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02/16/2010

 

This is an abstract of a talk prepared for the Microscopy & Microanalysis Annual Conference, Philadelphia, August 2000. The format is changed somewhat, some material added, and the figures are inserted within the text in color.

LISPIX: A Public Domain Scientific Image Analysis Program for the PC and Macintosh*

D. S. Bright+, and K. G. Milans++
+ Surface and Microanalysis Science Div., Nat'l Inst. of Stds. and Technology, Gaithersburg, MD. 20899-8371
++ undergraduate, Dept. of Computer Science, Carnegie Mellon University, Pittsburgh, PA.

 

MacLispix,1 a public domain image processing system for the Macintosh,* has been applied to a variety of image processing problems such as analysis of diffraction spots,2 uniform display of x-ray maps,3 determination of fractal dimension of particle outlines,4 and analysis of data cubes.5 Due to interest from the PC community, we have ported the software to Windows,* renamed it 'Lispix', and distributed it for both platforms, along with example images, source and documentation.6

Lispix reads TIFF files and raw files (no image header), both with pixel types of signed and unsigned 8, 16 and 32 bit integers, 4 and 8 byte IEEE standard floating point numbers, and 3x8 bit RGB color. Lispix has a variety of standard image processing operations, such as thresholding, edge finding (gradient), filtering, scaling, Linear Hough Transform, false coloring, RGB color overlays and particle measurement. Clipped scaling, (after trimming outliers) is especially useful for display of x-ray maps, and images with noise or very bright or very dark artifacts. Images can be grouped. A group of images can be selected, loaded all at once, enhanced, zoomed and tiled across the screen for viewing.

These examples illustrate some of the features of Lispix: Figure 1 shows the buttons for controlling Lispix, which have positions and colors (colors lost for printing) relating to their function.

FIG. 1 Window with buttons for controlling Lispix. Most buttons are pop-up menus.

In current verions of Lispix, the above buttons are in a menu bar.


 

Using control windows like these eased the task of making Lispix work nearly the same on both the PC and the Mac. Each button is a pop-up menu, except for the Single Mode and Widgets buttons. The Single Mode button controls how images are loaded and handled: singly, by groups, by selection, or all images at once (groups can be changed with the Group button). The Widgets button opens up more windows with buttons, for special purpose operations. One of the widgets is the periodic table of the elements, shown in Fig. 2a. This widget is an interface for selecting elements (e.g., that are required or prohibited for a data base query), but it is also useful by itself. Clicking on an element displays a list of its properties (Fig. 2b), and the table can be colored (shown in gray level in Fig. 2a) according to the numerical properties in the list.

   

 

FIG. 2 a) Periodic table - shaded according to density. b) List of elemental properties for Osmium.

Figure 3a shows part of an electron diffraction pattern, a 16 bit image requiring clipped scaling to be visible. Figure 3b is the gradient magnitude , and Fig. 3c the gradient direction. All three images are in the same group since they are derived from image a, and so they all zoom and scroll together using the navigator shown in Figure 3d. Note that the gradient direction image clearly shows dim spots that cannot be seen in either image 3a or 3b, and yet the center positions of the brightest spots are still clear.

FIG. 3 a) Electron diffraction pattern, 16 bit gray level image. Faint spots not visible, bright spots saturated. b) Gradient magnitude of a, enhanced to show faint spots. c) Gradient direction of a - shows faintest spots along with brightest spots. d) Navigator window for scrolling a, b and c together.
 
Figures 3e,f and g show another application of the gradient of direction filter. Fig. 3e is a light micrograph of asbestos fibers. Fibers are not seen in some areas of the micrograph because they are too thin or lack contrast. On the other hand, the direction of the gradient in Fig. 3f, shows the presence of fibers in all areas of the image. The faint fibers are visible, and the darkest are still perceived clearly. Due to the shading scheme for indicating the direction angle of the gradient with a gray level, and due to the directional nature of the fibers, a few fibers are not seen distinctly - those that lie parallel to the apparent direction of illumination, indicated by the radial direction indicator in Fig. 3g. Moving this indicator with the mouse changes the shading, adjusting the apparent direction of illumination for clearest visibility of particular fibers.
 3e  3f  3g
Figure 3e,f,g (added). e) Light micrograph of asbestos fibers. f) Direction of gradient filter of e. g) Shading control - changes apparent illumination direction of fig. f.  (download image)

Figure 4a, and navigator 4b, show a thresholded scanning electron micrograph of nickel spheres. After using the blob widget, various measurements of each sphere (blob) can be shown and listed, such as the maximum diameter (Fig. 4c) and the outline and blob index (Fig 4d.) About a dozen parameters are available. Fig. 4e shows the tab delimited table of area and maximum diameter, used for importing these measurements into a spread sheet.

 
FIG. 4 a) Electron micrograph of Ni spheres, 10 m m nominal diameter, thresholded to select spheres using a slider (not shown). b) Navigator. c) Maximum diameters of spheres. d) Sphere outlines and indices. e) Table of sphere properties.
 
 
Figure 5 illustrates exploration of a data set of several x-ray maps7 taken with an electron probe. Since the pixel intensities in the maps are proportional to element concentration, and since various combinations of elements correspond to different phases of this multi-phase material, scatter plots, such as Fig. 5f, (and RGB color overlays -- not shown) relating two or three of the maps indicate compositions and locations of the various phases.
 
FIG. 5 a-d) X-ray elemental maps for Sr, Bi, Pb and Cu respectively, of precursor for ceramic superconductor. (50 m m field width, 16 bit gray level images.) e) Window (another widget - see text) for selecting Bi and Cu images for the Concentration Histogram Image1, or scatter diagram shown in f. f) Scatter diagram for all pairs of corresponding pixels in Bi and Cu images. Parallelogram drawn with mouse to select feature in diagram. g) Traceback - pixels corresponding to points in parallelogram shown in white. White region corresponds to superconducting phase.

 

References:
 
1. D.S. Bright, Microbeam Analysis 4 (1995) 151-163.
2. D.S. Bright et al., Microscopy and Microanalysis 4 (Proc., suppl. 2)(1998) 60-61.
3. D. E. Newbury, and D. D. Bright, Microscopy and Microanalysis 5(5) (1999)333-343.
4. D.S. Bright, Microscopy and Microanalysis 3(Proc., suppl. 2) (1997) 897-898.
5. Bright, D.S. " PC/MAC* Image Processing Freeware For Examining Spectral Images.", in this proceedings.
6. Available from http://www.nist.gov/lispix/.
7. Maps courtesy of Ryna Marinenko, NIST. Figs. 3a and 3e courtesy of Eric B. Steel, NIST.

 

* Certain commercial equipment, instruments, or materials are identified in this report to specify adequately the experimental procedure. Such identification does not imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the materials or equipment identified are necessarily the best available for the purpose.