How to Optimize Imaging with Nikon Elements Software, Part 3

July 23, 2020

Advanced Measurement Applications

Optimizing your microscopy imaging with Nikon Elements software will streamline your workflow. In the final session of this three-part series, Technical Sales Representative James Bristol presents live tutorials for two advanced applications within this software platform:

  • Layer Thickness Measurement
  • Measurement Sequencer

Did you miss Part 1 or 2? View them here:

How to Optimize Imaging with Nikon Elements Software, Part 1

How to Optimize Imaging with Nikon Elements Software, Part 2: Using Imaging and Metrology Operations

    Add your contact information to our list, and we’ll let you know when new webinars become available.


    Charles Zona (CZ): Good afternoon, and welcome to another McCrone Group webinar. My name is Charles Zona, and today we welcome back Jim Bristol of McCrone Microscopes & Accessories. Jim is going to talk to us today about How to Optimize Your Imaging with Nikon Elements Software Part, 3. This is the third installment of the three-part series, so if you missed Part 1, there’s a recording of each episode on our website, and you can go there and access them by clicking on the resources tab.

    Before we get started, I would like to tell you a little bit about Jim’s background and experience. Jim is a technical sales representative from McCrone Microscopes & Accessories, with more than 30 years experience in optical instrumentation and software sales. Jim has successfully sold and supported complex imaging systems, such as laser scanning and spinning disc confocal microscopes, integrated systems for cell sterology and neuron tracing, as well as scanning electron microscopes and thermal microscope systems.

    Jim will field questions from the audience immediately following today’s presentation.

    Today’s webinar is a little different in that it is a recording, and not taking place live. However, you can still ask questions by typing them into the questions field. We will answer your questions individually in the coming days. This webinar will be available on The McCrone Group website under the Resources tab. And now, I will hand the program over to Jim.

    Jim Bristol (JB): Thank you, Chuck, And thank you, everyone, for joining us today for our third and final session on Nikon Elements image analysis software’s advanced measurment applications.

    Today, we’ll talk about two modules available with Nikon Elements: Measurement Sequencer, and Layer Thickness Measurement. So let’s get started.

    Measurement Sequencer

    This module is used to efficiently process repeated measurements of a lot or batch of samples or parts that require inspection. Now, I have an image up here in front of you. It’s black and white, it’s a stamping, and could be of any material, wood, metal, plastic. But it is calibrated, so we do know that we have a calibration to do proper measurements. What we’re doing here, is, under applications, we are selecting Measurement Sequencer Definitions, which is now open down here. And we are going to actually lay out and define the measurements that we want to repeatedly run on successive parts of the same type.

    Now the first thing we want to do over here is show the drawing, and make sure that we load that current document into the definitions. Why is that important? As we draw the lines, and the circles, and create the angles, we want to be able to have those lines and circles show up on this document to the lower right-hand side of the screen, so that we have a visual reference when we’re running successive measurements. Not only do we know where to draw the line, but we’re shown visually where we have to draw the line, so that we have that efficient repetition for future measurements.

    The first thing we’ll need to do is create this point of origin, usually in the lower left-hand corner. And because we have a rounded corner, and we don’t have a square, we’ll have to create a point of reference by two intersecting lines. So the first thing we’ll do is draw a simple line. In order to draw it, we have to tell it we’re editing the image. We’re going to click to put the line up.

    Now the next thing we’re going to do is you want to draw a perpendicular line to Line 1. We edit that, we bring it up, it shows up automatically because it knows what it’s doing, and we put it there, and there we now have Line 1 and Line 2.

    Let me now create an intersection to that line so that we have a point of origin. Line 1, Line 2, provides us with a point and we now have a point of origin for all of our measurements.

    The first measurment is, I want to measure the center of this circle to the point of origin to make sure it’s the right distance away. The first thing I’ll need to do is define the circle. So I go here to basic tools, and define a three-point circle. By rolling my mouse, I can increase the magnification of the image, and that allows me the ability to create my three-point circle.

    Now that I have my circle created, I can say that I want to measure a line, point-to-point, between Point 1 and Circle 1. And there is my measurement in microns.

    The next thing I want to be able to do here is measure the angle of this slot to my baseline. In order to do that, I first have to draw a line at that slot, so I’m going to do that; maybe magnify this a little bit. Click. Click, there’s my line. So now what do I want? I want to measure an angle. I want to measure an angle between Line 1 and Line 3. And now, I have an angle.

    As you can see over here, we’re now getting these lines, circles, etc. for reference, drawn onto our document, which will be important when we run the system…run the measurements later.

    Now I want to measure the distance between the width of this slot, here – to make sure the width of this slot is proper. So first I have to draw a line, so I’m going to draw a line, magnify just a little bit, click, and there’s my line.

    Now I want to draw a parallel line to that, so that I know that we have a square measurement. Parallel line to Line number 4…there is the line, and there is the other side of my notch. And now I want to measure the distance between those parallel lines—between Line 4 and Line 5, and I have that measurement.

