Copyright: © John J. Donovan


Help Contents
Contents

Introduction

Overview

Conventions

MicroImage Quick Start

MicroImage Menu Details

File Menu

Basic Menu

Advanced Menu

Acquire Menu

Setup Menu

Modes Menu

Window Menu

Help Menu

MicroImage Techniques

Choosing Colors

Registering an Image to a Coordinate System

How a 2d Histogram is Created

Image Processing

Configuring MicroImage

Initialization File Format


Overview

MicroImage, is an image acquisition and processing application, that allows users to rapidly acquire, enhance, manipulate and analyze digital images. MicroImage is a 32 bit Microsoft Windows application, which utilizes tools, icons, pop-up windows and pull-down menus to simplify complex operations and provide an easy to use interface for imaging operations. Intuitive point-and-click actions accomplish most MicroImage functions.

More:

Major Features of MicroImage

Image Processing

What You Should Know Before You Start


Major Features of MicroImage

For users who want to perform quick and easy image acquisition and processing techniques, the major features of MicroImage include:

•	Rapid image acquisition: acquire multiple analog, digital and pulse count data inputs simultaneously with just a few clicks of the mouse.

•	Rapid image enhancement and analysis: accomplish most functions within seconds.

•	Easy-access to functions via the Tool Bar: point and click an icon to activate many of the File, Basic and Acquire Functions.

•	Multi-image viewing and manipulation: MicroImage allows simultaneous display of multiple images (Multiple Document Interface). A click on the active window allows instant image manipulation.

•	Instant access to image histogram: with simultaneous display of image histogram and statistics.

•	Arbitrary Zoom: select any size to zoom in or out.

•	Print Image: print the entire image, or the current zoom of an image.

•	16 bit Image Depth Support: 64K gray level for large dynamic range images.

•	Real-world coordinate registration: images are registered in X and Y stage or beam coordinates and in Z (color depth), based on the input data type.

•	Image rectification: modify the aspect or perspective of an image using just two points or 4 or more control point geometries.


Introduction - Overview - Image Processing
Image Processing

Basic Image Processing

Advanced Image Processing


Basic Image Processing

The basic menu in MicroImage includes a number of simple image processing and enhancing functions:

•	Duplicate

•	Crop

•	Statistics

•	False Color

•	Set Gray Scale

•	Histogram Equalization

•	Brightness/Contrast

•	Linear Stretch

•	Size/Rotate

•	Optimize Palette


Advanced Image Processing

The advanced menu in MicroImage includes a number of sophisticated image processing and enhancing functions:

•	Rectification

•	Mask

•	Formula

•	Convolution

•	Composite

•	Filter

•	Histogram-Histogram processing (2D histogram images)

•	Histogram-Histogram trace-back

•	Classify (modal image analysis)

•	Mosaic imaging


What You Should Know Before You Start

Windows Operating Procedures

Hardware Requirements


Windows Operating Procedures

To use MicroImage, users should be familiar with standard Windows operating procedures, such as:

•	Window manipulation: opening, resizing, moving and closing

•	Menu manipulation: selecting commands

•	Dialog boxes: selecting options

•	Basic file manipulation procedures: opening, closing, saving, and exiting

Refer to your Microsoft Windows User's Guide for detailed information about these operations.  Users also should have a basic understanding of microscope, or photo image-processing, as well as familiarity with either PCX, TIFF or BMP image file types.  Users should have a working knowledge of capturing and saving images to at least one of these file types.


Hardware Requirements

MicroImage hardware requirements are:

•	Any Pentium II desktop or faster processor running Windows 95/98 or NT  4.0.

•	Minimum 32 Mb RAM and 200 Mb available hard disk space.

•	VGA high resolution video card with 16 bit (32K colors) or 24 bit color support.

•	High-resolution color monitor (17" minimum, 19" or 21" preferred) running in at least 800 x 600 screen resolution.


Conventions

MicroImage and the User's Reference manual follow these conventions described below for data formats, image coordinates and registration.

More:

Data Formats

Manual Conventions

Image Registration

Coordinate Systems


Data Formats

MicroImage recognizes a variety of standard image formats, including:

•	PC Paintbrush format (PCX), 8 bit

•	Tagged Information File Format (TIFF), 8 or 16 bit

•	Bit Map format (BMP), 24 bit, 8 bit, 4 bit, or 1 bit

•	Golden Software Grid (GRD) Surfer, 32 bit (real)


Manual Conventions

The first letter of key screen or menu items is capitalized throughout the manual, such as 'Tool Bar.'

•	'Click on an item' means to position the mouse so that the cursor is on the item then click the left mouse button once.

•	Double click means to follow the same routine, but click the left mouse button twice.

•	'Drag a box' means to position the cursor at the point where the upper left corner of a defined area begins.  Click and hold the left mouse button, then drag the mouse to create the box.  Position the cursor over the lower right corner of the box then release the button. Several MicroImage functions require the use of this operation.

•	'Pick images' mean to select one or more images by clicking once on the image area of each image.


Image Registration

All images acquired with MicroImage are "registered" for X-Y and Z dimensions. MicroImage stores this real world dimensional registration data in a private TIFF tag in the image file. This feature is only available for TIFF files. Programmers interested in accessing this TIFF tag for special processing options should contact Advanced MicroBeam for documentation of the TIFF tag registration fields.

The X-Y registration is determined by the "Cal Microns" and "Cal Y Microns" keyword values for relative or absolute image registration in the MICROIMAGE.INI file. In relative image registration the center of the image is 0,0 microns and the image registration is simply based on the magnification used to acquire the image. This method is used if no stage motors are specified in the MicroImage initialization file.

MicroImage will instead acquire images using absolute image registration referenced to stage coordinates if stage automation is present. The X-Y registration for absolute image registration is determined by both the "Cal Microns" and "Cal Y Microns" keyword values and the "Stage To Microns" keyword value in the MICROIMAGE.INI file along with the actual stage position at the time of acquisition. In  absolute image registration, the image coordinates are the actual stage coordinates in microns.

The Z registration for analog images is determined by the "zlo" and "zhi" keyword values in the MICROIMAGE.INI file. Digital and counter images store data in actual counts and so are Z registered to the image depth range (8 bit = 0-255 and 16 bit = 0-65535).

The image registration can be changed at any time from the Window | Properties menu. Note that Auto TIFF stage scan images from Probe for Windows and SURFER GRID (*.GRD) files imported into MicroImage are automatically registered for X-Y and Z dimensions using the default palette bar units keyword from the MICROIMAGE.INI file.


Coordinate Systems

Coordinates refer to the fixed x, y locations in an image.  The coordinate system may be any user-defined coordinate system, i.e., a scaled drawing of any unit. By default MicroImage assumes a micrometer or micron coordinate system for XY registration. However, images may be registered using any unit system.  See 'Registering an Image' for more information.


MicroImage Quick Start

The following key concepts are necessary to understand and successfully use MicroImage.  They include a screen overview, descriptions of the screen components, the main menu bar, tool bar and histogram and information windows.

More:

Installation

Screen Overview

Video Display settings

Editing the MICROIMAGE.INI File

Startup Files (INIWIN30.EXE)


Installation

From CD-ROM

From Internet Download


From CD-ROM

To install MicroImage, insert the MicroImage CD-ROM in the CD-ROM drive. Begin the installation from the Windows 95/98 or NT Start button. To begin the installation:

Step 1 Open the Start button on Windows Task Bar and click the Run menu.

Step 2 In the "Run" dialog box, type the drive where the CD-ROM is inserted and the command "setup."  For example, type "d:setup" if the CD-ROM is drive "D" drive, then click OK.  Follow the directions on screen.


From Internet Download

To install MicroImage from downloaded files from the Internet, first download the installation zip file from the Advanced Microbeam ftp site and save to a temporary directory on your hard disk (for example, C:\TEMP\MI-32). To begin installation:

Step 1 Unzip the downloaded zip file using Pkunzip or WinZip program with the password supplied by Advanced Microbeam to a temporary folder on your hard disk (for example, C:\TEMP\MI-32\EXTRACT).

Step 2 Using Explorer, browse to the folder where the unzipped files are and double-click on the file "setup.exe". Follow the instructions on screen.


Screen Overview

The MicroImage start up screen consists of these items:

More:

Menu Bar

Tool Bar

Histogram/Information Window

Image Information

Histogram Information

Percent Done Metering


Menu Bar

The main menu bar consists of eight items: File, Basic, Advanced, Acquire, Setup, Modes, Window, and Help.  These will be discussed in detail in the following sections.

An icon also exists for many menu commands so that functions are quickly accessible.  Access menu commands by clicking once on an icon, or by using pull-down menus in the menu bar.


Introduction - Screen Overview - Tool Bar
Tool Bar

The Tool Bar is the horizontal row of icons at the top of the screen. These icons provide quick access to commonly used function of the MicroImage program.

The first three icons in the Tool Bar are New, Open, Save. The remaining icons represent image processing or acquisition functions found in the Basic, Advanced and Acquire menus. Allow the mouse cursor to dwell over the button to see a short caption describing each icon.

The 4 individual tool bars may be dragged and docked to other locations, either as one row or as standalone windows.


Histogram/Information Window

The Histogram/Information window is a dockable window in the lower portion of the screen.  Both the image histogram and information about the image are displayed in this window. The information window displays additional information when the cursor is over the image and histogram statistics when the cursor is over the histogram.

Note that the Histogram/Information window can be inadvertently placed outside the visible area of the main window if the main window is resized. To avoid this it is suggested that the Histogram/Information window be "docked" to the main window by dragging and dropping it on the bottom of the main window.

An image must be opened for a histogram to be present in this window, since histograms are a graphic display of image brightness values.  The scale at the bottom  of the histogram ranges in value from 0 at the far left (black) to 255 at the far right (white) for 8 bit images and 0 to 65535 for 16 bit images.

When the cursor is within an image, the information window displays the image name, its size in pixels, the range of brightness values, and the x, y coordinates and pixel value (z) at the cursor. The window also identifies whether the image is registered to a real-world coordinate system and gives the real world coordinate vales.

The information also provides additional information on various acquisition and image processing elapsed time and percent done metering for extended operations.


Image Information

When the cursor is over an image, data about the image location appears in the information window. Data includes the image name, apparent scaled size and pixel and color dimensions. Also, the registration information and real world coordinates (if the image is registered) are separately displayed.

Here the cursor is on an image, which is being displayed at 99%.  The  pixel width is 157, the height is 157, and it has 256 colors.  Not Registered means there is no real world coordinates defined for this image.  The lower right says the cursor is on position 81, 73 and has a Z color value of 26 (out of 256).

This is a different image, one that is registered (that is has a world coordinate system defined).  The X, Y and Z coordinates indicate real world coordinates in this case are X = 23178.067, Y = 30669.62 microns and Z = 1841.1 data units.


Histogram Information

When the cursor is in the histogram window, data about its location appears in the information window.  The data includes the index number, which is the brightness value between 0 and 255, and the number and percentage of pixels having that particular value.

Placing the cursor in the histogram of a non Z-Registered image displays the Index number (170), how many pixels have 170 as an index (79), and the percentage of the image that are index 170 (0.56%)

This cursor here is on an image with a real world Z Registration defined for the image in Wt. Percent Fe.  It indicates that in this case, the cursor is on the histogram where the values represent a Wt. Percent of Fe of 9.7871.


Percent Done Metering

The lower right field in the Histogram/Information window indicates how far an operation has progressed.

In this case, the operation is 69% complete and has 2 seconds remaining.


Video Display settings

MicroImage is a 32 bit application software that requires Windows 95/98 or NT and benefits running in at least 800 x 600 screen resolution. MicroImage also requires more than 8 bit video for accurate display of multiple palettes. That means a minimum of 16 bits (64k colors) or 2 bytes for each pixel of video RAM.  This will ensure that the user will see multiple color and gray scale palettes in "True Color" at the same time.

To change the video settings for your desktop, simply right click the desktop in any blank area, select the Properties and click the Settings tab from the Display Properties dialog. Always, make sure that you have enough video RAM to support the selected video resolution and color depth before attempting to change the video driver. The following table provides some guidelines:

Resolution	Colors	Video RAM (minimum)
800 x 600	64K	960000    (1MB)
1024 x 768	64K	1572864  (2 MB)
1280 x 1024	64K	2621440  (4 MB)
1600 x 1200	64K	3840000  (4 MB)


Editing the MICROIMAGE.INI File

MicroImage reads an initialization file called MICROIMAGE.INI in the C:\Program Files\MicroImage (or installed) directory to obtain the microprobe, microscope or SEM hardware configuration and user preferences. This file must be present for MicroImage to run. If MicroImage does not find this file then it creates a default file using internally stored default values.

