Looking At A Grain!

Sia Afshari, Global Marketing Manager, EDAX

November seems to be the month when the industry tries to squeeze in as many events as possible before the winter arrives. I have had the opportunity to attend a few events and missed others, however, I want to share with you how much I enjoyed ICOTOM18*!

ICOTOM (International Conference on Texture of Materials) is an international conference held every three years and this year it took place in St. George, Utah, the gateway to Zion National Park.

This was the first time I have ever attended ICOTOM which is, for the most part, a highly technical conference, which deals with the material properties that can be detected and analyzed by Electron Backscatter Diffraction (EBSD) and other diffraction techniques. What stood out to me this year were the depth and degree of technical presentations made at this conference, especially from industry contributors. The presentations were up to date, data driven, and as scientifically sound as any I have ever seen in the past 25 years of attending more than my share of technical conferences.

The industrial adaptation of technology is not new since X-ray diffraction has been utilized for over half a century to evaluate texture properties of crystalline materials. At ICOTOM I was most impressed by the current ‘out of the laboratory’ role of microanalysis, and especially EBSD, for the evaluation of anisotropic materials for quality enhancement.

The embracing of the microanalysis as a tool for product enhancement means that we equipment producers need to develop new and improved systems and software for EBSD applications that will address these industrial requirements. It is essential that all technology providers recognize the evolving market requirements as they develop, so that they can stay relevant and supply current needs. If they can’t do this, then manufacturing entities will find their own solutions!

*In the interests of full disclosure, I should say that EDAX was a sponsor of ICOTOM18 and that my colleagues were part of the organizing committee.

Looking at the World of Microanalysis in Color

Tara Nylese, Global Applications Manager, EDAX

Several years ago, I was talking to a customer, who asked whether we could change the color scheme of the EDAX TEAM™ software. He said was that it was hard for him to tell the difference between the spectrum background and the cursor. I replied, “Well, the cursor is a lime green and the background is more like a gray-gre…..Oh, wait, you’re colorblind, aren’t you?” Surely enough he was, and while I can’t “see” his perspective, I can listen to and respect it. Thus, the motivation of this blog is to let our customers know that we in Applications listen to them and take their needs seriously.

In this specific case, I am happy to report that we just recently received feedback on the new EDAX APEX™ software, and one comment was that the user really liked the “contrast” of the red spectrum on the white background – see the image below.

More generally, it is one main goal of the EDAX Applications team to make sure that we capture the “real world” customer feedback and incorporate it as much as possible into future product enhancements, bug fixes and new generations of products. Each of our Worldwide Apps team members can talk to upwards of ten customers a week. These conversations are usually in interactions such as support calls, training sessions and demos. At each opportunity, we hear tremendously valuable real-world customer perspective, and very often we learn what we can’t “see” ourselves. Often, if I’m asked to share my thoughts, my words are just a colorful patchwork of years of customer ideas all melded into a microscopy amalgam.

Customer perspective is so important, in fact, that it is a cornerstone of the EDAX App Lab Mission Statement. A few years ago, I compiled about three pages of descriptions of what people thought of when they thought of Apps, and then condensed them down into the following statement that hangs on our HQ App Lab walls.

The EDAX US App Lab uses technical expertise and creativity plus a strong focus on understanding the needs of our internal and external customers to drive excellence in innovative analytical solutions. The applications group supports company-wide efforts to provide real-life value and benefits to our customers which differentiate our products in materials analysis.

Now to get back to the colors which are available for maps in our software. One of the lesser known functions is the ability to select and edit your color palette:

Using this option, you can choose from a 40-color palette, seen here. Remember to click on the element in the periodic chart first, then select your color.

Since I brought up the topic of colorblindness, I’ll also use a colorblind app that simulates how a Red/Green colorblind person sees the world (or our color palette).

Note the green color of O and P, and see how closely it compares to the yellow color of the lanthanide/actinide series!

Finally, to summarize the Applications message: to our current customers – thank you for sharing your thoughts; to all our applications team colleagues – thank you for gathering so much wide-ranging information and promoting the importance of it internally, and to all our future customers – when you chose EDAX, you’re choosing to join a dynamic microanalysis company, which strives to develop the most meaningful features and functions to meet your microanalysis needs.

Aimless Wanderin’ – Need a Map?

Dr. Stuart Wright, Senior Scientist, EDAX

In interacting with Rudy Wenk of the University of California Berkeley to get his take on the word “texture” as it pertains to preferred orientation reminds me of some other terminologies with orientation maps that Rudy helped me with several years ago.

