June 1, 2004

Contents

RGB Overlay of Three Gray Level Images

Superconductor Precursor Xray Maps Example

Examining corresponding regions in three images at once using RGB overlays.

The images will open and be stacked or cascaded. In ImageJ, the images will be opened into a stack.  On the PC, only part of the images were visible. Dragging the lower right corner (double headed diagonal arrow cursor appears) to enlarge the window seemed to 'snap' the image in place.

These xray maps are 16 bit images, rather than 8 bit. NIH Image requires that these TIFF files be imported. They are scaled to 8 bits as they are read, but the scale factors are retained so that the Info window shows an approximation of the original pixel value as the cursor is moved over the image. In ImageJ, the images are opened as 16 bit images, and they are not scaled, except for display.  The 16 bit values appear in the status bar.

If the images are zoomed, their titles will show. On the PC, it seemed necessary to scale (Edit -> Rotate and Scale menu) the images up by a factor of 3 or 4 to have them display properly. This is tedious. In ImageJ, the images tile, looking like this:


For ImageJ, ignore these steps:

All of the images have 'collapsed' into one. Each image can be shown one at a time using the Stacks -> (Next Slice, Previous Slice or Animate) menus. When animating the stack, the left and right arrows will quickly step from slice to slice.

 I kept these three images.  

 Color overlay  Zoomed version of the overlay along with the LUT.
   


The green phase is dark, because the green image (center in the line of seven above) was dark.  To correct this,

The color overlay of the xray maps shows at a glance the grains grouped by chemical composition, since the pastel shade is determined by the relative intensities of the (quantitated) xray maps.


Not applicable to ImageJ because the RGB overlay in ImageJ is a true RGB  image.

The zoomed overlay shows the individual pixels. Note that the colors are in no particular order in the LUT. This means that the gray levels of this 8 bit image are in no straightforward way related to the gray levels in any of the original xray maps. This is a 'false color ' or 'pseudo colored' image - most image processing such as smoothing or sharpening or thresholding will give meaningless results. Looking at the gray level version of this image indicates why:

If sharpening, smoothing, or other processing is to be done (in Image), the operations must be done on the three original gray level maps, and then the results combined into a color image.


ImageJ:  Process / Sharpen has this as the result: