Microanalysis That’s Out of This World!

Dr. Jonathan Lee, Application Scientist, Gatan

Working as a cathodoluminescence (CL) application scientist at Gatan, I observe a great variety of interesting specimens from semiconductor devices, plastics, and geological samples to novel nanoscale optical devices demonstrating the capabilities of the Monarc® Pro CL detector. In case you don’t know, CL is the visible, ultraviolet, and infrared light emitted by many specimens in the scanning electron microscope (SEM). Recently, I was contacted regarding a meteorite sample and asked what analysis I could demonstrate using CL. As a physicist and amateur astronomer, I was naturally very excited at the rare opportunity to analyze something that literally came from out of this world! You might say I was… over the moon !

The sample is a thin-section from a meteorite collected from Antarctica – Miller Range 090010, you can read more about the classification here: Meteoritical Bulletin: Entry for Miller Range 090010 ( Likely to have been a constituent of the asteroid belt, our specimen had a trajectory that eventually led it to fall to Earth. The study of these meteorites allows us to understand more about the age and history of our solar system. Given the origins and unusual conditions experienced by meteorites, the microstructure can be incredibly complex, but often, chondritic meteorites like this one contain calcium aluminum inclusions (CAIs) and corundum grains which are among the first solids to condense from the solar nebula! Now, before I get wrapped up with the Cosmic Calendar, let’s take a look at our specimen!

Figure 1. Image overlay from a CAI region of meteorite specimen (gray) secondary electron and (green) unfiltered CL.

CL revealed so much new information, and this was an exciting first result! For geological specimens, unfiltered CL images can be very useful to reveal mineral texture, but the real nitty-gritty information is found in the spectrum. So many of the grains showed such strong luminescence that I was eager to learn more.

Our friends at EDAX recently installed an Octane Elite Energy Dispersive Spectroscopy (EDS) Detector on the same SEM as the Monarc. EDS and CL are fantastically complementary techniques for sample analysis. EDS is great for elemental quantification but falls short when trying to identify trace elements, crystallographic phases, or grain boundaries – where CL shines! Equipped with these powerful tools, I collected my first multi-hyperspectral data, capturing CL and EDS signals simultaneously. Take a look at some of the results:

Figure 2. (left) True color representation of the CL spectrum image (color) overlaid with SE image (gray), and (right) extracted CL spectra from points 1 (aqua fill), 2 (red), and 3 (green).

Figure 3. (left) Elemental quantity maps extracted from the EDS spectrum image corresponding to aluminum (blue), calcium (green), and magnesium (red); and (right) extracted EDS spectra from points 1 (aqua fill), 2 (red), and 3 (green). Points 1, 2, and 3 are the same locations as in Figure 2.

Both techniques were very revealing. In addition to Mg, Ca, and Al, the EDS spectrum image (hyperspectral image) detected other elements, some in high abundance like O and Si, and others which were less abundant, including Fe, C, Ti, and Na. We discovered geological materials like hibonite, corundum, and apatite but could not discern which mineral complexes they were involved in. At first glance, the CL and EDS maps looked very similar, but the more I looked, the more I realized there were significant differences, and so I decided to dig a little deeper with the CL spectrum image. The CL spectrum shown in Figure 2 indicates the presence of several trace elements. By looking at the difference of intensities at the smaller sharp peaks in contrast with the surrounding intensities, I was able to differentiate two maps from the CL data, which likely correspond to the presence of trace elements, one with an emission peak at 460 nm (Fe in corundum) and the other at 605 nm (Sm in apatite).

Figure 4. Extraction of CL trace elements (Fe in corundum) found at 460 nm (red) and (Sm in apatite) 605 nm (green).

Figure 5. (left) Bandpass CL image displaying 580 ± 20 nm and (right) colorized EDS map for Al (blue), Ca (green), and Mg (red).

Figure 6. EDS and CL composite image including EDS elemental maps for aluminum(blue) and magnesium (yellow); and trace elements iron in corundum (green) and samarium in apatite (red) as revealed by CL.