    Now as you can see, all of those particular lines, circles, and points of reference are all laid out on this document. I can go ahead and save all of this, and create a Repetitive Measurement Sequence for future parts. So I’m going to go Save As, and I can call it Measurement Sample 1-1, and I will, and click, and that measurement sample is there.

    Now let’s go repeat what we did, but do it by being directed step by step.

    Measurement Sequencer Run. I’m going to run sample number one, we have everything here… okay, with the different lines, and you can see that those lines are on the document. So now we’re going to start at the top with Line 1, and the computer is going to actually give us these words that we’ve put in here, and I’ve added a few little tidbits as you can in this help text. So now as we go and click “Draw line. Initial X line for point of origin.” And we’re being told to draw the line, and where to draw the line. “Define perpendicular line. Initial Y line for point of origin.” Again, that purple line pops up. “Define large circle by three points.” Okay, so we’re going to zoom up and we’re going to define that part, and define that part, and define there… “Draw line. Draw line to measure angle of slot to X line of origin.” As you can see, we’re being shown where to draw. “Draw line. To measure width of notch, define parallel line” There. So we just stepped and did those three measurements very quickly, very effectively; everything’s okay.

    We can export this to a report and it pops up and it gives us the necessary measurements and tells us that the result was fine.

    Now what I’m going to do next is I’m going to go into Measurement Explorer I’m going go to Sample Measurement #1, I’m gonna make an edit, yes, okay, and everything is here. Sample 1…excuse me, is the one we want to make the edit on, and we want to make the edit on Sample 1-1, and we’re going to come down here, and what we’re going to do is, we’re going to—as we can in any of these measurements—put in a tolerance.

    So it shows a measurement is 893.221. I’m going to put in 895-900 and it’ll either pass or fail, and then we’re going to save that. And that’s Measurement Sample 1-1. So now if I go ahead here and apply, and go Sequence or Run, and I take Sample Measurement 1-1, I tell it to start “Draw line.” You’ll notice that I’m getting simpler commands. “Define perpendicular line. Define circle by 3 points. Draw line. Draw line. Define parallel line.”

    Boom. It failed. That tolerance tells us that we did not meet the max and min of 895-900 with a smaller line, and it failed. And as we export this to the report, we get a Failed aspect. We can label this part, print it off, and show graphically why this particular part did not meet the criteria.

    So that’s a very brief overview of the Measurement Sequencer using a simple stamping, and three simple measurements.

    Layer Thickness Measurement

    Layer thickness measurement is a module that allows you to identify and measure the thickness of layers or multiple layers of a sample image. It is best used in conjunction with the Auto Measure Module for greatest accuracy.

    Here we have a scanning electron microscopy image that has been calibrated and shows different layers that we want to be able to measure. So the first thing we’ll want to do in any image is understand what type of image do we have? Do we have a linear measurement, as we do here? Do we have a circular measurement? Think of a pipe with an inside and outside diameter and some kind of a protective coating on it, and we want to measure those individual layers…would be circular; general would be those that aren’t circular or linear; or a calo test. A calo test is a very specific and narrow function for paint coat and coating thicknesses, very thin paint thicknesses, such as in the automotive industry. Or very thin layers that might be on a specimen. A little bit narrow in its function. So if you have interest in working in that area, please touch base with us offline and we’ll work with you more individually.

    So back to linear. We need to define and be sure that we have as square an image as possible with our layers. We don’t want them to be skewed at a 40 degree angle or something to that effect. So we would define a baseline where we would click on this, and then trace across one of the layers to kind of square them up, and when we right-click, then the image would be skewed to even out those layers. And then we would use and apply limits to be able to make adjustments so that only the image itself is going to be looked at in order to measure our thicknesseses, and not the voids left by the skewing of the image. And we were quite square to start with, so we’ll just go back to that position.

    Again, it’s a calibrated image, so we have now the ability to set ourselves up and do these individual layers. So we start with a new layer. I’m going to call it the top layer. We can either use an auto detect function, a drawing function using the binary editor, or thresholding. Threshholding is predominantly done with color images where there already is a red, a green, and a blue image, and you want to separate that way. Being monochrome, this image won’t function very well, but just to give you an idea of what the defining work box looks like, here we have red, green, blue, or hue saturation intensity, but it doesn’t fit, so we’ll move on to the auto detect where we’re going to click on the auto detect function, bring our mouse up into the area, click on it, let it be drawn through that area, right click, and we fill it in.

    Now you’ll notice if I zoom up, we have one small area here that did not get drawn in, and as we get a little closer, you can see the irregularity shapes following a tracing. We have a couple of different ways we can deal with this one individual area. We can do something called gap closing, and here we have, under the the Question Mark, we have different ways with which we can deal with gaps there. We can either close all the gaps and just tell the software to work with the top and the bottom lines and include all the holes and the gaps. We can measure from the top down to the first hole or gap, from the bottom up to the first hole or gap, or we can define a maximal length between the gaps and provide the longest gap available. So in this case, we said close the gap, so that’s actually being ignored by the software. From a visual standpoint, though, if we’d like, we can go to the binary editor and we have a foreground and a background button, and here in the foreground I can go ahead and we can close this gap. There. And one more little…so now that gap has been closed.