If you want to customize the MICROIMAGE.INI file for your specific machine configuration, use a standard text editor such as NotePad, to change the number, type and name of the analog, digital, pulse counter, frame grabber or CCD input channels and the "probetype" field. Valid "probetype" values are "SEMQ", "JEOL", "CAMECA" and "DEMO". Some fields, such as "make", "model", etc. are for TIFF file informational purposes only. The entry fields are documented below in this help file. See "Editing the MICROIMAGE.INI File".

Note that the PROBEWIN.ELM file (if it is present) x-ray symbol and line channel names will overwrite the default digital and counter input channel names from the MICROIMAGE.INI file  if they are present. The PROBEWIN.ELM file is created by the Probe for Windows program and updated each time a tunable spectrometer is moved to another element position.

The PROBEWIN.EDS file is also used to store EDS ROI (region of interest) channel designations. The PROBEWIN.EDS file is created and updated by MicroImage each time the user modifies the channel names.


Startup Files (INIWIN30.EXE)

It will be necessary to add the MicroImage initialization utility (INIWIN30) program to the Windows 95/98 or NT Startup menu folder. Simply add a shortcut that points to the C:\Program Files\MicroImage\Iniwin30.Exe file and drop it in the Startup folder. The shortcut should be edited to use a command line argument to run the utility depending on the logic of the external beam control input and the desired analog to digital range and initial digital to analog level.

Usage:  'iniwin30 ([h|?] | {[b|u] [p|n] [value] [address]})'

h|? - print help syntax message and exit

b|u - A/D input range -5v->+5v or 0v->+5v

p|n - Control output high true or low true logic (positive or negative)

value - initial value for control logic port (A) range 0-255, preceded by "v"

address - base address (decimal) for Win95 Ueidaq driver, preceded by "a"

All arguments are optional. If a parameter is not given then the defaults are: bipolar, positive, 0, and 576. If the print help syntax argument is given, no other actions are taken. If the help syntax argument is not given, all actions are executed and a summary is echoed to the screen.

Example: "iniwin30 b p v0 a576" will give the same results as no arguments.

Note that under Win95 and Win98 the base address argument is required (unless the default baseaddress of 576 decimal (240 hex) is used by the board). This argument is not used when running under Win NT.

Remember to precede the value argument with the letter "v" and the base address argument with an "a". The base address default is 576 (hex 240) and the value must be in decimal. A non-default setting would look like this:

Example: "iniwin30 u n v255 a800" is a non default usage

Configures the Win30 card to unipolar A/D input, negative control logic polarity, control logic on and base address 800 decimal (320 hex).

If you installed MicroImage to a directory other than C:\Program Files\MicroImage, edit the shortcut accordingly.


File Menu

The File menu allows users to open, close, save and print files, or to exit from the program. File types are images and false color palettes, and the list of file types includes several standard and enhanced image formats including BMP, TIFF, PCX and others.

Open	Alt, F, O	Opens an existing image or false color palette file
Close	Alt, F, C	Closes the active image
Close All	Alt, F, L	Closes all images
Save	Alt, F, S	Saves changes to an existing file
Save As	Alt, F, A	Saves a new file; use file type as extension
Save History	Alt, F, H	Saves the current image history to a text file
Print	Alt, F, P	Prints entire image, current zoom, or prints to file
Print Preview	Alt, F, V	Print Preview entire image, current zoom
Print Setup	Alt, F, R	Open the Windows Print Setup dialog box
Exit	Alt, F, E	Terminate the MicroImage application


Basic Menu

The Basic menu provides a number of simple image processing functions that can be used to easily modify or enhance digital images.

More:

Duplicate

Crop

Statistics

Contrast Enhancement

False Color

Display Palette

Rotate/Flip

Normalize (16->8)


Duplicate

Many functions require the use of duplicate images.  To make a duplicate, load an image then select Duplicate from the Basic menu.  Tile the duplicate images for simultaneous viewing. Duplicate copies the following items from the source image:

•	Image Data (Pixel Values)

•	Image Palette (Color Lookup Table)

•	XY Coordinate Registration

•	Z Type Registration


Crop

Use the Crop function to isolate a smaller portion of the overall image, or to remove unwanted or unnecessary portions of the image. To use the crop function, click the crop icon or select Crop from the Basic menu. A dialog box identifies the active window and the x, y cursor coordinates.  Drag a box to define the cropped image, then release.

The cropped image appears as a new window.

If the original image was registered, the new cropped image will automatically contain the transferred correct proportional registration information.


Statistics

This function provides instant statistics for an image, an area of an image, or a transect through an image. With this function you may calculate:

•	Image or area size - width, height, and area in pixel units or real-world units

•	Center coordinates - center x and y of the image, area or transect

•	Average pixel value

•	Standard deviation

•	Minimum and maximum brightness values

•	Histogram - image, area, or transect

This dialog box appears when the statistics menu is clicked:

Calculated statistics instantly display for the corresponding open image.  When performing statistics on a masked or filtered images, the Exclude B & W checkbox may be used to ignore the contribution from pixels with values of 0 or 255 (0-65535 for 16 bit images).

To define an area for statistical calculations, click Choose Area and drag a box with the cursor to define it.  The dialog box gives the image name and x, y cursor coordinates at the left value box.  Click to select the upper left corner of the box, then drag a box to the lower right coordinates.  The right value box displays the x, y cursor coordinates for the lower right corner.

To define a transect, click Choose Transect then use the mouse to click the two end points.  Select the points and the dialog box gives the cursor coordinates.

Save statistics as a text file.  Before selecting an image, area, or transect, type in the label name.  You can create a new file to accommodate several statistics directly from the Statistics dialog box.  To do this, click the Log File box then type the destination drive and file.

For instance, to save the image statistics below, follow these steps:

1. Type the label name: 	Ore Sample 4-5746

2. Type the log file:	C:\Temp\5746.Txt

3. Click Choose Area

4. Drag a box to define the desired image area -- either all or part

Exclude B & W ignores brightness values of 0 and 255 so that these extremes do not affect the average value (mean).  This is a particularly helpful technique when calculating statistics on a filtered image, which has a black (0 value) background, or on a high-white image (255 value).


Contrast Enhancement

This menu contains a number of options to modify or enhance an image by either manipulation of the image palette or the image data itself.

More:

Histogram Equalization

Linear Stretch

Set Default Scale

Set Color Scale

Set Brightness/Contrast

Optimize Palette

Negate Palette

Stretch Palette

Unstretch Palette


Histogram Equalization

Histogram Equalization is a type of non-linear contrast enhancement useful for low-contrast images.  Applying this function will significantly brighten a dark image or darken a light image, making it easier to distinguish features for visual interpretation.

Pixel values redistribute into a set number of gray-scale classes, to make an equal number of pixels in each class.  This results in the most populated range of brightness values receiving the greatest contrast enhancement.  Depending on the image information content, fewer or greater numbers of classes may produce a more desired result.

To activate this function, click Histogram Equalization in the Basic | Contrast Enhancement menu.

Select the number of gray-scale classes for value reassignment by clicking in the dialog box.  You may select up to 15 classes.  Select whether the transformation should occur for the image or for the palette.  Transforming the image permanently changes the image data.  Transforming the palette only applies a "false coloring" to the image, and does not change the image data.  Click OK to continue


Linear Stretch

This type of linear contrast enhancement, sometimes called a contrast stretch, dramatically increases the contrast of an image having brightness values within a narrow range of the histogram. This happens by "stretching"' the original brightness values, or a percentage of the original values, to fit the entire gray scale.

The entire gray scale is 0 to 255 (0-65535 for 16 bit images).  Linear Stretch excludes the original brightness values in the minimum and maximum 5% of total area of the histogram (total number of pixels in the image).

Set the Starting and Ending Parameter pixel values or percentages, and Transformation Type which will determine whether the change will affect the palette or the image. As with other image transformation techniques, selecting Transform Image permanently changes the image data.  Selecting Transform Palette only applies a "false coloring" to the image, and does not change the image data.


Set Default Scale

Set Default Scale permanently applies the default color scale to an image. The image is immediately transformed to a normal color scale. This function is useful when it is necessary to "undo" false coloring previously applied to an image.


Set Color Scale

This menu allows the user to select a start and end color for quickly creating a two color interpolated palette.


Set Brightness/Contrast

This function alters the brightness and contrast of an image. To use it, load an image then select  Brightness/Contrast under Contrast Enhancement in the Basic menu. This dialog box appears:

Change brightness and contrast together or as separate functions.  To change either functions, drag the slider bar left or right.  You may preview the changes by clicking the Apply button.  Changes made in brightness and contrast are not fully implemented until you click OK.

Clicking Auto Apply automatically applies the changes as you move the slider bars. If Auto Apply is not selected, the changes do not occur until you click Apply. Click Cancel to quit the Brightness/Contrast function.


Optimize Palette

This function is useful when you want to reduce the color depth of an image. Usually, after applying a false color or classify procedure, the resulting image may have a less than optimal color palette and bits per pixel setting.  This function analyzes the image to determine if an optimization can be made.  If one can be made, it will indicate this by Enabling Sort, Compress, and Delete check boxes.

This function does not cause any loss of color data to the original image.  The resulting image will look exactly the same as the source.

Palette is Random

If this check box is enabled, it means that the color palette is not sorted by intensity.  This means if you view the image on a B&W screen (i.e. laptop or pentop), the image will not be accurate.  Click on Sort to sort the palette.

Duplicate Colors Present

Duplicate colors means that two different pixel indexes reference the same exact color.  Click on Compress to combine the two indexes into one.

Unused Colors Present

Unused colors are colors that are not referenced by the image.  Click on Delete to remove these colors.

Minimum Number of Colors Possible

Indicates the minimum number of colors given the chosen optimizations.

Minimum Color Resolution Possible

Indicates the minimum number of bits per pixel needed to represent the image after optimization.  The smaller this value, the less memory the image will consume.


Negate Palette

Inverts the colors in the palette. each RGB palette entry is replaced by values calculated from (255-R) (255-G) (255-B). The image data is unaffected.


Stretch Palette

This menu item is used to "stretch" the color palette to fit the actual image minimum and maximum. For example, if an 8 bit (0-255) image contains pixel values from 100 to 200 and the current palette is a thermal palette (black-brown-red-orange-yellow-white), then the unstretched image will display colors only from orange to yellow. To use the full palette for the actual image range, select the Stretch Palette menu item. A Pick Images dialog will appear allowing the user to select one or more images for the stretch palette operation. Click "OK" when the last image has been selected.

Note that disk files opened from the File | Open menu are not automatically stretched. If the opened disk image appears dark, then it may be necessary to use the Stretch Palette command to properly see the image.


Unstretch Palette

This menu item is used to "unstretch" the color palette to force the image display to a 1:1 relationship (assuming an 8 bit image) between palette color and pixel value. To use the minimum palette for the actual image range, select the Unstretch Palette menu item. Again, a Pick Images dialog will appear allowing the user to select one or more images for the unstretch palette operation. Click "OK" when the last image has been selected.


False Color

False Color allows you to assign a color to a gray-scale value, giving "color" to a normally gray image.  Assign the color to any range of pixel values, to unify and distinguish large blocks of values.

For example, you may want to examine the location of pixel values between 100 and 150 in an image. The false color function allows you to set the range of values, pick a color to assign to that range, and instantly apply the assigned color.

Choose the False color type you desire.  The following histograms illustrate the two different types of False Color.

Interpolated False Color

Pixel Range False Color

More:

Interpolate Mode

Pixel Range Mode


Interpolate Mode

Interpolate lets you choose distinct points in the histogram and assign a color to it.   The color is then "interpolated" or faded from one color to the next.  You need at least two colors defined before you will see any results.

You can select the location of the color by "clicking" on the histogram.  The cursor is then shown directly beneath the histogram. The following buttons operate uniquely to Interpolate:

ADD COLOR

Adds a new Interpolation Point to the histogram.  You choose the color for this point of the histogram.

DELETE COLOR

Deletes the color above your "interpolation cursor".  If the interpolation cursor is not on a color, this button is disabled.

CHANGE COLOR

Changes the color above your "interpolation cursor".  If the interpolation cursor is not on a color, this button is disabled


Pixel Range Mode

Pixel Range lets you assign colors to ranges of pixels.  Every pixel within that range is then assigned that color.  You may have one or more pixel ranges defined.

You can select a range by clicking and dragging over an area on the histogram.  The range is then shown directly beneath the histogram. The following buttons operate uniquely to Pixel Range Mode:

ADD COLOR

Assigns a color to the selected range.  This overwrites colors that may be defined within the range.