The data gathered from this sample may give a glimpse into the history of our solar system’s evolution. It also demonstrates the need for complementary techniques when analyzing complex samples. I want to thank NASA for generously providing the sample used in this study, Gatan and EDAX for providing me the opportunity to work with it, and the nature of the universe for generating this message in a bottle and letting it find its way to our lab!

Between the Lines

Dr. René de Kloe, Applications Specialist, EDAX

While I am testing new hardware and software versions, I use it as an opportunity to collect some data on unique materials. Testing detector speed or general software functionality is easiest on a simple material like an undeformed Ni or Fe alloy. But, I think it is a shame to perform longer duration tests on materials I have already seen many times before. For such occasions, I look through my collection of materials for something nice to map. During testing of the upcoming APEX 2.0 EBSD software, I collected a few larger scans on fossils that I had found during geological fieldwork and family holidays. This included large single-field scans and a Montage map, where we combine beam scans with stage movements for a large mosaic map.

Figure 1. a) Cross-section through a fossil crinoid stem. b) IPF on PRIAS center map of the fossil crinoid stem sample collected from the indicated area.

For example, Figure 1a shows a cross-section through a fossil crinoid stem. At the edge, the lighter areas represent the structure of the organism, while the darker areas are later sedimentary infill.

This is beautifully visible in the 2.1 x 1.7 mm IPF on PRIAS center map, where the biomineral structure appears smooth and fine-grained. In contrast, the infill is more equiaxed and shows topography due to compositional differences (Figure 1b).

Another beautiful scan was collected while I was trying out the new APEX 2.0 EBSD Montage map wizard. This wizard allows easy pre-imaging of the entire scan field to set the actual scan area. With the wizard, setting up such a large, 18 million point, 30-field Montage map over a 1.3 x 7 mm area can be done in a few minutes.

Figure 2. a) Calcite rock sample with fossils. b) EBSD Montage map of one of the nummulite fossils.

We collected these two scans on calcite rocks for which you can simply load the appropriate crystal structure. But collecting data is not always that easy, especially if you are not sure what phase(s) you have in your sample. And ultimately, EBSD data collection is based on pattern analysis and then matching the detected bands against a lookup table. In most cases, you can just search the included EDAX structure file database that contains close to 500 phases and covers most commonly studied materials, such as the calcite used for the scans above.

But where do these files come from? Partly, they are a result of our combined legacy. Over the years, we have seen many materials and often painstakingly identified which bands to select to get reliable indexing results. Nowadays, you can create phase files directly using atomic and crystallographic information. However, you can continue to extract the majority of “new” phase files from XRD databases, such as the AMCS, ICSD, or ICDD PDF databases. These databases contain 10’s to sometimes 100’s of thousands of phase descriptions that are based on XRD measurements. The XRD data shows which lattice planes are effective X-ray diffractors, and are also useful to construct a structure file for electron diffraction patterns.

Figure 3. Indexed olivine EBSD pattern.

And there the fun starts. Often there are multiple possibilities for phases or minerals (e.g., solid solution series) available in the database. Which one to select? And in many cases, there is no single-phase file that matches the pattern exactly. There are always bands that do not get labeled or are shown in the overlay that are not visible in the real pattern. This is due to the differences between X-ray and electron diffraction intensities or simply incomplete database entries. Time for some human intervention. The APEX EBSD software contains advanced tools to modify and optimize the reflector tables of imported or calculated structure files. First, the color-coding itself. All bands are labeled with a color that corresponds to the IPF color triangle, so equivalent lattice planes get identical colors. This allows a visual inspection if bands that are designated with the same color also appear identical.

Figure 4. IPF color triangle.

Then there is a band ID tool to help identify non-labeled bands in the diffraction patterns. When a pattern appears correctly indexed, but a number of bands are not labeled, the user can draw a line on the missing band. The software then shows which lattice plane corresponds to that band and also indicates all crystallographic equivalent planes. When it is still difficult to identify the correct indexing solution, it can be beneficial to bypass the Hough band detection and instead manually draw the bands for indexing. A good trick for low symmetry crystals is only to select the thinnest bands. These correspond to the lattice planes with the largest d-spacings and should be the important low-index crystallographic planes. By excluding the (often) large number of bands with similar bandwidths, you reduce the number of options and more quickly land at the best matching orientation or phase.

