JEOL 733 Electron Microprobe

I ran the JEOL 733 electron microprobe at Victoria University of Wellington from 1996 until the end of 2008. This is the web page I created for that instrument. The JEOL JXA-733 Superprobe was replaced by a JEOL JXA-8230 Superprobe in 2009. Apparently this page is still of some use, so I have made some additions and corrections.

Updated 9th February 2018

Picture of JEOL 733 Electron Microprobe


The Microanalysis facility runs a JEOL 733 Electron Microprobe purchased in 1979. It has three wavelength dispersive X-ray spectrometers. In 2006 the Electron Microprobe was upgraded with new Moran Windows based software and control electronics. Previous upgrades occurred in 1992 and 1998. A digital image capture system has also been added.


The Electron Microprobe is used for:

  • Mineral identification along with help from optical microscopy and X-ray diffraction.
  • Detailed analysis of minerals in rocks.
  • Geothermometry and geobarometry. Temperatures and pressures of rock formation can be derived from the analysis of minerals.
  • Experimental petrology, for example element partitioning between adjacent phases after heating.
  • Tephra analysis where glass deposited from a volcanic eruption is identified from its analysis. Sediments can be dated in this way.
  • Particle analysis in sedimentology and environmental studies.
  • Searching for rare phases. The X-ray signal of an element of interest creates an image map.
  • Studies of fossil materials, limestone, shells and corals. Element distributions may be significant in economic applications such as the performance of building materials. Element ratios can be used to calculate past temperatures.
  • Cathodoluminescence shows trace element zones in sample such as zircons. Micro-textures and overgrowths are readily observed even if compositional differences are very small.
  • A STEM attachment allows transmitted electrons to be observed from samples mounted on standard TEM grids.
  • A preamplifier modification allows very small differences in backscattered electron signals to be observed. This means we can see very small compositional differences such as zoning in a crystal.
  • The Electron Microprobe is also a high quality Scanning Electron Microscope.

Electron Microprobe

An Electron Microprobe is a specialised Scanning Electron Microscope designed primarily for elemental analysis of polished surfaces such as rock and mineral thin sections. It does this by measuring the intensities and wavelengths of characteristic X-rays emitted from the point on the sample where a stationary electron beam is focused. The wavelength of the X-ray identifies the element, and its concentration is related to the X-ray intensity by a procedure called a ZAF calculation. The finely focused electron beam can also be scanned over the sample to generate a corresponding magnified image on a high resolution screen.


The characteristic X-rays are electromagnetic radiations of very short wavelength and high energy. They result from an incident primary electron ionising an inner shell electron in a sample atom. The excited atom relaxes when an outer electron fills the space. Energy is lost by emission of a characteristic X-ray. Secondary and backscattered electrons are also emitted which are separately detected for imaging purposes.

X-ray monochromators

The X-ray monochromators contain crystals with molecular layers which act like diffraction gratings. The spacing between layers (d spacing) and the X-ray wavelength determines the angle of diffraction. Low energy X-rays require large d spacings (STE below) and higher energy X-rays require smaller d spacings (LiF) to reach a detector set at a convenient angle. The crystal is oriented to send only the wavelength of interest to the detector. By moving a crystal and a detector along a 140 mm radius circle (Rowland circle) other wavelengths can be selected. Crystals used are LiF (lithium fluoride), PET (pentaerithritol), STE (lead stearate) and TAP (Thallium acid phthalate). The angular range is from 25 to 130 degrees (2 theta angle). The crystals are also set for an X-ray take-off angle of 40 degrees. This angle is measured from the sample surface to the axis from the analysis point on the sample to the spectrometer entrance slit.