Map reconstructed form EBSD data showing the crystal orientation parallel to the sample surface normal

Joe Michael of Sandia National Lab has commented to me a couple of times his objection to the term “IPF map”. As you may know, the term is commonly used to describe a color map reconstructed from OIM data where the color denotes the crystallographic axis aligned with the sample normal as shown below. Joe points out that the term “orientation map” or “crystal direction map” or something similar would be much more appropriate and he is absolutely right.

The reason behind the name “IPF map”, is that I hi-jacked some of my code for drawing inverse pole figures (IPFs) as a basis to start writing the code to create the color-coded maps. Thus, we started using the term internally (it was TSL at the time – prior to EDAX purchasing TSL) and then it leaked out publicly and the name stuck – my apologies to Joe. We later added the ability to color the microstructure based on the crystal direction aligned with any specified sample direction as shown below.

Orientation maps showing the crystal directions aligned with the normal, rolling and transverse directions at the surface of a rolled aluminum sheet.

The idea for this map was germinated from a paper I saw presented by David Dingley where a continuous color coding schemed was devised by assigning red, green and blue to the three axes of Rodrigues-Frank space: D. J. Dingley, A. Day, and A. Bewick (1991) “Application of Microtexture Determination using EBSD to Non Cubic Crystals”, Textures and Microstructures, 14-18, 91-96. In this case, the microstructure had been digitized and a single orientation measured for each grain using EBSD. Unfortunately, I only have gray scale images of these results.

SEM micrograph of nickel, grain orientations in Rodrigues-Frank space and orientation map based on color Rodrigues vector coloring scheme. Source: Link labeled “Full-Text PDF” at

IPF map of recrystallized grains in grain oriented silicon steel from Y. Inokuti, C. Maeda and Y. Ito (1987) “Computer color mapping of configuration of goss grains after an intermediate annealing in grain oriented silicon steel.” Transactions of the Iron and Steel Institute of Japan 27, 139-144.
Source: Link labeled “Full Text PDF button’ at

We didn’t realize it at the time; but, an approach based on the crystallographic direction had already been done in Japan. In this work, the stereographic unit triangle (i.e. an inverse pole figure) was used in a continues color coding scheme were red is assigned to the <110> direction, blue to <111> and yellow to <100> and then points lying between these three corners of the stereographic triangle are combinations of these three colors. This color coding was used to shade grains in digitized maps of the microstructure according to their orientation. Y. Inokuti, C. Maeda and Y. Ito (1986) “Observation of Generation of Secondary Nuclei in a Grain Oriented Silicon Steel Sheet Illustrated by Computer Color Mapping”, Journal of the Japan Institute of Metals, 50, 874-8. The images published in this paper received awards in 1986 by the Japanese Institute of Metals and TMS.

AVA map and pole figure from a quartz sample from “Gries am Brenner” in the Austrian alps south of Innsbruck. The pole figure is for the c-axis. (B. Sander (1950) Einführung in die Gefügekunde der Geologischen Körper: Zweiter Teil Die Korngefüge. Springer-Vienna)
Source: In the last chapter (Back Matter) in the Table of Contents there is a link labeled “>> Download PDF” at

I thought these were the first colored orientation maps constructed until Rudy later corrected me (not the first, nor certainly the last time). He sent me some examples of mappings of orientation onto a microstructure by “hatching” or coloring a pole figure and then using those patterns or colors to shade the microstructure as traced from micrographs. H.-R. Wenk (1965) “Gefügestudie an Quarzknauern und -lagen der Tessiner Kulmination”, Schweiz. Mineralogische und Petrographische Mitteilungen, 45, 467-515 and even earlier in B. Sander (1950) Einführung in die Gefügekunde Springer Verlag. 402-409 . Sanders entitled this type of mapping and analysis as AVA (Achsenvertilungsanalyse auf Deutsch or Axis Distribution Analysis in English).

Such maps were forerunners to the “IPF maps” of today (you could actually call them “PF maps”) to which we are so familiar with. It turns out our wanderin’s in A Search for Structure (Cyril Stanley Smith, 1991, MIT Press) have actually not been “aimless” at all but have helped us gain real insight into that etymologically challenged world of microstructure.