Figure 5. Manual Band Selection tool.

When a solution is found that matches the thin bands, you can start drawing in the other ones. When drawing a band, the software automatically shows where all the crystallographic equivalent planes should be. If a line is drawn where no band is present, you have the wrong candidate, and you need to look further. If all the indicated bands match in appearance and width, you can enable the reflector. This way, it is easy to interactively generate a matching phase file. Just keep in mind that when you have optimized a structure file to a pattern, it is a good idea to find some more patterns from that phase (if necessary, just rotate the sample to get a different orientation) and verify that all the bands in the other patterns are also properly identified. This is especially important for low symmetry materials where few lattice planes are equivalent.

Figure 6. Band optimization sequence on an EBSD pattern from W2C. The initial reflector table (a) misses a number of strong bands. Manually selecting a band (b) shows which reflector this is and where the crystallographic equivalent bands should be. This can be repeated (c) until all clear bands have been labeled.

Although it can be rewarding to identify a new phase and optimize the structure file to allow for EBSD mapping of a new and interesting material, I would like to end with a word of warning. When you are working with a good pattern and successfully identify the phase and orientation, it is very tempting to keep looking for bands and completely fill the pattern with everything you can see. But that is often a bad idea, as the weaker bands will typically not get selected by the Hough transformation on the poorer patterns that are used during indexing. Enjoy playing with the materials and structure files, but don’t overdo it.

Figure 7. Diffraction pattern with all visible bands enabled for indexing.

How to Get a Good Answer in a Timely Manner

Shawn Wallace, Applications Engineer, EDAX

One of the joys of my job is troubleshooting issues and ensuring you acquire the best results to advance your research. Sometimes, it requires additional education to help users understand a concept. Other times, it requires an exchange of numerous emails. At the end of the day, our goal is not just to help you, but to ensure you get the right information in a timely manner.

For any sort of EDS related question, we almost always want to look at a spectrum file. Why? There is so much information hidden in the spectrum that we can quickly point out any possible issues. With a single spectrum, we can quickly see if something was charging, tilted, or shadowed (Figure 1). We can even see weird things like beam deceleration caused by a certain imaging mode (Figure 2). With most of these kinds of issues, it is common to run into major quant related problems. Any quant problems should always start with a spectrum.

Figure 1. The teal spectrum shows a strange background versus what a normal spectrum (red) should look like for a material.

This background information tells us that the sample was most likely shadowed and that rotating the sample to face towards the detector may give better results.

Figure 2. Many microscopes can decelerate the beam to help with imaging. This deceleration is great for imaging but can cause EDS quant issues. Therefore, we recommend reviewing the spectrum up front to reduce the number of emails to troubleshoot this issue.

To save the spectrum, right-click in the spectrum window, then click on Save (Figure 3). From there, save the file with a descriptive name, and send it off to the applications group. These spectrum files also include other metadata, such as amp time, working distance, and parameters that give us so many clues to get to the bottom of possible issues.

Figure 3. Saving a spectrum in APEX is intuitive. Right-click in the area and a pop-up menu will allow you to save the spectrum wherever you want quickly.

For information on EDS backgrounds and the information they hold, I suggest watching Dr. Jens Rafaelsen’s Background Modeling and Non-Ideal Sample Analysis webinar.

The actual image file can also help us confirm most of the above.

Troubleshooting EBSD can be tricky since the issue could be from sample prep, indexing, or other issues. To begin, it’s important to rule out any variances associated with sample preparation. Useful information to share includes a description of the sample, as well as the step-by-step instructions used to prepare the sample. This includes things like the length of time, pressure, cloth material, polishing compound material, and even the direction of travel. The more details, the better!

Now, how do I know it is a sample prep problem? If the pattern quality is low at long exposure times (Figure 4) or the sample looks very rough, it is probably related to sample preparation (Figure 4). That being said, there could be non-sample prep related issues too.

