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The term "concentration histogram Image" is used for historical reasons and because it is most used in conjunction with quantitated x-ray maps, where the axes do in fact denote concentrations. The CHI menu items can be used with any scaled images, and then the axes refer to intensities or pixel values. The histograms are also called scattergrams in the literature.
Concentration histogram imaging is one of the more important features of MacLispix. This function allows us to determine the populations of specific intensities within an image array or image array. For instance, in our laboratories we frequently use this technique to formulate compositional maps of weight percentages (reference). However, the applications of this function can be quite varied.
What is a Concentration Histogram Image (CHI)?
A CHI is formed by plotting the respective populations for a pair or triplet of images versus their intensity values. The CHI is a two or three dimensional generalization of a one dimensional histogram, which is a display of all the intensities within the image and the number of pixels that have each of those intensities (Figure 1).
The CHI is formed by finding the equivalent points in the selected images and then mapping the intensities of those points along their respective axes to a particular location or bin (for an example see Figure 2). The first three items on that list, X/Red Image..., Y/Green Image..., and Z/Blue Image..., are used to select the images that you wish to correlate with the CHI menu items. These are also used to select images for color overlays.
Images must be shown or displayed (scaled) before they are histogrammed -- this simplifies the 'binning' problem. All of the scatter diagrams have 256 bins per axis.
Traceback (super conductor precursor example)
The traceback function allows you to choose a specific region in the histogram and "traceback" the points in that region to find the areas in your original images that they correlate to. In our lab experience, we have found this function particularly useful in examining borderline or boundary regions in our images.
How do I use it?
To use this function you must first, of course, be working with a two or three dimensional scatter diagram. Make sure you have finished adjusting your histogram colors with the slider before starting the procedure for the traceback function. Next, click the traceback button. If there are more than one CHI windows, the front one will be used for the traceback. A window will appear on the screen asking you for a mask name for your CHI. A default name will be assigned, but these can sometimes be a bit long and you may want to use something shorter. When you finish selecting your name and have clicked the "OK" button, you will see a window flash in the upper left corner that says "mousing region". This indicates that you can now begin selecting your traceback region(s). To do this, use the mouse to position the arrow at some point around the region you wish to investigate. Then, while holding down the mouse button, outline the region you want to traceback. Be sure that you "close" the region, and when you are finished outlining, release the mouse button. You then place the arrow into each of the regions you selected, and while depressing the control key, click inside the regions. Upon doing this, your regions will be filled in, otherwise the region consists of the boundary only.
If you want to choose other regions, simply select those regions in the same way as you did this one. When you have completed highlighting all of your regions, depress the command key to activate the traceback.
You should now see your traceback window. This window will be the same size as your original images. If you like, you can now superimpose this image onto your originals. Simply select outline tcbk in the CHI menu item. You will first be asked to choose the traceback window which you can select using the given menu. Next, you will be asked which images or image arrays you wish to apply the outline to. You may select as many of these as you wish. When finished, click the "OK" and the traceback regions will be outlined in your original images.
The CHI's are displayed first as gray level images. These have limited visibility, so the thermalize option is used as a default. For small maps ( 128x128 or less) it usually is necessary to move these boundaries far to the left to see the bins with small populations - often the interesting areas of the CHI.
The scaling (thus the range) of the axes of the Concentration histogram Images are the same as the scaling of the im_scaled_array's of the associated windows.
Comparison of CHI's is sometimes easier if they are plotted with the same scales, that is, if the axes have the same ranges. This is done by scaling one set of images to the same ranges as the other set of images. Scaling can be done with the scale/linear button. When scaling is done on one set of images to match a range of another set, the images will usually appear dimmed.
3 Dimensional Plots (super conductor precursor example)
The 3D XYZ/normal option allows you to plot the data from three different images. It is created in much the same way as the two dimensional case except that you need a z/blue image. The orientation is controlled by the rotation button.