DELETE COLOR

Deletes the range.  The selected range must start and end within the range you wish to delete.  If this is not the case, this button is disabled.

CHANGE COLOR

Changes the color of a range. The selected range must start and end within the range you wish to delete.  If this is not the case, this button is disabled.

USE IMAGE TO SELECT RANGE

Allows you to define a rectangle on the image.  The minimum and maximum values in that rectangle will become the new range.

The following buttons operate the same under Interpolate mode and Pixel Range mode:

APPLY

Applies selected ranges to the image

SAVE

Saves defined color ranges as an .fc (false color) file

LOAD

Loads an existing color range which was previously saved

NEW

Eliminates all existing color ranges from the dialog box and any applied color

See Jenson, John. Introductory Digital Image Processing: A Remote Sensing Perspective.  Englewood Cliffs, New Jersey: Prentice-Hall, 1986.


Display Palette

Display the current full palette as an image window.


Rotate/Flip

Rotate/Flip allows you to rotate and/or flip an image.  Rotation may be done by flipping the image vertically or horizontally, or by turning the image in 90 degree increments either clockwise or counterclockwise.

To Rotate or Flip an image, select Rotate/Flip in the Advanced, Contrast Enhancement Menu. This dialog box appears:

To flip or rotate an image, click the desired option.


Normalize (16->8)

Converts a 16 bit image to an 8 bit image.

The 16 bit data values are normalized to 0-255 regardless of the true minimum and maximum data values. The actual minimum and maximum of the data are preserved in the z-axis registration of the new 8 bit image.

This function can be used before saving a 16 bit image to TIFF format for use by those programs which do not support the two byte integer (16 bit) TIFF specification.


Advanced Menu

The "Advanced" menu contains a number of useful operations for sophisticated image processing. They are used to provide advanced image processing techniques for acquired digital images.

An important part of image processing involves the use of image "masks". An image mask is merely a partial extraction of image information used to select regions of interest in the image data (histogram dimension) by setting a range of pixels to zero while maintaining the remaining pixel information. In MicroImage a mask is merely another image of the same pixel dimension (XY) created by an acquisition or derived from another source.

More:

Modify Image

Convolution

Filter

ReSize

Transfer Info

Rectification

Classify

Histogram-1d

Histogram-2d

Concatenate Images

Special Effects


Modify Image

Make Mask

Mask Image

Formula


Make Mask

The Make Mask function provides clarity in interpreting a source image by layering a mask image over it. In other words the mask image is applied to the source image to create an image with pixels that are zero wherever either the source image pixels are zero or the mask pixels are zero. Where the mask image is non-zero the source image is unchanged.

To use Mask, select make Mask in the Advanced, Modify Image Menu.  A dialog box appears that asks for the source band, or the band of interest.  Position the cursor on the source band and click once.

A second dialog appears that asks for the mask.  This is the band that will provide the clarity for the band being analyzed.  Position the cursor on the mask band and click once.

The function creates a new image that contains the masked image. The final image color appears the same as the source band.


Mask Image

The "Make Mask" menu item will create a black and white (pixels of value 0 or 255 only) image mask based on the pixel value of the selected pixel. All values less than the selected pixel will be colored black and all values greater will be colored white.

The user chooses pixels on any image. A mask is created that is of equal XY pixel size. Pixels that are greater or equal to the chosen pixel will be converted to 255, the remaining pixels of lower value are converted to zero.


Formula

The formula function enhances an image by modifying the intensities of grouped pixels from one or more images, each containing informationally related spectral bands.

A spectral band is image information that is related on a pixel by pixel basis to another images. For example: in acquiring BSE, Si Kα and Fe kα images on a specified sample area, one has obtained three related spectral bands that may be utilized for phase analysis and other purposes.

This function applies a formula, or algorithm, to each pixel. Adding or subtracting values to the image darkens or lightens the pixel values, resulting in a left or right shift of the histogram.

To apply a formula to the image, go to Formula in the Advanced Menu | Modify Image menu. This dialog box appears:

Scroll through the list of pre-saved formulas and click to select one, or type in a custom formula.  Next click the necessary color bands with the cursor.

Formulas do not always require the use of all spectral bands. For example, the Darken formula (A - 40) requires selection of only a single band. Remember, calculations occur only on gray scale (8 or 16 bit) pixel values, not on red, green, or blue values.

This function includes a pre-saved set of six formulas that function as follows:

Function	Displays image with:	Formula
flat field correction	pixel values corrected for background variation, where a is the flat field image and b is the signal image	(128/a)*b
brighten	pixel values lightened - histogram shifts right	A + 40
darken	pixel values darkened - histogram shifts left	A - 40
increase contrast	pixel contrast increased - histogram is lengthened	(A * 2) - 128
decrease contrast	pixel contrast decreased - histogram is compacted	(A * 0.5) + 128
average	pixel values averaged (for three bands)	(A + B + C) / 3
Note: You may permanently add your own formulas by editing the file FORMULAS.TXT

You may use a custom formula rather than a pre-saved formula.  Use standard mathematical symbols and numerals combined with single-letter variables representing the bands.  Complete the operation just as you would using a pre-saved formula.  Valid characters are A through Z,  1 through 9, period, (, ), *, /, +, and -.  Note: use parenthesis liberally since there is no mathematical precedence with the operators.

Note: adding one to all pixel values will insure that a mask will not contain zeros. Subsequently one may add or subtract mask images to include or exclude complex sets of pixels from images.


Convolution

The Convolution command applies a spatial filter matrix to each pixel that either enhances features or removes noise. The convolution applies to the entire image.

To apply a convolution to an image:

1. Select Convolution from the Advanced, Modify Image menu.

2. Choose one of the matrices in the pull-down list.

3. When you release the mouse button on a matrix selection the convolution automatically changes a duplicate of the active image.

4. The following convolutions -- all 3 x 3 kernels -- are available in the pull-down list:

Filter Name	Description and Function
Low Pass	Low pass (low frequency) filters enhance images by blocking high spatial frequency.  This image smoothing removes noise, but will blur the image at the edges.
High Pass	High Pass filters enhance detail by sharpening edges and contrast.
Shift Edge   Enhancement	A type of linear edge enhancement, these filters emphasize value gradients of the image.  Vertical (V) filters enhance vertical edges.  Horizontal (H) filter enhances horizontal edges.  The sum of these two enhances edges in any direction.
Gradient Edge Enhancement	These filters, also known as compass gradient masks, are used to perform two-dimensional enhancements in a directional orientation, and are useful for finding specific lines in an image.
Laplace Edge Enhancement	These filters highlight edges in any direction.
Note: You can permanently add your own convolutions by editing MATRIX.TXT.


Filter

Filtering an image allows you to isolate a defined cluster of pixel values within a range.  To use the filter function, load an image then select Filter in the Advanced, Modify Image Menu.  Enter low and high values in the dialog box to define the range of extracted pixel values.

Selecting 'Keep Inside' retains all pixel values within the selected range as they are, but changes all pixel values outside this range to a zero value, or black color (depending on the palette). The image displays with the selected range of pixels visible and all other pixels blacked out. Selecting 'Keep Outside' changes all pixel values within the specified range to a zero value (usually black), keeping the brightness values outside the selected range as they are. The histogram displays only for values outside the selected range.

Before selecting the low and high values for the isolated range, use the cursor and the information window to determine the values of interest.  For example, to isolate the pixel values in a large area on the image, move the cursor within the area.  Note the range of pixel values appearing in the information window, and use the apparent lowest and highest values as the low and high values in the Filter dialog box.

The Pick button provides another way to define the high and low values for the filter. This option defines a box within the image, from which the lowest and highest brightness values are identified and assigned to the filter.  To use it, click the Pick button.  A dialog box appears, identifying the active window and the x, y coordinates of the cursor.

Position the cursor at the point of the upper left corner of the box.  Click and drag the mouse to make the box, releasing the mouse at the point where the lower right corner should occur. The Filter dialog box stores the high and low values.

Selecting 'Create a B/W Mask' makes the selected values white and all other values black. No histogram displays for a filtered mask.  A filtered mask is helpful for visually enhancing the selected values, since these values display as white.


ReSize

To resize an image, type in the new pixel width and height. The image data points are resampled to produce a similar image with a different number of pixels. Three different methods are utilized for the resampling process.

More:

Fast

Nearest Neighbor

Bilinear Interpolation


Fast

The Fast method picks the next lower pixel in the original image. Since the lower number pixels are up and left in the image, a slight shift in image position may occur. Only data values already in the original image will be copied into the new image.


Nearest Neighbor

The "Nearest Neighbor" method is similar but rounds up or down to the nearest pixel. It is fairly fast, does not produce as much image shift, and does not add new data values to the result image.


Bilinear Interpolation

"Bilinear Interpolation" calculates the new pixel value using, in most cases, a linear interpolation between the four nearest pixels. When the result image is larger than the original image there are pixels near the edges of the result image that do not have four surrounding pixels in the original image. These pixel values are extrapolated from the four nearest pixels. Extrapolated values may be truncated to keep them within the allowed range of pixel values. In general, the result image will have different data values than the original and may require a larger palette for display.

Click OK when ready.


Transfer Info

This menu item is used to transfer the image info (including xy and z image registration) to another image. Sometimes the results of image processing  that utilizes several images will results in the loss of image registration in the final image. Therefore this menu may become useful to update the info fields of the resultant image.


Rectification

Rectification provides a way to align images so that north is at the top of the screen, and to transform coordinates in the image so that distortion is removed, making the image planimetrically correct.  The process involves relating pixel coordinates with their map coordinate counterparts (Jenson, p. 103).

To use the Rectification function, select Rectification in the Advanced Menu.  The dialog box appears. Using the Rectification function involves mapping x, y locations of pixels to their real world x, y locations.  These locations are known as Control Points, and a minimum of 4 control points is required to complete the function.

To begin the Rectification process, click Add to pick the first control point. This dialog box appears:

More:

Enter Control Points

Resampling

How MicroImage Selects Control Points

Other Features


Enter Control Points

Type in the Tag.  This is simply a label that identifies the control point.  The tag may be any alphanumeric label.

Enter the real world X and Y coordinates of the first control point in the Real X and Real Y windows.

Click Choose to match the real world X, Y to the corresponding pixel in the image.  After you click Choose, the cursor becomes an arrow.  Place the arrow's point at the X, Y location of the corresponding pixel and click.  This sets the X, Y location of the pixel, and adds the control point to the Control Points Available window.

You need a minimum of 4 control points to use the Rectification function, but you may have as many points as you wish.


Resampling

Once the conversion matrix has been determined, you need to decide how the new image pixel intensities will be derived.  This is called resampling.  There are two ways to resample: Bilinear Interpolation or Nearest Neighbor matching.

Bilinear Interpolation takes a weighted average of the surrounding eight pixels and does not preserve the original intensities.  The image will look smoother and is a good choice if the resultant image is to be used for display.

Nearest Neighbor takes the intensity of only the nearest pixel and does not average, thereby preserving the original pixel intensities.  Use this option if the resultant image is to be used for analysis rather than display.


How MicroImage Selects Control Points

When enough control points are typed in the Available Points window to comply with the selected number of points to use, MicroImage selects the best points within the Available group to use in the Control Points Used window.  For example, if you have seven available points, but the number of points designated to be used is four, MicroImage automatically calculates the best four points of the seven available, and positions those points in the Control Points Used window.

If, however, you wish to ensure that certain points are absolutely used in the Control Points Used window, you can lock those points in the Control Points Available window.  To lock a point, click once on the lock symbol in the point description.  When a point is locked, it automatically appears in the Control Points Used window.

After the required number of points appears in the Control Points Used window, click OK to complete the Rectification.  A duplicate of the original image appears and Rectification is applied to the duplicate.


Other Features

To save a group of control points, click Save after building the list of control points in the Available window.  Locate the desired drive and directory on which to save the control points file, and save the file using .cp as the file extension.

To Load a previous control point file, click Load then locate the desired .cp file.  Once located, click OK to load the .cp file.

To Edit an existing control point list, click the point you wish to edit, click the Edit button, then type in the changes to be made.

To Delete an existing control point, click the point to highlight it, the click the Delete button.

To select a new width for the Rectified image, type in the desired width in the New Width window at the bottom of the Image Rectification dialog box. The unit of width is pixels.


Classify

The Classify feature is used to identify regions of interest in an image using one or more spectral "bands" for a given image area. Classification, also known as thematic mapping, is a method of extracting information from analytical data. It employs the use of training sites, or areas that represent uniform examples of known phases.