Figure 4. This pattern is probably not indexable on its own. Better preparation of the sample surface is necessary to index and map this sample correctly.

For general sample prep guidelines, I would highly suggest Matt Nowell’s Learn How I Prepare Samples for EBSD Analysis webinar.

Indexing problems can be challenging to troubleshoot without a full data set. How do I know my main issues could be related to indexing? If indexing is the source, a map often appears to be very speckled or just black due to no indexing results. For this kind of issue, full data sets are the way to go. By full, I mean patterns and OSC files. These files can be exported out of TEAM/APEX. They are often quite large, but there are ways available to move the data quickly.

For the basics of indexing knowledge, I suggest checking out my latest webinar, Understanding and Troubleshooting the EDAX Indexing Routine and the Hough Parameters. During this webinar, we highlight attributes that indicate there is an issue with the data set, then dive into the best practices for troubleshooting them.

As for camera set up, this is a dance between the microscope settings, operator’s requirements, and the camera settings. In general, more electrons (higher current) allow the experiment to go faster and cover more area. With older CCD based cameras, understanding this interaction was key to good results. With the newer Velocity cameras based on CMOS technology, the dance is much simpler. If you are having difficulty while trying to optimize an older camera, the Understanding and Optimizing EBSD Camera Settings webinar can help.

So how do you get your questions answered fast? Bury us with information. More information lets us dive deeper into the data to find the root cause in the first email, and avoids a lengthy back and forth exchange of emails. If possible, educate yourself using the resources we have made available, be it webinars or training courses. And always, feel free to reach out to my colleagues and me at!

Teaching is learning

Dr. René de Kloe, Applications Specialist, EDAX

Figure 1. Participants of my first EBSD training course in Grenoble in 2001.

Everybody is learning all the time. You start as a child at home and later in school and that never ends. In your professional career you will learn on the job and sometimes you will get the opportunity to get a dedicated training on some aspect of your work. I am fortunate that my job at EDAX involves a bit of this type of training for our customers interested in EBSD. Somehow, I have already found myself teaching for a long time without really aiming for it. Already as a teenager when I worked at a small local television station in The Netherlands I used to teach the technical things related to making television programs like handling cameras, lighting, editing – basically everything just as long as it was out of the spotlight. Then during my geology study, I assisted in teaching students a variety of subjects ranging from palaeontology to physics and geological fieldwork in the Spanish Pyrenees. So, unsurprisingly, shortly after joining EDAX in 2001 when I was supposed to simply participate in an introductory EBSD course (fig 1) taught by Dr. Stuart Wright in Grenoble, France, I quickly found myself explaining things to the other participants instead of just listening.

Teaching about EBSD often begins when I do a presentation or demonstration for someone new to the technique. And the capabilities of EBSD are such that just listing the technical specifications of an EBSD system to a new customer does not do it justice. Later when a system has been installed I meet the customers again for the dedicated training courses and workshops that we organise and participate in all over the world.

Figure 2. EBSD IPF map of Al kitchen foil collected without any additional specimen preparation. The colour-coding illustrates the extreme deformation by rolling.

In such presentations, of course we talk about the basics of the method and the characteristics of the EDAX systems, but then it always moves on to how it can help understand the materials and processes that the customer is working with. There, teaching starts working the other way as well. With every customer visit I learn something more about the physical world around us. Sometimes this is about a fundamental understanding of a physical process that I have never even heard of.

At other times it is about ordinary items that we see or use in our daily lives such as aluminium kitchen foil, glass panes with special coatings, or the structure of biological materials like eggs, bone, or shells. Aluminium foil is a beautiful material that is readily available in most labs and I use it occasionally to show EBSD grain and texture analysis when I do not have a suitable polished sample with me (fig 2) and at some point, a customer explained to me in detail how it was produced in a double layer back to back to get one shiny and one matte side. And that explained why it produces EBSD patterns without any additional preparation. Something new learned again.

Figure 3. IPF map of austenitic steel microstructure prepared by additive manufacturing.