Higher energy X-rays are detected with a sealed xenon filled detector with several hundred volts across it. The counter window is a very thin beryllium foil. An X-ray photon ionises the gas momentarily and causes a brief electrical pulse to be detected by a preamplifier and registered by computerised counting electronics. The total count accumulated over a fixed period corresponds to the X-ray intensity. The lower energy X-rays are detected with a proportional counter containing a flowing gas mixture of argon and 10% methane. This counter window is made from thin aluminised mylar. The purpose of the methane is to quench the electron cascade in the counter giving a short duration pulse. This allows high count rates to be measured


The Electron Microprobe is calibrated using standard minerals of known composition. For example Si and Ca are calibrated with a polished, carbon coated section of wollastonite. Some synthetic minerals such as titanium dioxide and alumina are also used. A wide range of standards are mounted on a standards bar which resides inside the instrument. The bar is periodically repolished and re-coated with carbon.

ZAF calculation

The counts are processed through a ZAF calculation which corrects for inelastic electron scattering and energy loss related to atomic number (Z), absorption of X-rays by the sample (A) and a fluorescence X-ray correction (F). Once these factors are accounted for a correct analysis is usually obtained after calibration. The calculation is complex and is part of the control computer program.


Electron back scattered images or X-ray maps can be obtained which may be further computer enhanced and coloured, if necessary, to reveal details such as zoning.

Optical microscope

The Electron Microprobe also has an coaxial polarising microscope set on the same axis as the electron beam. This is mainly used for focusing the sample using incident light and for selecting areas of high reflectance (polish) for analysis. Transmitted light viewing assists in selection of mineral phases. The coaxial polarising microscope magnifies 414 times and resolves 1 micron. A colour video camera produces an image at 1600 times on a colour monitor

Sample stage

Stage movements are X: 32mm, Y: 50mm, Z: 2mm and rotation to 4 positions. The working distance from the objective to the sample stage is set at 11mm.

Backscattered electron detector

The backscattered electron detector is primarily used for imaging samples because it responds to the average atomic number at the electron beam focus point. Regions with a high average atomic number show up as brighter regions. In silicate rock samples bright areas are often associated with increased iron content or the presence of sulphide or metallic ores. Backscattered electrons have higher energy compared with secondary electrons. They are emitted and detected at higher angles relative to the specimen plane. The emission results from elastic events between the incident electrons and bound electrons.

The backscattered electron detector preamplifier on our Microprobe has been modified to allow a fivefold gain increase for elements in the upper part of the periodic table (silicates, glasses). This modification has allowed small changes in compositional zoning to be imaged. Image processing allows even more subtle changes to be resolved.

Atomic Number vs Stage Current

Note: stage current (nA) = beam current (12nA) - backscattered electron current (nA).

Cathodoluminescence detector

Many samples produce light when stimulated by electrons. This is called cathodoluminescence. The intensity and colour of the light is often determined by small differences in trace element content, such as rare earths. Although the electron microprobe may not have the sensitivity to measure the trace elements directly the distribution can be observed by imaging with the light produced by cathodoluminescence. The photomultiplier detector can be placed to either observe light from above the sample using the incident light optical system, or from below using the transmitted light optical path. Both positions gather a good percentage of the available light so there are usually no problems with sensitivity. There is room to insert a filter if a specific light colour is of interest. In the longer term a monochromator may be added.

Sample preparation - slides

Normal petrographic slides, without cover slips, can be used for microprobe analysis. The slides are usually cut to a size of 28 x 48mm. The slides need to be polished well with regions of interest showing strong scratch free reflections when viewed using incident light microscopy.

Sample preparation - marking regions

The slide must be clean. Detergent in warm water followed by a distilled water rinse works well. Ethanol, isopropanol or petroleum ether can also be used on a cloth or tissue to wipe the slides clean. It is best to avoid fingerprints in the first place.

The regions of interest are circled with a black ink pen.Indian ink is ideal. The circles are linked by arrowed lines. The first line should lead in from the edge of the slide and the last line should finish with an arrow at another point on the edge. Each line should be crossed with marks using roman numerals, I, II, III, IV, V, VI, VII, VIII,etc. Alternatively the circles can be numbered with small numerals close to each circle. Block mounted samples can be scribed with a fine point in the same way. Circles should be small, a few mm across, as the minimum magnification , on screen, is 40 times.