    Next we can add another layer. First we exit out of the binary editor. And now we can add another layer, and this, of course, will be called the middle layer. We’re going to auto detect it, and you can see—there—follow that, and if we were to go ahead and show both, you can see how that interface overlaps very nicely.

    Now there are a couple of spots here, or voids, that we know belong to the bottom layer, so again we go to the binary editor. And we’re going to go to background, and we’re going to select our box, and we’re going to eliminate these areas from the middle layer because we know they belong to the bottom layer. Exit the editor.

    Add a layer. Minimize out. Now these areas with the binary editor, we’re going to go to foreground and we’re going to fill them in so that they do belong to the bottom layer. And this one here, I’m going to use a poly line instead of a square and just surround it, close it in. And for sake of, just an example, we’re going to leave this area open and just show it, that it is actually just an irregular part of the bottom of that layer. Exit the editor.

    We now have three layers, and we have our measurements showing mean, min, max, and standard deviation of the thicknesses. We chose to close gaps on all of the individual layers. We can then take this Excel and, and export it out to Excel, and immediately have that information available in that fashion.

    Now I’m going to go ahead and clear these, and I’m going to show you one of the other methods, which is the draw method. And we’ll do this in the same basic fashion, but we have here a transparency. And I’m going to put the transparency on zero for a second so that it’s—the colored sections are very opaque—and we’re going to go ahead and on the Draw. And that automatically brings up the binary editor. I’m going to click, click, and I’m going to fill in my section, and there. My section has been filled in, and I exit the editor. Now it’s very opaque. I’m going to clear that again. I’m going to draw it once more, and then before I fill it in, I’m going to roll my mouse. And you can see how the bottom line is moving down. Now this is just for sake of an example. I want to show you that, and I’m going to right click and we fill it in. Okay. We exit the editor.

    We’re now going to go to the middle section and we’re going to draw the middle section, fill it in, and there it is. So now we’ve exited that. If we show both of these in a full transparency, we just see the colors; we don’t see the actual edge of the samples. But if we go down to 50 degree transparency, we can see as we zoom up that the top layer does look like it’s evading into the middle layer, and there may be times where you have to make that visual judgement because the software can’t be 100% accurate all the time. So to maintain the math correctly, we have what we call “Keep Edges.” So here I’m going to say, for the top edge, I want the bottom, now watch what happens to my numbers when I click on Bottom, not much, but what happens when I go to Top here and adjust the edges? The numbers change. We go from None to Bottom, and you see how the numbers are changing, they go from None to Top. So this allows you to adjust your mathematics so that you can take into consideration these adjustments that you had to make a visual judgement on. Okay, that’s clear. Let’s clear that.

    Let’s zoom back—so that is basically how we would work with a linear image. So let’s work one now with a general image. So we’ll go here and open up a slightly different image, come back to our layer thickness measurement, and here is a curved section now—it’s not circular, so we’re going to do what’s called a “General,” and we’re going to clear both sides here. and the first thing we need to do is to define a polyline—a line that tells us the basic aspects of the edges or the layers we’re working with. So we’re going to click on Define a Polyline, and I’m going to start here, not directly at the edges; somewhat into the image, and we give the software some vectors that we’re now going to look at, and we’ll do our measurements inside these vectors, leaving blank the areas outside of the vectors.

    So we have two different layers here that we want to look at: the top and the bottom layer. If we go to Layer 1 and click on Draw, and come up with our pen and click, right-click, there’s our first layer. If we exit the editor, go to our second layer, Draw, left-click and then right-click, that’s filled in. Now we’ve got a little bit of an issue here so we’ve got to take a look at how we’re going to handle that. We can do it a couple of different ways. We can exit the editor, and we can come back here and clear the entire layer and we can try it again. That’s much better. Now we again make a visual judgment that this is part of that layer that has, you know, has infiltrated what looks like the substrate. But again, we’re going to keep that layer as is. And now when we take a look at what we have here, we have our two different layers. We have our mean, min, max, and standard deviation.

    So that’s how we would work with something semi-circular as well as linear, and this is the Layer Thickness Measurement Module on Nikon Elements.

    As in past sessions that we’ve presented to you, I want to thank Ryan McGaha from Nikon Metrology for his help and support in preparing this presentation. You can view this third and final webinar, as well as the entire Nikon Elements series, on our website at

    CZ: Thanks, Jim, for doing this presentation, and thanks to all of you who tuned in today. We really appreciate your time. We’re going to leave the questions field open for a while, so feel free to type in your questions, and as I mentioned at the beginning of this webinar, we will answer your questions individually offline in the coming days. And please check out our webinars page for upcoming McCrone group webinars. Thank you.


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