A relatively new development is additive manufacturing or 3D printing where a precursor powdered material is melted into place by a laser to create complex components/shapes as a single piece. This method produces fantastically intricate structures (fig 3) that need to be studied to optimise the processing.

With every new application my mind starts turning to identify specific functions in the software that would be especially relevant to its understanding. In some cases, this then turns into a collaborative effort to produce scientific publications on a wide variety of subjects e.g. on zeolite pore structures (1, fig (4)), poly-GeSi films (2, fig (5)), or directional solidification by biomineralization of mollusc shells (3).

Figure 4. Figure taken from ref.1 showing EBSD analysis of zeolite crystals.

Figure 5. Figure taken from ref.2 showing laser crystallised GeSi layer on substrate.

Such collaborations continuously spark my curiosity and it is because of these kinds of discussions that after 17 years I am still fascinated with the EBSD technique and its applications.

This fascination also shows during the EBSD operator schools that I teach. The teaching materials that I use slowly evolve with time as the systems change, but still the courses are not simply repetitions. Each time customers bring their own materials and experiences that we use to show the applications and discuss best practices. I feel that it is true that you only really learn how to do something when you teach it.

This variation in applications often enables me to fully show the extent of the analytical capabilities in the OIM Analysis software and that is something that often gets lost in the years after a system has been installed. I have seen many times that when a new system is installed, the users invest a lot of time and effort in getting familiar with the system in order to get the most out of it. However, with time the staff that has been originally trained on the equipment moves on and new people are introduced to electron microscopy and all that comes with it. The original users then train their successor in the use of the system and inevitably something is lost at this point.

When you are highly familiar with performing your own analysis, you tend to focus on the bits of the software and settings that you need to perform your analysis. The bits that you do not use fade away and are not taught to the new user. This is something that I see regularly during the training course that I teach. Of course, there are the new functions that have been implemented in the software that users have not seen before, but people who have been using the system for years and are very familiar with the general operation always find new ways of doing things and discover new functions that could have helped them with past projects during the training courses. During the latest EBSD course in Germany in September a participant from a site where they have had EBSD for many years remarked that he was going to recommend coming to a course to his colleagues who have been using the system for a long time as he had found that the system could do much more than he had imagined.

You learn something new every day.

1) J Am Chem Soc. 2008 Oct 15;130(41):13516-7. doi: 10.1021/ja8048767. Epub 2008 Sep 19.
2) ECS Journal of Solid State Science and Technology, 1 (6) P263-P268 (2012)
3) Adv Mater. 2018 Sep 21:e1803855. doi: 10.1002/adma.201803855. [Epub ahead of print]

Endless Summer

Matt Nowell, EBSD Product Manager, EDAX

My family and I love the beach. We love to swim in the water, ride the waves, and play in the sand. Each summer we typically spend time at Sunset Beach, North Carolina. After years of seeing the cool stuff in the SEM, materials science and microscopy are always topics of discussion. This year, after enjoying the musical Hamilton, my wife was inspired to start working on a periodic table of elements rap song. My 13-year-old learned more about metalworking watching the History Channel show, Forged in Fire, where participants are challenged to make different weapons from assorted metallic sources. My favorite part was watching them evaluate different parts of a bicycle for heat-treatable steel to recycle. One of my favorite moments though was unpacking my beach shoes on the first day.

Generally, when we visit a beach, we try to bring home a shell or a piece of driftwood. However, when I was putting on my shoes for the first time, I noticed some sand was still present. My last beach trip had been to the Cayman Islands. I immediately noticed that this sand looked much different than the sand at Sunset Beach. I decided to save a little bit of each for some microscopy and microanalysis when I got back home.

When I looked at them both more closely, I saw that the sand from Sunset Beach (SB) on the left was much darker with black flecks, while the sand from Grand Cayman (GC) was much lighter. Thinking about the possible composition of the sand got me thinking about the bladesmithing competition held at the TMS annual meetings. One year, the team from UC Berkeley created a sword using magnetite found at local beaches using magnets. I thought it would be interesting to examine both of these sands with my SEM, EDS, and EBSD tools.

