Color Mix Tutorial
Gatan, Inc.
5933 Coronado Lane, Pleasanton, CA 94588 Tel: (925) 463-0200 Fax: (925) 463-0204
May 2001
Contents
1 2 Introduction The Color Mix dialog
3 Simple map generation 4 Aligning the images 4.1 Coarse alignment 4.2 Fine alignment 5 Generating a final map
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1
Introduction
The Color Mix package has been developed as an aid to the visualization of multiple images within the DigitalMicrograph (DM) environment. Color Mix allows an aligned, color composite to be formed by assigning selected images individually to the red, green and blue orthogonal color channels. This tutorial describes the process of aligning the component images and generating the final color composite. Color Mix requires no special hardware or software beyond that supplied by the standard DigitalMicrograph environment.
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The Color Mix Dialog
To display the Color Mix dialog select COLOR MIX… from the ANALYSIS menu, as shown in Figure 2-1.
Figure 2-1. The Color Mix menu option.
The routine assigns each of the three frontmost images to the red, green, and blue channels of the final composite. If there are only two images, the frontmost image is assigned to the red channel, while the second image is assigned to both the green and blue channels. You can change the image assignment by selecting alternates from the 3 popup menus at the top of the dialog.
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KEY: 1. 2. 3. 4. 5. 6. 7. Specification of red, green & blue images Display limits for extremum values of component image Specification of reference and shift images for alignment Coarse alignment button Arrow buttons for alignment of channels in RGB composite Button to generate RGB map Button to generate a final, cropped RGB image
5 6 7 Figure 2-2. The Color Mix Dialog
By default, the intensity range of each image is mapped into the range 0-255 of the color composite image. You can change these limits using the fields in area 2 of the Color Mix dialog. The effect of doing so is addressed in the following section.
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Simple map generation
If the images are spatially aligned then you can simply hit the “Generate” button. This will combine them into a composite color image without applying any offsets . The process will apply the intensity ranges set up in area 2 of the dialog. You can adjust the strength of the red, green, or blue components in the final composite by changing the ranges in area 2 of the dialog from their default values. Figure 3-1a) shows a particular color composite built using the default ranges 0 – 255 for each of the red, green, and blue channels. Figure 3-1b) shows the same composite, but with the enhanced strength of the red component now lying in the range 100-255. You can see that in figure 3-1c, we have decreased the strength of the red component by setting the red range to be 0 – 100.
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a)
b)
c)
Figure 3-1. The Color Mix Dialog
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Aligning the images
It is often necessary to align the individual images before combining them to produce the color composite. Typically this might be necessary if the images are elemental maps acquired in the presence of spatial drift. Figure 4-1a shows a composite of carbon, nitrogen and oxygen generated without aligning the maps. Notice the yellow and purple edges that correspond to regions of overlap resulting from misalignment of the component images. 4
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b)
Figure 4-1. a) Composite formed without spatial alignment, b) composite formed after alignment. The Alignment section of the Color Mix dialog allows you to perform both coarse and fine alignment.
4.1 Coarse Alignment
In coarse alignment you grab and move each image in turn to align it with a reference image. To perform a coarse alignment 1. Select a reference image. Use the “Reference” popup menu to choose the image. The default reference image is the front most one. 2. Select an image to align. Use the “Shift” popup menu to choose the image. 3. Click the “Coarse Align” button. The button remains depressed and a copy of the image to be aligned is overlaid on the reference image (see figure 4-2 below). A number of Color Mix dialog elements are disabled in this mode.
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Figure 4-2. Reference image with image to be aligned overlaid. 4. Press the CTRL key and drag the image to be aligned over the reference image. Observe the images appear to “flash”. In addition, in the general,misaligned case, features in the images will appear to oscillate laterally. The images are aligned correctly when this oscillation is minimized. 5. When you are happy with the alignment click the “Coarse Align” button. Color Mix will note the required x and y offsets for this image. 6. Select the third image for alignment from the “Shift” popup menu. Repeat steps 4 and 5 for this image. All 3 images have now been roughly aligned. If you are happy with the image alignment at this stage then hit the “Generate” button to build the composite image. At this point Color Mix lists the offsets used in the Results window as shown in Figure 4-3 below.
Figure 4-3. Alignment offsets output on pressing the Generate button
4.2 Fine Alignment
If you find that the coarse alignment does not give you sufficient control over the image alignment you can use the arrow buttons to effect single pixel positioning of the images. 6
To align the images using the arrow buttons 1. Select the reference image and image to align as described for Coarse Alignment. 2. Click on the relevant arrow button to move the “Shift” image. Each button press moves the second image by one pixel. You can increase the step size to 5 pixels by pressing the CTRL key while clicking. The RGB image updates on each click – you can therefore view directly the alignment on the composite image. Note also that if the corresponding RGB image is not present, clicking on the arrow buttons immediately generates one. 3. Repeat step 2 on the third image.
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Generating a final map
If any of the images combined into the color composite has to be shifted by more than a few pixels, then the composite image will contain noticeable artifacts (streaks) at the edge where there is incomplete overlap (Figure 5-1a). You can crop the composite image to remove these artifacts by pressing the “Crop” button at the bottom left of the Color Mix dialog. Color Mix creates an image based on the common sub-area of the individual components. The resulting image looks cleaner but will not be of the same size as the originals (Figure 5-1b). a) b)
Figure 5-1. a) Uncropped color composite image b) composite that is cropped to common sub-area.
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