Classification involves either of two methods:  supervised or unsupervised.  Supervised classification involves some determination on the part of the analyst regarding location of training sites, based on an understanding of the image configuration.  The analyst sets the number of classifications, then each pixel is evaluated and reassigned to one of the classifications, based on its proximity to the pixels normally occurring in that class.

Unsupervised classification relies entirely on computer grouping of brightness values into classes determined by mathematical criteria. This type classification is useful when image features are not well-defined. To activate the function, go to Classify in the Advanced Menu.

More:

Starting a Classification

Unsupervised Classification

Details of Unsupervised Classification

Supervised Classification


Starting a Classification

Pick up to 10 bands on the same image that you wish to use in the classification. Choose which type of classification you wish to perform:

•	Manual (Supervised Classification)

•	Automatic (Unsupervised Classification)


Unsupervised Classification

If you choose automatic (unsupervised) classification, the dialog box appears. The information required is:

Number of Classes: maximum number of clusters to be identified by the algorithm.

Spectral Distance: a radius in spectral space used to determine when a new cluster should be formed.

Class Merge Distance: a spectral space distance parameter used when merging clusters.


Details of Unsupervised Classification

Assume the following input variables:

•	N = Number of classes (signatures) to find

•	S = Spectral distance

•	C = Class merge distance

Lets take the case where you have a two band image (two dimensional).  This algorithm works equally well for n-band images.  Each class is an single average value (0 .. 255 for 8 bit images or 0 .. 65535 for 16 bit images) for each of the bands.  For instance here are some classes:

•	Class 1: {201,42}

•	Class 2: {18,245}

Now lets go through every pixel in the source images.  Each pixel is compared to all the existing classes.   For the very first pixel, there will be none.  A distance function is performed to every class.  For our 2-dimension case, it would be:

where CB1 is "Class Band 1" and PB1 is "Pixel Band 1".

The class that has the smallest distance to the pixel is chosen.  If the distance between the chosen class and the pixel is less than S or the number of classes is equal to N, then that pixel is merged into the class.  This is done by adjusting the weighted average for that particular class.  If it is not merged with a class, then a new class is created.

After 2000 pixels, the classes are analyzed.  Each class is compared to every other class.   If the distance between any two classes are less than C, then the two classes are merged. This process is continued until all pixels have been processed.

For more information on unsupervised Classification, See John Jenson's Digital Image Processing,  page 215, "Unsupervised Classification."


Supervised Classification

Supervised classification allows you to train the computer to recognize certain pixel signatures. When you do supervised classification, you get the following box:

1. Set the minimum distance for pixel classification.  All values that are not within the minimum distance from any defined classification receive a value of zero (black).

2. Click Add to build each classification.  Drag the cursor to draw a box defining the training site.  As each classification builds, the average pixel value for the training site displays next to the color bar in the dialog box.  This becomes the value used for comparisons in determining the reassignment of pixels to each classification. To change the color, click on the bar then click the cursor to select a new color from the palette.

3. After all classifications are built, click Apply, then drag the cursor to define a box for a test area.

The test area provides a preview of the classification before its completion.  A complete classification may take several minutes, but a test area is complete in seconds.

4. If the test area is suitable, click OK in the main dialog box to complete classification of the entire image.  To change the range of classifications, do one of the following:

• Choose New to clear all existing classifications

• Choose Delete to clear a highlighted classification

• Choose Add to make additional classifications

5. Save stores a group of classifications as a text file with the extension .cy.  This is a convenient way to use pre-defined classifications using the Load button.


Histogram-1d

The "Histogram-1d" menu item displays a simple one dimensional histogram of the currently selected image in a re-sizable window that can be saved to disk or printed. The histogram is displayed using white on black so that all parts of the histogram are easily visible.


Histogram-2d

Calculate

Kill Pixel

Trace-back


Calculate

The "Calculate 2d-Histogram" menu item allows the user to select 2 images for displaying a histogram-histogram scatter plot. For example, if two images are acquired on a sample for say Fe kα and Zn kα, and the two images are selected for "Calculate 2d-Histogram" then the resulting image will contain a plot of the histogram of Fe kα versus the histogram of  Zn kα. The images selected for this process can be either qualitative intensity images from MicroImage or quantitative concentration images from Probe for Windows using the stage scan feature.

This histogram-histogram plot can be very useful for interpretation of images of complex phases. Each distinct phase will cluster in a specific region of the plot to allow identification of the individual phases and their range of intensity or concentration. To determine the exact spatial relationship between the phases, use the "Trace-back" menu item described in the following section.

For more information see the figure on 2-d histograms in the MicroImage Techniques sections below or the reference "Concentration Histogram Imaging: a Quantitative View of Related Images", by D.S. Bright, R.B. Marinenko, in Microscopy: The Key Research Tool, v. 22, No. 1, 1992.


Kill Pixel

The "Kill Pixel" menu item can be used to erase single pixels in the current 2-d histogram image. This can be useful when a single bright pixel is preventing the stretch palette function from revealing image detail. Simply click on the offending pixel (usually bright) and re-stretch the palette for the image.


Trace-back

The "Trace-back" menu item allows the user to determine spatial or distribution relationship for phases mapped using the "Histogram-2d" menu item described in the previous section.

If a histogram-histogram plot has been created, then clicking this menu allows the user to select a region of interest in the plot image and then creates a "trace back" mask image of the selected pixels. This process may be repeated indefinitely for as many phases as exist in the 2-d histogram plot.

If at least three "trace-back" masks are created then the user can then use the Composite menu to create a 3 color map of the selected phases.


Concatenate Images

Mosaic

Pave

Combine

Composite


Mosaic

The "Mosaic" menu item allows the creation of "mosaic" images by combining multiple images to create a single registered image. The images selected for the mosaic process must be registered in absolute coordinates. This usually means the images have been acquired with the stage motors properly configured (see Number of Stage Motors keyword in the MICROIMAGE.INI file) so that the actual stage coordinates can be saved with the image registration

If the microscope stage is not automated and the mosaic process must be used on relative registered images, it might be best to note the actual stage coordinates of the image, by entering them in the image description field at the time the images are acquired. This field is found by clicking on the Window | Properties menu. In this way, the stage coordinates of the image are available for subsequent absolute registration calculations as described below.

To convert an image to absolute registration, by using a "back of the envelope" calculation based on the stage position the image was acquired at and the relative image registration, simply convert the image stage position (previously noted) to microns and add the appropriate relative micron offsets from the image registration to the stage position in microns (relative image registration is from the center of the image). After two opposite corners of the image are calculated in absolute microns, just click the Window | Properties menu and click the XY registration button and modify the image registration vector fields. Once you have done this for at least two images, you can use the mosaic process to combine the images into a single image as described below. For more on image registration please refer to the "Image Registration" paragraph in the "Image Processing Techniques" section below.

To use the Mosaic feature, simply click the menu and a "Pick images" dialog will appear allowing the user to select up to 20 images to mosaic. When all images are selected, simply click "OK". Click "Cancel" at any time to cancel the mosaic process.


Pave

This menu allows the user to select a large number of images that will then be "tiled" together into a single image. This is useful when it is desired to print multiple spectral bands (BSE, SE, X-ray, etc.) on the same page.

Use the mouse to select each image that will be included. Generally the images should be spectrally related (that is, all from the same acquisition) and will therefore have the same aspect ratio for proper concatenating.


Combine

The "Combine" menu item is used to create a "stereo" pair of images. Generally the use a stereoscopic viewer will be required, although some individuals can defocus their eyes sufficiently to discern a stereo effect.


Composite

This function creates a composite color image by combining selected red, green, and blue bands to produce a full-color image.  This requires either using three 8-bit spectral band images or a single 24-bit image such as a 24-bit BMP.

Open the three 8-bit spectral band images or a single 24-bit image and tile the windows to view the individual bands. Then go to the Composite menu in the Advanced menu.  Select each successive band as prompts occur.

A Pick RGB band dialog box appears to allow the user to select each band.

A Convert Colors dialog with three selections for level of composite image color optimization in creating the composite: quick, slightly optimized, and fully optimized.

Optimization refers to the way in which the computer "reads" the colors and converts them to one of the 256 available colors. Selecting Quick prompts the computer to assign "nearest fit" color to individual pixel values.  Selecting Slightly Optimized makes the computer examine pixels in every 10th line of the image and calculate the closest values. A Fully Optimized conversion tells the computer to examine pixels in every 2nd line of the image for calculations.

Selecting Slightly or Fully Optimized allows selection of the number of colors used in the conversion process, from 16 to 256 in exponential order (24 to 28). The greater the range of values, the more realistic the composite image appears, but the longer the conversion process takes to complete.  Click to select a number.

Click an optimization selection and value range to start the conversion. Upon completion a new window displays the composite image.


Special Effects

Erode

Dilate

Median

Negate Data

Burn In


Erode

The "Erode" menu item performs a filter operation on each pixel, based on a 3 X 3 pixel region, that returns the minimum pixel value in the pixel area. For example, repeated "Erode" processing of a feature with a concavity, usually results in dividing the feature at the concavity, allowing the separation of overlapping objects in an image. Information relating to original size and shape may be degraded, but a better count of the number of features may be obtained.


Dilate

The "Dilate" menu item performs a filter operation on each pixel, based on a 3 X 3 pixel region, that returns the maximum pixel value in the pixel area. Hence, the "Dilate" process is the opposite of the "Erode" process. Repeated erosion and dilation tends to smooth an image and separate features.


Median

The "Median" menu item performs a filter operation on each pixel, based on a 3 X 3 pixel region, that returns the middle value of the sorted values in the 3x3 pixel area. Single pixels that are very different in value from the others nearby are ignored. This operation is useful in "cleaning up" an image that has been degraded with noise that affects only a few pixels at a time, such as static or a missing scan line. Some information in the image is lost but visually the error is much reduced.


Negate Data

This function creates a negative of the image by inverting the image palette. Each pixel is converted by calculating 255-pixel value for 8 bit images and 65535-pixel value for 16 bit images.

To use Negate, load an image then select Negate Data in the Advanced | Special Effects menu. A negative image displays over the previous image, reversing the histogram to reflect the opposite pixel values.

If the image disappears it may be necessary to re-stretch the palette using the Basic | Contrast Enhancement | Stretch Palette menu item. To reverse a negative image, repeat the process.


Burn In

This menu item is used to copy the current active (selected) image window to another image window. This menu allows the capture of the entire image area, including the scale and palette bars (if visible), plus the window frame and title bar.


Acquire Menu

The following "Acquire" menu items are used to actually acquire analog/digital images. In order to first acquire an image, each input channel must already be enabled from the MICROIMAGE.INI file and then selected for input by either editing the MICROIMAGE.INI file defaults or using the "Setup" menu. Channels that are ready for acquisition are immediately opened as windows in the MicroImage client image area.

A progress indicator will run during the acquisition to indicate how the acquisition is proceeding. Both the percent completion and time remaining are displayed. Note that if any counter inputs are enabled, the acquisition will take considerably longer. Normally MicroImage updates the window display at 20% intervals during the acquisition, however the data already acquired can be seen by simply selecting "Cascade" or "Tile" from the "Window" menu.

For ease of use, these acquire menu items are duplicated in the tool bar. See Image Acquisition Buttons section below.

More:

Single

Continuous

Average

Finish

Halt


Single

Click this menu item to start a single frame acquisition of the selected channels. Analog data is normalized to the image depth (0-255 for 8 bit images and 0-65535 for 16 bit images). Digital and counter timer channel data is simply accumulated. If analog pixel averaging is selected, each analog channel pixel will be the average of the specified number of average acquisitions specified under the "Setup" | "Scan Type" menu.


Continuous

Click this menu item to start a series of single frame acquisitions of the selected channels.  If analog pixel averaging is selected, each analog channel pixel will be the average of the specified number of average acquisitions specified under the "Setup", "Scan Type" menu. The image acquisition will continue until the "Finish" or "Halt" menu items are clicked.


Average

Click this menu item to start an frame average acquisition of the selected channels. Analog channels will be averaged using a running average of the form :

where :	i is the previous count intensity

i' is the new count intensity

n is the frame number of the acquisition

Digital images will simply accumulate the count data for each frame average. If the number of frames to be averaged will be greater than 255 (for digital I/O inputs), or the signal levels greater than 255 counts per specified count time (for counter inputs) be sure that 16 bit images are selected from the appropriate input dialog box under the Setup menu. The program will simply set pixel values to the maximum image depth if the digital data overflows the maximum image depth (255 for 8 bit images and 65,535 for 16 bit images).