Sand grains from Sunset Beach.

Sand grains from Grand Cayman.


Initially I placed a bit of sand on an aluminum stub for SEM and EDS analysis. To reduce charging effects, I used the Low Vacuum capability of our FEI Teneo FEG-SEM, running at 0.1 mbar pressure. Images were collected using the Annular BackScatter (ABS) detector for atomic number contrast imaging. The sand grains from Sunset Beach were generally a little smaller than the Grand Cayman sand, as expected from visual inspection. Both sands exhibited cracking and weathering, which isn’t surprising in hindsight either. Many grains show flat surfaces, with internal structure visible with ABS imaging contrast.

I followed the imaging work with compositional analysis using EDS. The Sunset Beach sand was primarily composed of silicon and oxygen grains, which I suspect is quartz. The single brighter grain in Figure 3 was composed of an iron-titanium oxide. The Grand Cayman sand was primarily a calcium carbonate (Ca-C-O) material. The more needle shaped grains were primarily sodium and chlorine, which I assume is then salt that has solidified during the evaporation of the water. All this leads me to believe I really didn’t do a good job of cleaning my shoes after Grand Cayman.

While quartz being present in sand wasn’t surprising to me, the observation of calcium carbonate did remind me of some geological homework I did on the island. The water in Grand Cayman was very clear, which made it great for snorkeling. We swam around and saw a coral reef, a sunken ship, lots of fish, and stingrays. To understand why the water was so clear, I read that it was the lack of topsoil, and the erosion and runoff of topsail to the water that was responsible for the clarity. Looking again at this reference, it mentions that the top layer of the island is primarily composed of carbonates. The erosion of this material would explain the primary composition of the beach sand in my shoes.

Of course, the next step now is analyzing these sands with EBSD to determine the crystal structure of the materials. I’ve started the process. I’ve mounted some of the sand in epoxy, and hand polished to get some flat surfaces for analysis. I’m able to get EBSD patterns, but getting a good background is going to be tricky. I think the next step will be to watch my colleague Shawn Wallace’s webinar on Optimizing Backgrounds on MultiPhase samples to be presented on September 27th. You can also register for this here.

In the meantime, I’ll keep the sand samples on my desk to remind me of summer as the colder Utah winters will be approaching. It will be a good reason to stay inside and write the next chapter of this analysis for another blog post.

Vacationing Between a Rock and a Hard Place?

Shawn Wallace, Applications Engineer, EDAX.

One of the perks of both my degree (Geology) and my current job is that I have travelled extensively. In all those travels, I had been to 47 of the 48 contiguous US States, with Maine being the missing one. This year, I decided to be selfish and dragged the family to Maine on vacation, so I that could tick off the final one.

Being a member of the Wallace family means vacation is a time for strenuous hikes and beating on rocks to unlock their inner goodies, to add to our ever growing rock and mineral collection. This vacation was no different. Maine is home to some of the best studied and known Pegmatites, and they quickly became our goal. Pegmatites are neat for a several reasons, the main two being that they tend to form giant crystals (a 19 foot long Beryl found in Maine) and weird minerals in general tend to form in them.

I was able to track down some publicly accessible sites, found a lovely home base to rent for the week, and we set off for a week long rockhounding adventure. Ok not all week. We took a couple days off to go swimming, as it got up over 90F (>32C).

Figure 1. Dendrites cover this massive feldspar sample on nearly all faces.

Our first stops yielded the usual kind of rocks I was expecting, but another site did not. There we found dendrites everywhere. The rock itself is a massive feldspar (Fig. 1). You can see that most of the dendrites nucleate at the edge of a fracture surface and then do their fractal thing on the surface itself. Wanting to better understand the sample, I started searching for previous EBSD work on geological dendrites. While a lot exists in the metals world, very little exists in the geological world. To me, this means I have work to do. Let’s see what I can do to get some useful data on this sample!

P.S. I have Alaska and Hawaii to go. Who needs an onsite training in those states?