Tutorial 4: Using the Phase Tool


The Phase Tool allows the user to examine maps, identify compositional distinct regions (“phases”) and assemble a cumulative image that shows which areas of the specimen have been identified and which remain.  For the purpose of this tutorial, the term “phase” will apply to chemically distinct regions; excepting those phases that are structurally different, but chemically identical.  Other definitions for terms found in this tutorial are as follows:

Phase: a compositionally distinct region of a map

Phase Map: a cumulative image containing one or more phases defined from individual compositional maps

Compositional Map: an image of 1 element that has been fully corrected to convert from intensity to concentration

Thresholding: the process by which a user may select pixels whose brightness is within a defined range


This tutorial is meant to familiarize users with the recently developed phase tool, and to suggest a process for using it.  Unlike other tutorials which were meant to walk the user through a variety of techniques, this tutorial is very process specific.  That being said, the author wishes to stress that the technique shown in this tutorial is not the only way to use the Phase Tool. 

Note on the example used:  The author wishes to thank Dr. Richard Lindstrom for providing the material (a NIST soil SRM), as the example in this tutorial.

Note on the image files used:  The author has elected to use compositional X-Ray maps in this example.  These maps have been generated by creating K-Ratio maps (where K is the intensity of the unknown divided by the intensity of a pure standard) with Lispix, then applying a ZAF correction to each pixel.  While it is not necessary to use compositional maps (the threshold values will work regardless of the data range), it is very useful to do so because the compositional information can be checked against known minerals and phases.

The Lispix Window

Step 1: Opening Maps

Open the Phase Tool by clicking Tools / Phase.  Once opened click on the “Setup” button in the Phase Tool and select “Select and Load Maps.”  This will open a dialogue screen allowing the user to choose X-Ray maps previously generated.  For instructions on how to generate X-Ray maps from a data cube, refer to tutorials 1 and 2.  Once selected, the images will open “stacked”, thereby allowing Lispix to bring the appropriate image to the front for processing.

Alternatively, if the maps of interest are already open, click the “Setup” button and select “Select Map Images Already Open”.  This will display a dialogue box showing the names of the images already opened along with their sizes.  Choose the maps of interest and click “OK”.  This process will not stack the maps.

When the maps are correctly loaded, the number of maps will be shown left of the “Help!” button.

Step 2: Adding 1 Phase

At the top left corner of the Phase Tool, there is a “Define Phase” button.  This button actually toggles between the Phase and Map tools.  The Lispix phase tool follows the following process:

To add a phase, make certain the toggle switch says “Define Phase”.  Click the “Add” button to add a new phase.  In the example, the author has added a “Silicon Dioxide” phase to the list.

The name of the phase will appear at the bottom left in the tool.  Click the “Edit Color” button to change the color.  Lispix will automatically assign a unique color to each phase.


Step 3: Thresholding Maps in a Phase

Once a phase is listed in the Phase tool, click the “Define Phase” button.  The toggle will switch to say “Choose Map” and will once again be blank.  Now click the “Add” button to add a map to the Silicon Dioxide phase.  A list will appear with all of the maps that were loaded into the tool in step 1.  In this example, the silicon map titled “Si” has been added.

Below the selected map, a threshold slider will appear.  Below the threshold slider, a message box containing instructions will also appear.  Slide the threshold slider until the appropriate region of the map is colored in red.  Remember that pixel values that fall within the threshold are colored red.  When the appropriate pixels are colored, click “Continue” on the message box to save the threshold.


There are 4 values on the Threshold slider.  As listed from left to right, the values are:


Step 4: Generating the Phase Map

When the appropriate images have been thresholded (after the “Continue” button has been pressed) the Phase Tool can generate a phase map.  Press the “Show Results” button and select “Show Combined Phase Maps” to generate the cumulative phase map. 

Lispix will generate 3 images.  The first (shown at the farthest left) is the actual color phase map.  The second (middle) image is the multi use map.  Pixels colored white on this binary image indicate that two or more phases have been assigned to that pixel.  When analyzing a data cube, it is advisable to keep the number of multi-use pixels to a minimum.  Any pixel that is assigned to more than one phase will appear white on the color phase map.  The final map (right) is the zero use map.  Pixels colored white on this binary image indicate that no phase is assigned to the pixel.  For this map, the user is trying to decrease the number of pixels in it. 

Step 5: Editing Phases

Steps 2, 3 and 4 may be repeated until the user is satisfied with the phase results.  Add phases as necessary, add maps to the phases, threshold the maps, and generate the phase map.  As the process progresses, it may be necessary to change the attributes of the phase.  As of version 102, the user may only change the color of the phase.  Click the “Edit Color” button while the “Define Phase” toggle is activated. 

Note: As a list of phases is generated, click on the name of the phase to highlight it in red.  This selects the phase whose properties will be edited.

Step 6: Editing Maps

When the “Choose Map” toggle is activated, the user may edit the threshold values for any of the maps in the selected phase.  First, select the appropriate phase (when the “Define Phase” toggle is activated), then switch to “Choose Map”.  Select one of the maps (again, the selected map will be highlighted in red), and then click “Edit Threshold” to bring up the map and threshold slider.  Follow the same process as in Step 3 to threshold the map.

Step 7: Printing and Saving the Phase Tool

Click the “Setup” button in the Phase Tool to bring up some options for saving and printing the tool.  The “Save Tool” option will write a text file with the extension .lisp.  Opening this file using the “Load Tool” option will allow the user to load in all of the phases and thresholds.  Important note:  If you changed the name of the images using the “Change Name” button, you need to reopen the images and change the name to match those listed in the phase tool.

The “Print Tool” option will produce a text file that shows the phases, colors, maps and thresholds of all the tools in the phase map.  The text file is tab delimited and can be copied and pasted directly into MS Excel®. 


Tips, Tricks and Alternative Methods

This section is intended to document some tricks or useful methods for analyzing complex, heterogeneous materials using the Phase Tool.  Again, these methods may not be the best for all materials, but the author’s experience with concrete and soils characterization has led him to develop these additional methods.


(Alternative Title: Using the Phase Tool as an Interrogative Technique)

There are many instances in microanalysis where the analyst will be considering samples of unknown morphology and composition.  The distribution of phases and their subsequent chemical makeup is frequently unknown.  This was the case with the soil sample shown in this tutorial.  To solve this problem, author relied on three techniques to determine the phases present.

First, the user should start with the identification of large, easily recognizable phases.  In many soil systems, such a phase might be silicon dioxide or orthoclase.  Once these phases cover large portions of the map, more interrogative techniques can be used.

Second, the user should try to minimize zero use and multi use.  As the user creates phases, the zero use maps will ideally approach zero while the multi use map will stay at an ideal minimum value.  Even though the thresholded images may colorize pixels, they do not necessarily overlap, and thus, the pixels may not be included in the phase.  Consequently, should the pixels overlap too much, the multi use map will increase its percentage.  Given these criteria, the user can analytically determine the value or validity of a given phase. 

For example, let us assume that phase X covers ten percent of the map, but the addition of the phase causes the zero use map percentage to jump eight percent.  It is likely that only two percent of phase X is a genuine phase.  At this point, the user can adjust the thresholds for the phase, or delete the phase all together.

Finally, the zero use map can be used as a mask to determine what compounds have yet to be identified.  Using the Data Cube tool, click on the Plot button and select “Sum Spect with Mask.”  From the list of possible images, choose one of the zero use maps (preferably the most recent one).  Lispix will generate a plot showing spectra of the compounds present in the unidentified pixels.