Slide scanner

A slide scanner is available for scanning whole slides in plain light. A modified photographic slide mount holds standard 28x48mm slides.

Sample preparation - blocks

Granular samples can be mounted in 25mm diameter epoxy blocks using standard plastic moulds. The grains are sprinkled across the base of the mould. Epoxy is poured in to a level of about 20mm. The grains are bisected on a diamond lap and polished to a high standard. If a number of different grain types are to be analysed then a pre-drilled epoxy block may be used with 6 holes 5-6 mm in diameter set around the edge and one in the middle. One face is cut flat, This face is stuck on a glass or perspex plate with wide double sided tape. The grains are placed in the bottom of the holes using a small funnel to avoid cross contamination.

Epoxy is dripped into the holes using a small stick until the holes are completely filled. When set the block is removed from the double sided tape and polished after bisecting the grains. Do not substitute perspex rod sections for the epoxy blocks.Problems with degassing, sample insulation and charging are likely. Blocks can also be set onto petrographic slides. They are then cut and polished to the same thickness as petrographic sections.

Sample preparation - examination

To obtain the best use of your time on the Microprobe a preliminary examination of the sample with an optical microscope is necessary. An incident light examination ensures that the region of interest is well polished and suitable for probing. Colour, with or without polars, can assist in selecting regions of interest. A transmitted and polarised transmitted light examination can be used to select minerals and zones of interest.

Sample preparation - carbon coating

Samples need to be coated with a carbon film of a standard 25nm thickness to make the surface conductive. This prevents the sample charging up and reducing the effective electron energy. The coating is deposited in a high vacuum chamber by electrically heating a narrow carbon rod. A polished brass plate is also coated. A royal blue interference colour on the plate corresponds to a coating thickness of 25 nm.The coating quality is important for successful analyses. For this reason coating should be done here as the thickness will be the same as on our standards. The coated sample is connected to the brass sample holder by a combination of metallised tape and a silver based paint.

Analysis programs

The following includes program elements and typical probe conditions. Settings depend on sample type, size and stability with the beam induced temperature rise. There are many other special purpose programs.

  • SILICATES: F Na Mg Al Si P S Cl K Ca Ti Cr Mn Fe Co Ni Zn Sr Ba Zr V. Electron energy 15kV, beam current 6 to 12 nano-amps (recorded on printout), beam spot size less than 1 micron up to 30 micron.
  • TEPHRAS: Na Mg Al Si K Cl Ca Ti Cr Mn Fe Ni. Electron energy 15kV, beam current 6 to 8 nanoamps (recorded on printout), beam spot size from 10 micron up to 30 micron. Alkali elements are run first to reduce changes from electron beam heating during analysis.
  • SULPHIDES: S Mn Fe Co Ni Cu Zn As Se Mo Pd Ag Cd Sb Te Pt Au Hg Pb Bi. Electron energy 25kV, beam current 6 to 15 nanoamps (recorded on printout), beam spot size from less than 1 micron up to 30 micron.
  • SYNTHETIC GLASSES: F Na Al Si Zr Ba La Ti Ca Cr. Electron energy 15kV, beam current 6 to 12 nanoamps (recorded on printout), beam spot size less than 1 micron up to 30 micron.

Picture of JEOL 733 Electron Microprobe



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Biotite, backscattered electron image Biotite, backscattered electron image

X-ray spectrometer X-ray spectrometer

X-ray proportional counter X-ray proportional counter

Clinopyroxene, backscattered electron image Clinopyroxene, backscattered electron image

Zoned garnet Zoned garnet, backscattered electron image

Cathodoluminescence image of zircon Cathodoluminescence image of zircon

Marked up slide Marked up slide, circular polarised light image

Drilled Block mounted on slide Drilled Block mounted on slide

Block mounted on slide after cutting, polishing and carbon coating Block mounted on slide after cutting, polishing and carbon coating

Ant, Secondary Electron image Ant, Secondary Electron image

Ant upper leg, Secondary Electron image Ant upper leg, Secondary Electron image