My Fossil Background

Dr. René de Kloe, Applications Specialist, EDAX

Call me old-fashioned, but when I want to relax I always try to go outdoors, away from computers and electronic gadgets. So when I go on vacation with my family we look for quiet places where we can go hiking and if possible we visit places with interesting rocks that contain fossils. Last summer I spent my summer vacation with my family in the Hunsrück in Germany. The hills close to where we stayed consisted of shales. These are strongly laminated rocks that have been formed by heating and compaction of finegrained sediments, mostly clay, that have been deposited under water in a marine environment. These rocks are perfect for the occurrence of fossils. When an organism dies and falls on such a bed of clay and is covered by a successive stack of mud layers, it can be beautifully preserved. The small grains and airtight seal of the mud can give a very good preservation such that the shape of the plant or animal can be found millions of years later as a highly detailed fossil. Perhaps the most famous occurrence of such fossil-bearing shale is the Burgess shale in British Columbia, Canada which is renowned for the preservation of soft tissue of long-extinct creatures. The Hunsrück region in Germany may not be that spectacular, but it is a lot closer to home for me and here also beautiful fossils have been found.

Figure 1. Crinoid or sea lily fossil found in the  waste heap of the Marienstollen in Weiden, Germany.

Figure 2. Detail of sulphide crystals.

Figure 3. Example of a complete crinoid fossil (not from the Hunsrück area). Source

So, when we would go hiking during our stay we just had to pack a hammer in our backpack to see if we would be lucky enough to find something spectacular of our own. What we found were fragments of a sea lily or crinoid embedded in the rock (Figures 1,3) and as is typical for fossils from the area, much of the fossilised remains had been replaced by shiny sulphide crystals (Figure 2). Locally it is said that the sulphides are pyrite. FeS2. So of course, once back home I could not resist putting a small fragment of our find in the SEM to confirm the mineral using EDS and EBSD. The cross section that had broken off the fossil showed smooth fracture surfaces which looked promising for analysis (Figure 4). EDS was easy and quickly showed that the sulphide grains were not iron sulphide, but instead copper bearing chalcopyrite. Getting EBSD results was a bit trickier because although EBSD bands were often visible, shadows cast by the irregular surface confuse the band detection (Figure 5).

Figure 4. Cross section of shale with smooth sulphide grains along the fracture surface.

Figure 5. EBSD patterns collected from the fracture surface. Indexing was done after manual band selection. Surface irregularities are emphasized by the projected shadows.

Now the trick is getting these patterns indexed and here I do like computers doing the work for me. Of course, you can manually indicate the bands and get the orientations of individual patterns, but that will not be very helpful for a map. The problem with a fracture surface is that the substrate has a variable tilt with respect to the EBSD detector. Parts of the sample might be blocking the path to the EBSD detector which complicates the EBSD background processing.

The EDAX EBSD software has many functions to help you out of such tight spots when analyzing challenging samples. For example, in addition to the standard background subtraction that is applied to routine EBSD mapping there is a library of background processing routines available. These routines can be helpful if your specimen is not a “typical” flat, well-polished EBSD sample. This library allows you to create your own recipe of image processing routines to optimize the band detection on patterns with deviating intensity gradients or incomplete patterns due to shadowing.

The standard background polishing uses an averaged EBSD pattern of more than ~25 grains such that the individual bands are blended out. This produces a fixed intensity gradient that we use to remove the background from all the patterns in the analysis area. When the actual intensity gradient shifts due to surface irregularities it is not enough to just use such a fixed average background. In that case you will need to add a dynamic background calculation method to smooth out the resulting intensity variations.

This is illustrated in the EBSD mapping of the fossil in Figure 6. The first EBSD mapping of the fossil using standard background subtraction only showed those parts of the grains that happened to be close to the optimal orientation for normal EBSD. When the surface was pointing in another direction, the pattern intensity had shifted too much for successful indexing. Reindexing the map with optimised background processing tripled the indexable area on the fracture surface.

Figure 6. Analysis of the fracture surface in the fossil. -1- PRIAS center image showing the smooth sulphide grains, -2- Superimposed EDS maps of O(green), Al(blue), S(magenta), and Fe(orange) -3- EBSD IPF on IQ maps with standard background processing, -4- original IPF map, -5- EBSD IPF on IQ maps with optimized background processing, -6- IPF map with optimized background.

In addition to the pattern enhancements also the band detection itself can be tuned to look at specific areas of the patterns. Surface shadowing mainly obscures the bottom part of the pattern, so when you shift the focus of the band detection to the upper half of the pattern you can maximize the number of detected bands and minimize the disturbing effects of the edges of the shadowed area. It is unavoidable to pick up a false band or two when you have a shadow, but when there are still 7-9 correct bands detected as well, indexing is not a problem.

Figure 7. Band detection on shadowed EBSD pattern. Band detection in the Hough transform is focused at the upper half of the pattern to allow detection of sufficient number of bands for correct indexing.