 If analog pixel averaging is selected, each analog channel pixel will be the average of the specified number of average acquisitions specified under the "Setup" | "Scan Type" menu.


Finish

Click this menu item to allow the current frame to finish the acquisition. This will prevent any image artifacts due to an incomplete image acquisition from being incorporated into the image.


Halt

Click this menu item to immediately halt the current image acquisition. Note however, that if any the counter inputs have been selected, it may take some time for the current scan line to finish, before returning control to the user.


Setup Menu

The "Setup" menu is used to select the input channels and configure the imaging and acquisition parameters. For instance, click "Analog Inputs", "Digital Inputs" or "Counter Inputs" to select the analog, digital of pulse counter inputs. Next click "Magnification" and/or "Image Size" to select the image magnification and size. Note that acquired image will not be properly registered unless the correct magnification factor is selected before the acquisition is started.

More:

Analog Inputs

Digital Inputs

Counter Inputs

Magnification

Stage Scan Setup

Image Size

Scan Type

Scale Bar Setup

Palette Bar Setup

Load Setup

Save Setup

Faraday Setup


Analog Inputs

Click the "Analog Inputs" menu item to open the Analog Inputs dialog box.

Use the Analog Inputs dialog box to select the analog inputs, choose 8 or 16 image depths and/or rename channel labels. The "Auto Stretch" option will perform a linear palette stretch automatically after each image frame is acquired. Click "OK" to save the changes or "Cancel" to exit without saving the changes.


Digital Inputs

Click the "Digital Inputs" menu item to open the Digital Inputs dialog box.

Use the Digital Inputs dialog box to select the digital inputs, choose 8 or 16 image depths and/or rename channel labels. In most cases, an 8 bit image depth will be satisfactory for digital image acquisition. The "Auto Stretch" option will perform a linear palette stretch automatically after each image frame is acquired. Click "OK" to save the changes or "Cancel" to exit without saving the changes.


Counter Inputs

Click the "Counter Inputs" menu item to open the Counter Inputs dialog box.

Use the Counter Inputs dialog box to select counter inputs, choose 8 or 16 image depths and/or rename channel labels. Note that the counter inputs use the same signal source as the digital inputs, but the signals are pulse counted instead of input using digital I/O. You can also select "Beam" to acquire an image using the beam counts for an absorbed current image of the sample area. The "Auto Stretch" option will perform a linear palette stretch automatically after each image frame is acquired.

Note that the count time for the pulse counter can be set here. This is the count time used for each pixel acquisition. The valid ranges for the pulse counter is .01 to 1,000,000 seconds. The default count time is 0.1 seconds, unless otherwise specified in the MICROIMAGE.INI file.

Note that a 512 X 512 image using a pulse count time of 0.5 seconds per pixel will require at least 36 hours to acquire. Plan your imaging sessions accordingly!

Click "OK" to save the changes or "Cancel" to exit without saving the changes.

More:

Imaging and Detection Limits


Imaging and Detection Limits

In order to compare the detection limit of a typical quantitative analysis, with that obtained using a x-ray imaging, consider that for a quantitative sample under typical operating conditions (assume 10 sec count time and 50 nA of sample current) the detection limit for most elements will be on the order of 1000 ppm (0.1 weight percent) at 99% confidence levels.

If one attempts the same detection limit for say a 128 X 128 pixel acquisition in MicroImage, the time required for counting time alone will be 128 X 128 X 10 = 163,840 seconds or about 45.5 hours. For an image at twice the resolution (256 X 256 pixel), an acquisition at the same count time will be 256 X 256 X 10 = 655,360 seconds or about 182 hours or 7.5 days! Therefore, most of the time, a minimal count time of 0.1 to 0.5 seconds is used for the counter inputs, resulting in a significantly lowered detection limit. As a rule of thumb, for x-ray imaging, assume 10 minutes to 1 hour for major elements, 1 to 8 hours for minor elements and think twice before attempting trace element imaging (possibly use the low resolution but quantitative mapping feature in Probe for Windows instead).

Remember also that these are qualitative images, not corrected for background, matrix, interference and spectrometer defocusing effects. To produce quantitative images it is recommended that you acquire background images with the spectrometer positioned off the peak or use the Probe for Windows X-Y area stage scan features to produce fully quantitative data and then export it using the "SURFER .BAS" feature from the Plot! window. After gridding from the GS Scripter application you can import and display the quantitative data in gray or false color scales using MicroImage or as contour or surface plots using Surfer for Windows.


Magnification

Since MicroImage provides only a reference beam scan to the microscope's analog electronics, it is necessary to control the SEM or microprobe magnification (and rotation) using the analog electronics. In addition, in order for the image registration and scale bar to be valid, the actual magnification currently in use must be indicated in the Magnification dialog by either selecting one of the pre-set magnification options or entering an intermediate value in the magnification text field.

Remember, forgetting to set the correct magnification for an image acquisition will result in an improper image registration. Always double check the magnification before starting a stage/beam scan image acquisition.

The allowed range of magnification ("min" and "max") is specified in the MICROIMAGE.INI file. However the pre-selected values are loaded as follows for Semq, Jeol and Cameca microprobes, based on the value of the "probetype" keyword in the MICROIMAGE.INI file :

Semq	Jeol	Cameca
100	40	100
200	100	200
500	200	400
1000	400	800
2000	1000	2000
5000	2000	4000
10,000	4000	8000
20,000	10,000	20,000
50,000	20,000	40,000
Click "OK" to save the changes or "Cancel" to exit without saving the changes.


Stage Scan Setup

Click the "Stage Scan Setup" menu item to open the Stage Scan Setup dialog box. This dialog will allow the user to specify the stage area to be scanned using the stage X and Y motors.

The area to be scanned is defined by specifying two opposite corners of a rectangular area and is used for both stage only scanning and combined stage and beam scanning. The correct aspect ratio of the scan area is preserved by MicroImage regardless of the pixel dimensions of the image.

The Center Stage button shifts the current stage scan size to the current position of the microscope stage, preserving the image aspect ratio and size.

The Stage Scan Setup dialog only pertains to installations which have motion control for the microscope stage hardware. If motion control is specified in the MICROIMAGE.INI file, then all images acquired will be registered in absolute stage coordinates based on the units defined in the MICROIMAGE.INI file.


Image Size

Click the "Image Size" menu item to open the Image Size and Orientation dialog box. Use the Image Size and Orientation dialog box to change the number of pixels in an image and it's orientation as viewed on your monitor.

Simply click on one of the option buttons for a square image using pre-defined image sizes of 32 X 32 to 4096 X 4096 pixels. Be aware that increasing the image size, increases the acquisition time by the square. For example, a 64 X 64 image will take four times longer to acquire than a 32 X 32 image.

Both the beam and stage scan orientations are handled independently. The "Reverse Axis" check boxes will allow the user to reverse the direction of the beam or stage scan acquisition for each axis independently. These items are normally set in the MICROIMAGE.INI file to produce an image geometry that is the same as the optical light image or CRT monitor image.

Click "OK" to save the changes or "Cancel" to exit without saving the changes.


Scan Type

Click the "Scan Type" menu item to open the Scan Type dialog box. Use the Scan Type dialog box to change the general scan characteristics.

For example, from this menu you may select stage only or beam only or a combination of stage and beam scanning. Both the beam and the stage scans use a raster scan pattern to eliminate any non-linearity in the beam or stage scan microprobe hardware.

The stage scan only maintains a stationary beam while only moving the stage. The combined stage and beam scan moves both the stage and the beam. The stage area is defined by the Stage Scan Setup menu and the beam scan is defined by the Magnification menu.

Use the combined stage and beam scan with a relatively high magnification for WDS imaging of large sample areas when lower magnifications would suffer from excessive Bragg defocusing.

Note that use of this combined stage and beam scan feature requires extremely accurate calibration of the beam scan coils in both X and  Y in stage microns and the scan coil rotation on the instrument must be precisely orthogonal (that is, parallel to the stage motion). See the "cal microns" and "cal y microns" parameters in the MICROIMAGE.INI file.

If stage backlash is required for stage and combined stage and beam scanning, be sure to define a non-zero backlash parameter in the [stage x] and [stage y] sections of the MICROIMAGE.INI file.

More:

Scan Averaging

Analog Pixel Averaging


Scan Averaging

The Scan Averaging section tells MicroImage the maximum frame averages to perform for all channel types. You can acquire fewer frames by simply clicking "Finish" or "Halt" during the acquisition.


Analog Pixel Averaging

The "Analog Pixel Averaging" section is used by MicroImage to determine the number of initial A-D conversions to discard and the number of A-D conversions to average for each pixel. Use the "Samples to Discard" to give the DAC more settling time and use the "Samples to Average" to produce smoother data on a pixel basis. Generally there is no advantage to acquiring more samples than the bit resolution of the A-D converter. For the WIN30PG that corresponds to 16 bits.

Click "OK" to save the changes or "Cancel" to exit without saving the changes.


Scale Bar Setup

The scale bar setup may be modified by clicking the "Scale Bar Setup" menu items under the "Window" menu. All scale bar setup defaults are defined in the MICROIMAGE.INI file.

To change the preferred scale bar position simply click the scale bar position location. Note that if an off image display position is selected (those outside the embossed frame), the scale bar may not always be visible depending on the window tiling. It may be necessary to click and drag the window border to a rectangular shape to see the off-image scale bar.

Click "Hide" to turn the scale bar display on or off. Click "Label" to have the  program display a label string or not. Click "Large" to have the program use a large scale bar versus a small scale bar.

Click the "Orientation" and/or "Color" options to change the scale bar from horizontal to vertical or vertical to horizontal display and the color of the scale bar and label from black to white.

The default "XY Units" is that specified in the MICROIMAGE.INI file. To use a different XY label for all images, enter a new value in the text box.

The "Thick" option is used to display the scale bar thicker for a more prominent display using the value defined in the MICROIMAGE.INI file.


Palette Bar Setup

The palette bar setup may be modified by clicking the "Palette Bar Setup" menu items under the "Window" menu. All palette bar setup defaults are defined in the MICROIMAGE.INI file.

To change the preferred palette bar position simply click the palette bar position location. Note that the palette bar may not always be visible depending on the window tiling.  It may be necessary to click and drag the window border to a rectangular shape to see the off-image palette bar.

Click "Hide" to turn the palette bar display on or off. Click "Label" to have the  program display a label string or not. Click "Black" to have the palette bar label display as black characters, otherwise white characters are used.

To change the palette bar units label for a single image, click the "Z Registration" button in the Properties dialog.


Load Setup

Click the "Load Setup" menu item to open the Load Setup dialog box. Use the Save Setup dialog box to recall a previously saved image acquisition setup. This option allows a user to load a specific imaging setup without having to change the program defaults in the MICROIMAGE.INI file. Enter a filename with a .SET extension and click "OK" to load the previous setup or "Cancel" to exit without loading a previous setup.


Save Setup

Click the "Save Setup" menu item to open the Save Setup dialog box. Use the Save Setup dialog box to save the current image acquisition setup to a .SET file for use later on. Once the setup is saved, it can be recalled at any time using the "Setup" | "Load Setup" menu item described above. Enter a filename with a .SET extension and click "OK" to save the current setup or "Cancel" to exit without saving the setup.


Faraday Setup

Click the "Faraday Setup" menu item to change the default beam blank mode in the software. To leave the beam always unblanked (faraday cup removed), leave the check box unchecked. To have the program remove the faraday cup before each image acquisition and insert the faraday cup after each image acquisition, check the check box.


Modes Menu

The "Modes" menu contains an assortment of image mode selections. Most of the menu items will indicate their current state by a menu check mark.

More:

Pixel Snap

Stage Snap

Release Beam

Center


Pixel Snap

To move the current beam position to an arbitrary position on the image, simply click the "Pixel Snap" menu item. A dialog box will open and prompt the user to indicate where the beam should be positioned by simply clicking a pixel on the currently selected image. The beam position will be indicated by a cross hair on the image.

The beam will remain in the selected position until another image acquisition is performed, or an additional "Pixel Snap" operation is selected. To re-center the beam use the "Center" menu item described below. To release the computer control of the scan, click the "Release Beam" menu item.

Be aware that the program will move the beam based on how the image was acquired. If the image was acquired using a beam scan only, then using Pixel Snap will move the beam only. If the image was acquired using a stage scan only, then using Pixel Snap will move the stage only. If the image was acquired using both the beam and stage scan, then using Pixel Snap will move both the beam and the stage.

However, if the image was saved to a registered TIFF file and opened again, using Pixel Snap will move the stage only. Note that the beam is normally returned to the center position after an image acquisition or the program is terminated.


