
  • J-cut
  • Lift-out
  • Thinning
  • Polishing
  • 3D Tomography
  • Credits
  • Introduction
  • AFM
  • Background information
  • Imaging: Interactions
  • What can you measure?
  • Imaging modes
  • Intro
  • Contact mode
  • Tapping mode
  • Non-contact mode
  • Specimen
  • Specimen choice
  • Contact and tapping modes
  • Non-contact mode
  • Data display
  • Artefacts
  • Image artefacts
  • Tip artefacts
  • Scanner artefacts
  • AFM in practice
  • Laser alignment
  • Laser alignment on cantilever
  • Cantilever tuning
  • Image quality optimisation
  • Scan rate
  • Gains
  • Set-point
  • Contact mode
  • Tapping mode
  • Feedback
  • Control signal
  • Control modes
  • Discontinuous
  • Continuous
  • Proportional control (P)
  • Integral control
  • Derivative control
  • Composite control (PID)
  • Other Techniques
  • Scanning Tunneling Microscopy (STM)
  • Near-field scanning optical microscope (NSOM/SNOM)
  • Tip enhanced Raman spectroscopy (TERS)
  • Credits
  • Introduction to SIMS
  • What is SIMS?
  • Mass analysers in SIMS
  • Applications of SIMS
  • Basic principles of SIMS
  • Ion–Sample Interactions
  • Static vs dynamic SIMS
  • ToF-SIMS
  • Primary-Ion Sources for ToF-SIMS
  • Liquid-Metal Ion Guns
  • Cluster Sources
  • Pulsing
  • Bunching
  • Collection optics
  • Time of Flight analysers – overview
  • Inside the analysers
  • Inside the ToF analyser
  • Reflectron-TOF
  • ESA TOF
  • Detectors
  • Data
  • Sample preparation
  • Sample requirements for ToF-SIMS
  • Powders
  • Suspensions and solutions
  • Applications of ToF-SIMS
  • Typical applications
  • Pharmaceutical science
  • Geology and mineralogy
  • Forensics
  • Large Geometry SIMS and NanoSIMS
  • Common features
  • Common features of the Large Geometry and NanoSIMS
  • Primary Ions and Primary column
  • Sample chamber and stage
  • Dynamic mode
  • Secondary column
  • Double focussing mass spectrometer - overview
  • Inside the mass spectrometer
  • Electrostatic analyser
  • Magnetic sector analyser
  • Collection system
  • Magnetic sector analyser operation
  • Detectors
  • Sample preparation for LG and Nano-SIMS
  • LG-SIMS - specific capabilities
  • Benefits of LG-SIMS
  • Data Output from LG-SIMS
  • Instrument performance
  • Calibration
  • Matrix effect
  • LG-SIMS for isotope geochemistry
  • Applications of LG-SIMS in geoscience
  • LG-SIMS for Nuclear Safeguards and Forensics
  • NanoSIMS - high resolution imaging mass-spectrometry
  • Benefits of Nano-SIMS
  • NanoSIMS applications
  • NanoSIMS – Cancer therapeutics
  • NanoSIMS – Environmental processes
  • NanoSIMS – Medical
  • NanoSIMS – Geology
  • NanoSIMS – Materials Science
  • Credits
  • What is research data?
  • Introduction to research data management
  • Maintaining quality and integrity
  • Benefits of managing research data
  • FAIR data principles
  • What is FAIR data?
  • The FAIR principles explained
  • Persistent identifiers
  • Are FAIR data and open data the same?
  • The CARE principles
  • What are CARE principles?
  • What are Indigenous data?
  • The CARE principles explained
  • Be FAIR and CARE
  • FAIR and CARE are complementary
  • Global guidelines
  • Research data management plans
  • Credits
  • Introduction
  • Typical hazards at a microscopy facility
  • Your specimen
  • Microscopy specimen preparation
  • Microscope operation
  • Local rules
  • Supporting documentation
  • Summary
  • Credits
  • Microscopy Concepts
  • Scanning Electron Microscopy
  • Transmission Electron Microscopy
  • Light & Fluorescence Microscopy
  • Cryo-Electron Microscopy
  • X-ray Diffraction
  • Energy Dispersive Spectroscopy
  • Atom Probe Tomography
  • Focused Ion Beam
  • Scanning Probe & Atomic Force Microscopy
  • Work Health and Safety
  • Research Data Management
  • SEM Simulator
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