In the images below are a few suggestions of background processing recipes that can be useful for a variety of applications.

Of course, you can also create your own recipe of image processing options such that perhaps you will be able to extract some previously unrecognized details from your materials.

A Bit of Background Information

Dr. Jens Rafaelsen, Applications Engineer, EDAX

Any EDS spectrum will have two distinct components; the characteristic peaks that originate from transitions between the states of the atoms in the sample and the background (Bremsstrahlung) which comes from continuum radiation emitted from electrons being slowed down as they move through the sample. The figure below shows a carbon coated galena sample (PbS) where the background is below the dark blue line while the characteristic peaks are above.

Carbon coated galena sample (PbS) where the bacground is below the dark blue line while the characteristic peaks are above.

Some people consider the background an artefact and something to be removed from the spectrum (either through electronics filtering or by subtracting it) but in the TEAM™ software we apply a model based on Kramer’s law that looks as follows:Formulawhere E is the photon energy, N(E) the number of photons, ε(E) the detector efficiency, A(E) the sample self-absorption, E0 the incident beam energy, and a, b, c are fit parameters¹.

This means that the background is tied to the sample composition and detector characteristic and that you can actually use the background shape and fit/misfit as a troubleshooting tool. Often if you have a bad background, it’s because the sample doesn’t meet the model requirements or the data fed to the model is incorrect. The example below shows the galena spectrum where the model has been fed two different tilt conditions and an overshoot of the background can easily be seen with the incorrect 45 degrees tilt. So, if the background is off in the low energy range, it could be an indication that the surface the spectrum came from was tilted, in which case the quant model will lose accuracy (unless it’s fed the correct tilt value).

This of course means that if your background is off, you can easily spend a long time figuring out what went wrong and why, although it often doesn’t matter too much. To get rid of this complexity we have included a different approach in our APEX™ software that is meant for the entry level user. Instead of doing a full model calculation we apply a Statistics-sensitive Non-linear Iterative Peak-clipping (SNIP) routine². This means that you will always get a good background fit though you lose some of the additional information you get from the Bremsstrahlung model. The images below show part of the difference where the full model includes the steps in the background caused by sample self-absorption while the SNIP filter returns a flat background.

So, which one is better? Well, it depends on where the question is coming from. As a scientist, I would always choose a model where the individual components can be addressed individually and if something looks strange, there will be a physical reason for it. But I also understand that a lot of people are not interested in the details and “just want something that works”. Both the Bremsstrahlung model and the SNIP filter will produce good results as shown in the table below that compares the quantification numbers from the galena sample.


While there’s a slight difference between the two models, the variation is well within what is expected based on statistics and especially considering that the sample is a bit oxidized (as can be seen from the oxygen peak in the spectrum). But the complexity of the SNIP background is significantly reduced relative to the full model and there’s no user input, making it the better choice for the novice analyst of infrequent user.

¹ F. Eggert, Microchim Acta 155, 129–136 (2006), DOI 10.1007/s00604-006-0530-0
² C.G. RYAN et al, Nuclear Instruments and Methods in Physics Research 934 (1988) 396-402

What Kind of Leaves Are These?

Dr. Bruce Scruggs, XRF Product Manager, EDAX

This year is shaping up to be an interesting year for travel. Five countries and counting, and I’m not even including a stopover in Texas. The last trip was to Brazil. Beautiful country. But, there’s a reason you see snack and beverage vendors roaming the side of the highways in Rio and Sao Paulo..…

I started out with a micro-XRF workshop at the Center for Mineral Technology at the Federal University at Rio de Janeiro. We were working out of the Gemological Research Laboratory with Dr. Jurgen Schnellrath. At the end of the technical presentations, we analyzed some various pieces of jewelry that participants from the workshop brought. I must admit that this makes me a bit nervous to analyze anything with unforeseen sentimental value and I refuse to analyze engagement and wedding rings. A large pair of blue sapphire earrings turned out to be glass. (Purchased at a garage sale at a garage sale price. So, no big surprise …) Another smaller set of blue sapphire earrings were found to be natural sapphires accompanied by a sigh of relief from the owner. (They came from a reputable jewelry shop with a reputable jewelry shop price.)