Stage Snap

To move the current stage position to an arbitrary position on the image, simply click the "Stage Snap" menu item. This feature is intended for quantitative analysis of small features where a vertical beam is desired. Therefore only the stage will move regardless of how the image was acquired. A dialog box will open and prompt the user to indicate where the stage should be moved to.


Release Beam

Clicking on the "Release Beam" menu item will release the beam from computer control. Normally this is done after using the above "Pixel Snap" feature to lock the beam to specific image locations, in order to return the scan back to analog control. Note that the program will automatically release the beam once an image is acquired, after using the "Pixel Snap" feature.


Center

Clicking on the "Center" menu item will force the beam back to the image center position. This is useful after using the "Pixel Snap" option and the user decides to re-center the beam for quantitative analysis. Note that the beam is normally returned to the center position after an image acquisition or the program is terminated.


Window Menu

The window menu contains a number of window-handling menus including: Zoom, Properties, History, Global History, Tile, Cascade, Arrange Icons, etc.

More:

Zoom

Properties

History

Global History

Cascade

Tile

Arrange Icons

Tool Bar

Status Bar

Histogram

Zoom Bar

Acquisition Bar


Zoom

Zoom provides a way to enlarge or decrease the viewing size of the image. This table illustrates various zoom functions:

Option	Result
In	Zoom in on a defined area
Out	Zoom out by a factor of two
Extents	Make the window fit the image
Set	Set an arbitrary zoom (any %)
More:

Using Zoom


Using Zoom

To zoom in or out of an image, go to Zoom in the Window menu, select In, Out, Extents or Set in the active window only.


Properties

The Properties menu opens a dialog that display both general and registration information about the currently selected image.

More:

TIFF Info

Technical Info


TIFF Info

This group displays textual information that is contained inside TIFF image files.  You may edit Author and Description.


Technical Info

This group displays information regarding size, number of colors and memory usage.

The storage type is either RAM or DISK.  This indicates if the image is being stored in RAM memory or Disk Memory. Normally images are stored in RAM unless the total memory requirements of all loaded images exceeds the physical memory.

Resolution

This group displays the resolution of the image in real world values.  This example indicates the image has a resolution of 282.72 units per pixel.  For this image, the units are microns, therefore the image is obviously a stage scan image.

You can overlay your own coordinate system on an image by clicking Change Registration.  Select a pair of points on the image and establish corresponding coordinates. The registration screen displays X and Y coordinates for both raster (image) and vector (real-world).

See Registering an Image to a Coordinate System.

Z Type

This group displays the arbitrary scale that is overlaid on the intensity spectrum.  You can change the Z Type by clicking on Change Z Registration.

Low is the real world value for pixel values of 0.  High is the real world value for pixel values of Number Colors (usually 256).  Description is the textual description of this scale.

By assigning the low and high, intermediate values can then be interpolated.  This information is displayed in the Information Window of the main screen.


History

This menu item displays a text box containing a history of image modifications to the currently selected image.


Global History

This menu item displays a text box containing a history of general MicroImage events that may be useful for test or debugging purposes.


Cascade

When only a glimpse of each image is necessary, the Cascade  command in the Window menu will layer all the open images so that the image titles are visible in a "stacked" manner.


Tile

With several images loaded in the MicroImage screen, the Tile command in the Window menu arranges the windows in a tiled pattern. This makes all windows visible at the same time, with no window overlap.


Arrange Icons

This menus sorts the images that have been minimized to title bars.


MicroImage Menu Details - Window Menu - Tool Bar
Tool Bar

The is a status menu that indicates if the Tool Bar should be displayed. Normally this is displayed and docked at the top of the screen. Click the menu to toggle the Tool Bar state.


Status Bar

The is a status menu that indicates if the Status Bar should be displayed. Normally this displayed at the bottom of the screen. Click the menu to toggle the Status Bar state.


Histogram

The is a status menu that indicates if the Histogram should be displayed. Click the menu to toggle the Histogram state.

Color Palette

The is a status menu that indicates if the Color Palette should be displayed. Click the menu to toggle the Color Palette state.


Zoom Bar

The is a status menu that indicates if the Zoom Bar should be displayed. Click the menu to toggle the Zoom Bar state.


Acquisition Bar

The is a status menu that indicates if the Acquisition Bar should be displayed. Click the menu to toggle the Acquisition Bar state.


Help Menu

The Help Menu gives you access to two tools, the MicroImage Help file and the About MicroImage dialog.

More:

Help On MicroImage

About MicroImage


Help On MicroImage

The Help file (this document) includes all topics related to MicroImage operation.  To use it, select the Help. Click a selection to view a brief description of the subject.


About MicroImage

About displays information about MicroImage.


Choosing Colors

Several of the image processing functions allow you to choose colors.  For instance, Classification and False Color both let you choose colors for certain operations.   They both display the following dialog box:

Here, you can click on the color you want, then hit OK.  You can also save the color list to a file and load a color list from a file with the Load and Save Buttons.

If you want, you can add your own colors to the list by clicking Add. The following dialog box then appears.

Simply type a name for the color, then click on the color.


Registering an Image to a Coordinate System

This is done by clicking on Properties under the Window Menu.  Click on the Change Registration button.

More:

To register an image to a coordinate system

Methods of establishing coordinates


To register an image to a coordinate system

1.	Enter the x and y coordinates for the two real-world coordinates in the Point 1 Vector and Point 2 Vector boxes.

2.	Using the cursor, click the Point 1 Raster box, then locate the first point on the image and click the mouse.

3.	Follow the same procedure for the second point: click in the Point 2 Raster box then click the second point on the image.

4.	After clicking OK, MicroImage displays the image registered to the selected coordinates.

In the example below, the two real-world coordinates are 1278360, 345404 and 1279825, 346374 (these appear in the Vector x and y boxes).  These points correspond to the two image points designated with the Select tool: 0, 345 and 475, 0 (in the Raster x and y boxes).


Methods of establishing coordinates

•	By locating vector coordinates from a drawing file of your image

•	By creating a user-defined coordinate system for a particular application,  i.e., using a scaled drawing to locate known points.

•	Using control points in the image that are correlated with coordinates gathered from a survey or other mapping.


How a 2d Histogram is Created

The steps involved in creating a 2-d histogram. Note that two spectral bands are mapped in histogram space to create a new image. In this example the oxygen image histogram represents the x axis and the silicon image histogram represents the y axis of the resultant image. The resultant image contains spectral image information that reveals correlations between to two spectral bands.

More:

Example of a 2d Histogram:


Example of a 2d Histogram:


MicroImage Techniques - Image Processing
Image Processing

Histograms

Filters

Look-Up Table (Palette)


Histograms

Histograms are a graphic representation of the frequency distribution of brightness values in an image.  This is defined as the graphic display of a set of data that shows the frequency of occurrence (along the vertical axis) of individual measurements of light intensity values (along the horizontal axis).


Filters

Spatial filters de-emphasize or emphasize designated spatial frequencies. They enhance features or remove noise by accentuating or diminishing high frequency information in the image. Spatial frequency is a characteristic of remotely sensed images defined as "the number of changes in brightness value per unit distance for any particular part of an image.2

A convolution is a filter type that applies a mathematical matrix to individual pixel values based on the surrounding pixel values.  In MicroImage, a "kernel" of pixels is an odd-numbered square of pixels, such as 3x3 or 5x5.  The center pixel in the kernel is the basis for the convolution calculations.

Applying a matrix of numerical values (convolution) to the kernel of pixels results in either:

•	 The center pixel of each kernel is replaced with an average value calculated from surrounding pixels; or

•	 A reassignment of all pixel values, based on the multiplied and summed values calculated from the mathematical matrix. This happens when each pixel is multiplied by its corresponding matrix value, then summed to produce a common value.

•	The mathematical results occur from the kernel moving throughout the image and applying the formula to all pixels.


Look-Up Table (Palette)

Lookup tables (LUT) are devices that assign color to gray-scale values.  As a pixel value passes through the lookup table, it is reassigned a new value, then passed out as a new value.  A LUT applies the same treatment to each pixel of the same intensity.  For example, values of 0 may enter the LUT then exit the LUT with a reassignment of Red.


Initialization File Format

The MICROIMAGE.INI file is read by MicroImage when the program is first launched to configure a number of program defaults and to describe the hardware interface. Changes made to the setup may be saved using the "Save Setup" menu under the "Setup" menu as either the default MICROIMAGE.INI file or as a user specified setup (.SET extension).

The MICROIMAGE.INI is a standard Windows initialization file format. That is, entries are under each section header may be in any order and may even be left out altogether. Be sure to not change the actual names of the entry items, because the MicroImage program will only search for items having a exact match with the entry names defined in this document. In addition, do not move an entry item from one section to another, since the MicroImage program will only search for an item in the section designated for that item as defined in this document.

If the program cannot find an entry, a default value is loaded in it's place. The default entries are documented below under each section. If an entry requires that it be enclosed in quotes, always use double quotes. Entries in double quotes will preserve mixed case characters for naming channel input labels, etc.  MicroImage will save modified parameters back to the INI file when it is terminated, so that the same configuration will be reloaded the next time the program is run, with a few noted exceptions.

The section entry keyword strings and the entries themselves are not case sensitive. Entries that require an "on" or "off", will also accept "true" or "false". Note that entries that do not require enclosing in double quotes, can be enclosed in double quotes if desired.

More:

[software]

[hardware]

[faraday]

[scalebar]

[palette bar]

[analog]

[digital]

[counter]

[stage x]

[stage y]


[software]

Under the software heading all entries pertaining to the general program setup are specified. Note that the "corfile", "elmfile" and "default palette" entries must be enclosed in double quotes if spaces are required in the file name or path.

xsize = 256

ysize = 256

X polarity = 1

Y polarity = 1

Stage X polarity = 1

Stage Y polarity = 1

Display X polarity = 0

Display Y polarity = 0

Registration X polarity = 0

Registration Y polarity = 0

maximum scans = 10

pixel discard = 3

pixel average = 5

magnification = 200

min = 100

max = 50000

corfile = "c:\Program Files\Probe for Windows\Probewin.cor"

elmfile = "c:\Program Files\Probe for Windows\Probewin.elm"

edsfile = "c:\Program Files\Probe for Windows\Probewin.eds"

default palette = "c:\Program Files\MicroImage\Thermal.fc"

make = "Your Micro Probe/SEM Here"

model = "Your Model Number"

author = "Your Name Here"

description = "Your Description Here"

host computer = "Your Computer Here"

retrace = 10

ImageDataDirectory="C:\MicroImage\UserImages"

Xsize = the default horizontal size of the image in pixels and must be an integer from 2 to 4096. The default is 128. The "xsize" entry does not have to be the same as the ysize entry.

Ysize = the default vertical size of the image in pixels and must be an integer from 2 to 4096. The default is 128. The "ysize" entry does not have to be the same as the xsize entry.

X polarity = the default direction of the horizontal beam scan. The entry must be either 0 or 1, "on" or "off" or "true" or "false".

Use this entry (along with "y polarity") to modify the beam scan direction in the microscope. Normally this option can be ignored unless there is a reason to set the beam scan direction due to scan coil hysterisis effects.

The default is 0 or false. This option will affect the Display and Registration polarity options.

Y polarity = the default direction of the vertical beam scan. The entry must be either 0 or 1, "on" or "off" or "true" or "false".

Use this entry (along with "x polarity") to modify the beam scan direction in the microscope. Normally this option can be ignored unless there is a reason to set the beam scan direction due to scan coil hysterisis effects.

The default is 0 or false. This option will affect the Display and Registration polarity options.

Stage X polarity = the default direction of the horizontal stage scan. The entry must be either 0 or 1, "on" or "off" or "true" or "false".

Use this entry (along with "stage y polarity") to modify the stage scan direction in the microscope. Normally this option can be ignored unless there is a reason to set the stage scan direction due to stage backlash effects.

The default is 0 or false. This option will affect the Display and Registration polarity options.

Stage Y polarity = the default direction of the vertical stage scan. The entry must be either 0 or 1, "on" or "off" or "true" or "false".

Use this entry (along with "stage x polarity") to modify the stage scan direction in the microscope. Normally this option can be ignored unless there is a reason to set the stage scan direction due to stage backlash effects.

The default is 0 or false. This option will affect the Display and Registration polarity options.

Display X polarity = the default polarity of the horizontal image display orientation. The entry must be either 0 or 1, "on" or "off" or "true" or "false".

Use this entry (along with "display y polarity") to change the image orientation to correspond with the orientation of the optical image in the microscope. The default is 0 or false.

Display Y polarity = the default polarity of the horizontal image display orientation. The entry must be either 0 or 1, "on" or "off" or "true" or "false".

Use this entry (along with "display x polarity") to change the image orientation to correspond with the orientation of the optical image in the microscope. The default is 0 or false.

Registration X polarity = the default polarity of the horizontal image registration display orientation. The entry must be either 0 or 1, "on" or "off" or "true" or "false".

Use this entry (along with "registration y polarity") to change the image registration orientation to correspond with the orientation of the stage coordinates in the microscope. The default is 0 or false.

Registration Y polarity = the default polarity of the horizontal image registration display orientation. The entry must be either 0 or 1, "on" or "off" or "true" or "false".

Use this entry (along with "registration x polarity") to change the image registration orientation to correspond with the orientation of the stage coordinates in the microscope. The default is 0 or false.

Maximum scans = the maximum number of frame averages per "average" acquisition cycle. Increase this value to change the default for better digital x-ray statistics. The default is 10.

Pixel discard = number of A-D conversion samples to discard before starting the actual analog image acquisition. Increasing this value will allow more time for the DAC beam control to settle. The default is 0.

Pixel average = number of A-D conversion samples to average per pixel. Increasing this value greater than 16 for a 16 bit A-D will have minimal effect. The default is 1.

Magnification = the default microscope magnification used for initialization of the microscope. This may be any value between the magnification "min" and "max" as defined below. The default is 200. The intermediate magnification values loaded by the program depend on the definition of the "probetype" parameter in the MICROIMAGE.INI file.

Min = the minimum enabled value in the Magnification dialog box. The default is 100 for "SEMQ".

Max = the maximum enabled value in the Magnification dialog box. The default is 50000.

Corfile = the path and filename containing the spectrometer and stage motor coordinate and offset values. This ASCII file is created by Probe for Windows and it's companion programs and is usually found in the C:\Program Files\Probe for Windows directory.

The default is no file. If the program is used as a standalone imaging application without the quantitative option, simply indicate no file with a set of empty quotes "".

Elmfile = the path and filename containing the currently tuned spectrometer element, x-ray line and analyzing crystal descriptions for naming the digital and counter input channels. This ASCII file is created by Probe for Windows and it's companion programs and is usually found in the C:\Program Files\Probe for Windows directory.

Make sure that the "max" entries in the [digital] and [counter] sections correctly reflect the number of spectrometer entries in the PROBEWIN.ELM file.

However, please note that if the first channel of the counter-timer inputs is used for beam current input, then the "max" entry in the [counter] section must be equal to the number of spectrometers plus one. See also the use of the "beamchannel" keyword in the [digital] and [counter] sections below.

The default is no file. If the program is used as a standalone imaging application without the quantitative option, simply indicate no file with a set of empty quotes "".

EDSfile = the path and filename containing the current EDS digital ROI (region of interest) channel names (element and x-ray line) for naming the digital counter input channels.  This ASCII file is created by MicroImage and is usually found in the C:\Program Files\MicroImage directory.

Make sure that the "max" entries in the [digital] and [counter] sections correctly reflect the number of channel names in the Probewin.eds file.

Note that if the first channel of the counter-timer inputs is used for beam current input, then the "max" entry in the [counter] section must be equal to the number of spectrometers + one. See also the use of the "beamchannel" keyword in the [digital] and [counter] sections below.

The default is no file. If no EDS ROI channels are available or the program is used as a standalone imaging application without the quantitative option, simply indicate no file with a set of empty quotes "".

If EDS ROI channels are indicated with the "MaxEDS" keyword (see "Digital" and "Counter" sections below), and the "EDSFile" keyword is blank, the program will create a default EDS file name based on the "ElmFile" keyword and populate it with defaults.

Note that it may be necessary to delete the current EDS file, if the value of "MaxEDS" is changed in either the "Digital" or "Counter" sections, so that an EDS file of the correct size can be automatically created.

Default Palette = the path and filename containing the default palette file. The default palette file determines the palette used for image acquisition, it will not change the palette of previously acquired images. The default is no file.

The palette file must be a MicroImage palette file with the extension .FC. If the Default Palette file is not specified, or the specified palette file cannot be located, or the specified file is not a valid MicroImage palette file, then the default gray scale palette will be used for all image acquisition. Image palettes can of course be modified after they are acquired using the False Color option.

The THERMAL.FC, RAINBOW.FC and BLUERED.FC false color palette files are supplied with MicroImage. The user can also create their own false color palette by using the "False Color" menu or tool bar button to specify a new palette and save it as a .FC file. This new palette file can then be specified in the "default palette" entry for use as the default palette for image acquisition.

Make = the manufacturer's name of the imaging instrument should appear here in this entry. Be sure to enclose the string in double quotes. All of the following image descriptor strings will be saved when the TIFF file save or save as option is used. Other image formats may or may not support saving this information to disk. This entry is for informational purposes only.

Model = the model number or description of the instrument used to acquire the images should appear here in this entry. Again be sure to enclose the description in double quotes. This entry is for informational purposes only.

Author = this entry should designate the instrument operator. In a single user laboratory, simply edit this string to include your name. In multi-user laboratories, use a generic label and use the Image Info tool bar item to change the "author" and "description" fields once the images are acquired and before they are saved to disk. The default is "user".

Description = this entry can be used to provide a verbal description of the image. Generally, this parameter is left generic and instead the user can use the "Image Info" tool bar item to change the "author" and "description" fields once the images are acquired and before they are saved to disk. The default is "microprobe image".

Host computer = use this entry to provide a description of the host computer used to acquire the images. This entry is entirely optional and is only for informational purposes.

Retrace = the number of analog samples to be discarded after the beam scan is "retraced" back to the beginning of the scan line. On fast Pentium computers the microprobe scan coils will often need additional time for the beam to "settle" after a large change in the voltage. This delay is applied independently from the pixel discard described elsewhere and is applied even if no analog image is being acquired. The default is zero analog sample discards for no retrace delay. Normally a fairly large value of 5 to 20 may be applied without affecting the acquisition time significantly since the delay is only applied once for every scan line.

ImageDataDirectory = this entry is used to define the default path for opening and saving images (TIF, BMP, PCX and GRD), false color palettes (FC) and setup files (SET). This parameter is not saved back to the INI file when the program is terminated.


[hardware]

Under the hardware heading all entries pertaining to the general hardware setup are specified.

probetype = "JEOL"

adtype = "win30pg"

datype = "win30pg"

iotype = "win30pg"

cttype = "dcc20ax"

mctype = "dcx"

Win30pgBaseAddress=576

CounterTimerDeviceName = "IOMapper0"

CounterTimerNumberofBoards = 1

cal mag = 100

cal microns = 1260

cal counts = 4095

cal y microns = 1260

cal y counts = 4095

units = "u"

stage to microns = 100

cal kilovolts = 15

user kilovolts = 15

spectrometer motors = 4

stage motors = 3

adrange="unipolar5"

control logic=on

SX50InterfaceBoardType = 1

SX50SEMDeviceName="IOMapper5"

SX50WDSDeviceName="IOMapper6"

Probetype = use this entry to define the instrument type. Be sure to enclose the entry in double quotes. Default = "SEMQ". At the current time the only valid entries are defined here :

SEMQ	for ARL SEMQ microprobes

JEOL	for JEOL microprobes

CAMECA	for Cameca microprobes

DEMO	for testing and demonstration purposes

The only difference between the "probetype" for the various manufacturers is the default intermediate magnification values for loading the Magnification dialog as shown here :

SEMQ	JEOL	Cameca
100	40	100
200	100	200
500	200	400
1000	400	800
2000	1000	2000
5000	2000	4000
10,000	4000	8000
20,000	10,000	20,000
50,000	20,000	40,000
Adtype = this entry is used to indicate the board type for analog to digital conversion of input signals for the program. The only valid entries at this time are "win30pg" and "simulate". The simulate board type is used with a "Probetype" other than "DEMO" to allow some hardware interfaces to be ignored.

Datype = this entry is used to indicate the board type for digital to analog (analog output) conversion of beam raster signals for the program. The only valid entries at this time are "win30pg" and "simulate".

Iotype = this entry is used to indicate the board type for x-ray digital input signals and magnification control for the program. The only valid entries at this time are "win30pg" and "simulate".

Cttype = this entry indicates the counter timer board type for digital pulse counting x-ray signal input for the program. The only valid entries are "dcc20ax"  and "simulate" for the 32 bit timer board.

Mctype = this entry indicates the motor controller type for control of the microscope stage for the program. The only valid entry is "dcx", "sx50" or "simulate".

Win30pgBaseAddress = this entry is used to specify the I/O port base address for the Win30PG A/D-D/A card for the UEIDAQ Win95 driver. This parameter is only used for the Win95 driver as the UEIDAQ driver under Win NT already has this information. The default is 576 decimal (240 hex).

CounterTimerDeviceName = this entry is used to define the counter timer board device name on the PC I/O bus used by Probe for Windows. The default device name is "IOMapper0". If more than one counter timer board is installed, the DIP switches of all the counter-timer boards must be set to consecutive 8 bytes address ranges.

CounterTimerNumberofBoards = this entry indicates the number of DCC20AX counter timer boards installed in the system and used by Probe for Windows. Normally 1 or 2 boards are used. The default is 0.

Cal mag = this entry indicates the magnification condition which is used to measure the "cal microns" calibration value in the next entry. The default is 200.

Cal microns = this entry specifies the actual number of "units" (usually microns and defined below) measured at the "cal mag" magnification condition for calibration of the image registration. The "cal microns" should refer to the maximum horizontal or vertical extent of the image display. The use of a calibration grid is recommended for this procedure. Contact Advanced MicroBeam for details. The default is 630 (assumes SEMQ at x100).

Cal counts = this entry refers to the maximum number of D/A counts in the image scan. It should normally never be adjusted. The only valid setting is 65535 for the 16 bit D-A board. The default is 65535 (16 bit digitizer).

Cal y microns = this entry specifies the actual number of "units" (usually microns and defined below) measured at the "cal mag" magnification condition for calibration of the image registration of the Y beam scan axis. The "cal microns" should refer to the maximum vertical extent of the image display. This and the cal y counts keywords are only to be used for microprobes that have a non-square scan coil response (that is a rectangular image display as in the Cameca SX-50).

The use of a calibration grid is recommended for this procedure. Contact Advanced MicroBeam for details. The default is equal to the Cal Microns (above).

Cal y counts = this entry refers to the maximum number of D/A counts in the image scan of the Y beam scan axis. It should normally never be adjusted. The only valid setting is 65535 for the 16 bit board. The default is the Cal Counts (above).

Units = use this entry to specify the label string used in the scale bar and image labels. Make sure that the string is enclosed in double quotes. The "cal microns" entry is in "units" units. The default is "microns".

Stage to microns = this entry defines the stage unit to micron conversion factor. For example, the SEMQ microprobe stage is calibrated in 0.1 mm units, therefore the conversion factor for the SEMQ should be 100. On the other hand, the JEOL and Cameca microprobe stages are calibrated in 1 mm units and should therefore use a "stage to microns" factor of 1000 (microns times 1000 equals 1 mm). The default is 100 (SEMQ).

Note that all imported and exported grid files will have the XY data values adjusted using the "stage to micron" conversion factor.

Cal kilovolts = this entry defines the operating voltage of the microprobe for the purposes of the magnification calibration. Be sure to enter the actual operating voltage of the microprobe that was used to measure the "cal microns" entry above. The default is 15.0.

User kilovolts = this entry defines the default operating voltage of the microprobe. The value is usually the same as the "cal kilovolts" above but is not required to be. The "user kilovolts" entry can be changed from the Magnification dialog box from the "Setup" | "Magnification" menu. The ratio of the "cal kilovolts" to the "user kilovolts" is used to modify the "cal microns" value for the purposes of image scale registration. The default is 15.0. The calculation is shown here :

where : 	is the actual "cal microns" calibration value for the current operating voltage

is the "cal microns" value for the "cal kilovolts" operating voltage

is the "cal kilovolts" value

is the current operating voltage

Spectrometer motors =  this entry defines the number of tunable spectrometer motors in the microprobe. This must not include any fixed or monochromator spectrometers in the microprobe.

Stage motors = this entry is the number of microscope stage motors. Enter either 0, 2, 3 or 4.

adrange = this entry specifies the input voltage range of the A/D conversion channels. The WIN30PG board only supports "unipolar5" and "bipolar5" ranges.

control logic = this entry specifies the logic of the external control output line for using an external beam scan input on the microprobe or SEM. The default is on (JEOL and SEMQ instruments). If "control logic" is off, then the A7 control line on the DAC board is low during image acquisition.