Gold leaf “Gold leaf'” embedded in resin

At the end, we analyzed what was termed “gold leaf” jewelry, i.e. a ring and a pair of earrings. The style of these pieces was thin gold leaf foil embedded in resin. The owner was one of the younger students in the lab and she had purchased the jewelry herself from a relatively well-known designer’s collection. The goal was to measure for the presence of gold. Since the gold leaf was embedded in resin, XRF was the ideal tool to measure the pieces non-destructively. The jewelry also had some rather odd topography at times given the surrounding resin, but the Orbis had no problem to target the gold leaf given the co-axial geometry of the exciting X-ray and video imaging. I would have liked to have used the excuse that we couldn’t target the sample accurately because of XRF system geometry. There was no gold. Copper / Zinc alloy. That was it. She had paid about $30 US for the earrings and she said she felt cheated. I kept thinking “Cheated? Maybe … live a little, wait until you buy a house!” Later, I was searching the internet looking for a technical definition for “gold leaf”. I knew I was onto something when I found a webpage that said that gold leaf was “traditionally” 22K gold thin foil used for gilding. The page later described modern Copper/Zinc alloy metal leaf “… offering the same rich look of gold leaf, but at a fraction of the price….” Apparently, this metal leaf can be found at art stores. Who knew?

From there, we went on to the state of Sao Paulo and did a workshop at the Center for Nuclear Energy in Agriculture at the University of Sao Paulo. During the workshop, some of the students gave presentations on their work. I saw a very interesting experimental setup with live plants being measured in the Orbis. The plant’s roots were placed in a water bath doped with various forms of minerals or fertilizers. The whole plant, roots, stem, leaves, was then inserted into the Orbis and the stem was measured to monitor the uptake time for the relevant components in the bath. The plants could be moved in and out of the chamber to monitor the uptake over extended periods of time and over various portions of the plant.

On the way to the Sao Paulo airport, I had the pleasure of sitting in the longest traffic jam I have ever endured with the monotony being broken by roaming snack and beverage vendors. It was quite the sight to watch the peanut vendors carrying propane fueled peanut warmers traversing the lane dividers on the highway with the occasional motorcycle speeding between the cars along the same lane dividers.
Tip for next time … buy the Brazilian produced chocolate before going to the airport. The selection at the airport is rather limited and you never know when you may be having more fun than humans should be allowed to have watching motorcycles and peanut hawkers.

Journey of Learning: Teaching Yourself the Power of EBSD

Shawn Wallace – Applications Engineer, EDAX

The joy of learning is sadly something that many people forget about and some never really feel. One of the things I like to keep in mind when I am learning something new is that learning is usually not a eureka moment, but a process of combining concepts and ideas already known, to reach a new solution or idea. The reason I was thinking about learning as a process is because recently I found myself forgetting that. A customer sample came in that was, for EBSD, hard in every way: Difficult crystal system/orientation, sample prep issues, poor diffractor. With all those factors, the sample was putting up a fight and winning, mainly because I allowed it to. I had tried all my normal tricks and was not making much headway. I knew the sample was analyzable, but I was not treating the process as a personal learning opportunity, instead I was treating it as a fight that I had to win. I was quickly bouncing from potential solution to potential solution and trying them, without spending much time on thinking what would be best to try and how to tackle the problem as a problem, and not a challenge. I didn’t even frame it that way in my own head until a week later when I was visiting a customer site to do some training.

During the training session, a sample came up with a very different set of problems, but still ones that were stymieing us as we sat at the microscope. I found the user resorting to what I had done previously; just try this and see if it works, without thinking about what the best course of action was. As I sat there, I told them to take a step back and evaluate what the issue was and how we could use our knowledge of all the functions available to us in the TEAM™ software and/or our microscope to find a solution. We sat and talked about the issue and the user was able to come up with a game plan and try some things that would help him reach a solution or gain additional knowledge, aka LEARN. I learned that day – that I sometimes need to treat myself the way I would treat a user. There will always be cases when I don’t know the answer and I have to teach myself the solution.

That leads us to an open question. How do you learn EBSD as you go along? With that in mind, here at EDAX we are going to start a new series of blog posts to discuss the basics of EBSD, from pattern formation, the Hough Transform, and finally indexing. More importantly, I hope to touch on how to troubleshoot issues using your newfound understanding of these concepts and tie the entire processes together as they all play off each other.

My final goal is get your creative juices flowing to dive deeper into understanding the kind of questions that EBSD can answer, and how that, in the end, can provide you with an incredible understanding of your analysis challenges and ultimately a solution to the problem. EBSD is one of the most powerful analytical techniques that I know. It can answer the simple questions (what phase is my sample?) to the incredibly complex (if I squeeze my sample this way, which grains will tend to deform first?). As your knowledge grows, EBSD is one step ahead of you, egging you on to learn more and more. I hope to be your guide on this Journey of Learning. I think I will learn quite a bit too.