SX50InterfaceBoardType =

SX50SEMDeviceName=

SX50WDSDeviceName=

These entries are only used for Cameca installations which call the SX50 DLL interface for stage motion and control. The "mctype" parameter must be set to "sx50" above. The SX50InterfaceBoardType must be set to 0 for the null test mode, 1 for the PC11 interface board and 2 for the Logical interface board. The default is 1.

The SX50 SEM and WDS device names must be set according the device names defined in the IOMapper applet. The defaults are "IOMapper5" for the SEM device name and "IOMapper6" for the WDS device name. These values should match the SX50 parameter values defined in the PROBEWIN.INI file.

Note that the SX50 interface requires the following three DLL files:

SX50_32.DLL	high level library

SX-NULL.DLL	test driver

SX-PC11.DLL	pc11 driver

SX-DCI13.DLL	logical driver

These files are installed automatically by the IOMapper installation. Contact Advanced Microbeam for help on this and other installation issues.


[faraday]

This section describes how the faraday cup or beam blank circuit is utilized in the software. The true and false entries should not be enclosed in double quotes.

FaradayCupPresent = false

DefaultBeamBlankFlag = false

FaradayWaitInTime = 0.5

FaradayWaitOutTime = 0.5

FaradayCupPresent = this entry indicates whether a faraday cup is present in the hardware configuration. Use true for present or false for not present. If not present, then a beam blank circuit is assumed present. The default is false.

DefaultBeamBlankFlag = this entry saves the beam blank mode for the software. True indicates that the software should remove the faraday before the image acquisition and insert it after the image acquisition. False indicates that the software should always leave the faraday cup removed. The default is false.

FaradayWaitInTime = this is the delay in seconds that the software will wait after inserting the faraday cup (or blanking the beam). The default is 0.5 seconds and the allowable range is 0 to 100 seconds.

FaradayWaitOutTime = this is the delay in seconds that the software will wait after removing the faraday cup (or unblanking the beam). The default is 0.5 seconds and the allowable range is 0 to 100 seconds.


[scalebar]

This section is used to define the default setup for the image scale bar used for displaying the image size on screen or for hard copy purposes. The true and false entries should not be enclosed in double quotes.

horizontal = true

label = true

black = false

hide = false

large = false

position = 15

thick = 4

thin = 2

print factor = 4

Horizontal = the entry must be specified as 0 or 1, "on" or "off" or "true" or "false". Specify true for a horizontal scale bar or false for a vertical default scale bar display. The default is false.

Label = the entry must be specified as 0 or 1, "on" or "off" or "true" or "false". Specify true for a scale bar label to be displayed or false for no scale bar label display. The label string displayed is defined under the [hardware] section above as the "units" entry. The default is false.

Black = the entry must be specified as 0 or 1, "on" or "off" or "true" or "false". Specify true for a black scale bar and label or false for a white scale bar and label. The default is false.

Hide = the entry must be specified as 0 or 1, "on" or "off" or "true" or "false". Specify true to not display a scale bar or false to display a scale bar. The default is false.

Large = the entry must be specified 0 or 1, "on" or "off" or "true" or "false". Specify true for a large scale bar or false for a small scale bar. The default is true.

Position = this entry is used to define the position of the scale bar display on or off the image. The default is 10. See the drawing below to select the default display position of the scale bar and label :

	0	1	2
3	4	5	6	7
8	9	10	11	12
13	14	15	16	17
	18	19	20
Position values of 4, 5, 6, 9, 10, 11, 14, 15 or 16 will place the scale bar on top of the image area, while values of 0, 1, 2, 3, 7, 8, 12, 13, 17, 18, 19 or 20 will place the scale bar outside the image area. Based on this mapping, a position entry value of 8 will place the scale bar off the image to the left, and a position entry of 15 will place the scale bar on the image near the middle lower edge of the image.  Only integer values indicated above are valid entries for the scale bar position display.

Thick = the thickness of the displayed scale bar if the "Thick" option is checked in the Scale Bar Properties window. 0 is minimum thickness or 1 pixel thick. Use this option to have the scale bar displayed more prominently when printing images to paper.

Thin = the thickness of the displayed scale bar if the "Thick" option is NOT checked in the Scale Bar Properties window. 0 is minimum thickness or 1 pixel thick.

Print factor = the factor applied to the scale bar thickness when printing. Specifically the pixel to DPI conversion factor (screen to printer). Default is 4 which assumes approximately a 100 DPI screen and a 400 DPI printer.


[palette bar]

This section is used to define the default setup for the image palette bar used for displaying the image Z unit data on screen or for hard copy purposes. The true and false entries should not be enclosed in double quotes.

label = true

hide  = false

black = true

units = "units"

position = 1

Label = the entry must be specified as 0 or 1, "on" or "off" or "true" or "false". Specify true for a palette bar label to be displayed or false for no palette bar label display. The default is false.

Hide = the entry must be specified as 0 or 1, "on" or "off" or "true" or "false". Specify true to not display a palette bar or false to display a palette bar. The default is false.

Black = the entry must be specified as 0 or 1, "on" or "off" or "true" or "false". Specify true for a black palette bar label or false for a white palette bar label. The default is false.

Units = Default unit label for palette bar.  Normally overloaded by channel units labels defined below. The default is "counts".

Position = this entry is used to define the position of the palette bar display off the image. The default is 2. See the drawing below to select the default display position of the palette bar and label :


[analog]

The following entries define the analog channel input defaults.

autostretch = on

max = 4

ch1 = "SEI"

ch2 = "AEI"

ch3 = "COMPO"

ch4 = "TOPO"

en1 = on

en2 = off

en3 = off

en4 = off

bits1 = 8

bits2 = 8

bits3 = 8

bits4 = 8

pol1 = true

pol2 = true

pol3 = true

pol4 = true

zunit1 = volts

zlow1  = 0.

zhigh1 = 10.

zunit2 = volts

zlow2  = 0.

zhigh2 = 10.

zunit3 = volts

zlow3  = 0.

zhigh3 = 10.

zunit4 = volts

zlow4  = 0.

zhigh4 = 10.

programmable gain1 = 2

programmable gain2 = 2

programmable gain3 = 2

programmable gain4 = 2

Autostretch = this entry specifies if a linear palette stretch should be applied automatically to the image acquisition by default. The entry must be one of the following choices : "on", "ON", off" or "OFF". The enabled values can be enclosed in double quotes or not. The default is on.

Max = use this entry to specify the maximum number of analog input channels in the microscope system. Analog inputs may include any analog signal between 0 - 10 volts. Examples include backscattered electron, secondary, and cathodo-luminescence detector signals. The default is 1.

All input channels greater than the Max value, will be disabled and unavailable to the user.

Ch[n] = use the Ch[n] (for channel) entries to indicate the default name of the analog channel as it should appear in the image window. The character [n] in Ch[n] should be from 1 to "max" and there should be a unique label entry for each valid channel.  For example : if the first analog input channel is for backscattered electron signals, specify the channel name by using the string "ch1= "BSE" or "ch1="BS" or whatever is preferred. Spaces in the channel name will be converted to underscores. The default is "Analog[n]".

In addition, the name can be edited and changed from the "Analog Inputs" dialog box while the program is running. The channel string name must be enclosed in double quotes.

En[n] = the En[n] (for enabled) entry is used to indicate if the channel is selected or not by default when the program is started. The character [n] in En[n] should be from 1 to "max" and the entry must be one of the following choices : "on", "ON", off" or "OFF". The enabled values can be enclosed in double quotes or not. The default is off.

Bits[n] = use the Bits[n] (for bits per pixel) entry to specify the default image depth for each channel image. The character [n] in Bits[n] should be from 1 to "max" and the only valid choices are 8 or 16. An invalid entry will default to 8 bit image depth. Use "8" to specify an image depth of 8 bits per pixel (256 possible pixel values) or "16" to specify an image depth of 16 bits per pixel (65535 possible pixel values). The default is 16.

pol[n] = The default polarity of the analog input channels. The default is true for positive voltage equals high signal. If set to false (SX-50), the A/D conversions are inverted using a 1's complement.

zunits[n] =  The default label for the analog channel. Enclose in quotes if spaces are used. The default is "volts".

zlow[n] =  the real world value that corresponds to an A-D conversion of 0, usually zero volts. The character [n] in En[n] should be from 1 to "max". The default is 0.0.

zhigh[n] =  the real world value that corresponds to an A-D conversion of 65535 (16 bits for WIN30PG board), depending on the resolution of the A-D converter. The character [n] in En[n] should be from 1 to "max". The default is 10.0.

programmable gain[n] = is used to define the programmable gain for WIN30PG boards only. The allowable values are 1, 2, 4 or 8. This will provide additional gain for analog signals less than 10 volts full scale. The default gain is 1. The specified gain is applied to each analog input separately.


[digital]

The following keywords define the digital channel input defaults.

beamchannel = false

autostretch = on

max = 8

maxelm = 8

ch1 = "Si"

ch2 = "Fe"

ch3 = "Ca"

ch4 = "Al"

ch5 = "1"

ch6 = "2"

ch7 = "3"

ch8 = "4"

en1 = off

en2 = off

en3 = off

en4 = off

en5 = off

en6 = off

en7 = off

en8 = off

bits1 = 8

bits2 = 8

bits3 = 8

bits4 = 8

bits5 = 8

bits6 = 8

bits7 = 8

bits8 = 8

Beamchannel = this entry specifies if the first channel on the digital inputs is a beam current input. If true, then the program will offset the ElmFile text strings by one channel. Default = false.

Autostretch = this entry specifies if a linear palette stretch should be applied automatically to the image acquisition by default. The entry must be one of the following choices : "on", "ON", off" or "OFF". The enabled values can be enclosed in double quotes or not. The default is on.

Max = use this entry to specify the maximum number of digital input channels in the microscope system. Digital inputs may include any digital signal which switches between 0 to 5 volts. Examples include x-ray PHA signals. The default is 1. All input channels greater than the "max" value, will be disabled and unavailable to the user. "Max" should less than or equal to 16 for the WIN30 boards for digital inputs.

MaxElm = use this entry to specify the maximum number of labels to read from the .ELM file specified by the "ElmFile" keyword (usually C:\Program Files\Probe for Windows\Probewin.elm). This value must be less than or equal to the number of spectrometer channels (or lines) found in the .ELM file. If the keyword is missing, the default is calculated as "MaxElm" = "Max" - "BeamChannel".

MaxEDS = use this entry to specify the maximum number of labels to read from the .EDS file specified by the "EDSFile" keyword (usually C:\Program Files\Probe for Windows\Probewin.eds). This value must be less than or equal to the number of digital EDS ROI channels (or lines) found in the .EDS file. If the keyword is missing, the default is calculated as "MaxEDS" = "Max" - "MaxElm" - "BeamChannel".

Ch[n] = use the Ch[n] (for channel) entries to indicate the default name of the digital input channel as it should appear in the image window.

Note that the name of the digital input and pulse counter input channels can be the same and will in fact normally be the same, since they are loaded in real time from the PROBE.ELM file (if it was specified in the [software] section above). MicroImage will automatically append an "_d" to digital channel names and an "_c" for pulse counter input names, to differentiate the digital inputs from the pulse counter inputs in the image window names.

The character [n] in Ch[n] should be from 1 to "max" and there should be a unique entry for each valid channel.  For example : if the first digital input channel is for tunable spectrometer #1, specify the channel name by using the string ch1= "Spec1" or ch1="Sp1" or whatever is preferred. Spaces in the channel name will be converted to underscores. The default is "Digital[n]".

In addition, the name can be edited and changed from the Digital Inputs dialog box while the program is running. The channel string name must be enclosed in double quotes.

En[n] = the En[n] (for enabled) entry is used to indicate if the channel is selected or not by default when the program is started. The character [n] in En[n] should be from 1 to "max" and the entry must be one of the following choices : "on", "ON", "off" or "OFF". The enabled values can be enclosed in double quotes or not. The default is off.

Bits[n] = use the Bits[n] (for bits per pixel) entry to specify the default image depth for each channel image. The character [n] in Bits[n] should be from 1 to "max" and the only valid choices are 8 or 16. An invalid entry will default to 8 bit image depth. Use "8" to specify an image depth of 8 bits per pixel (256 possible pixel values) or "16" to specify an image depth of 16 bits per pixel (65535 possible pixel values). The default is 8.

X-ray images acquired using digital inputs can only increment a pixel value at most by 1 count for each image frame acquisition, unless pixel averaging is used. Therefore, without pixel averaging, it would require at least (and usually much more than) 256 image frames to be acquired before an 8 bit image will overflow.

Pixel values that overflow the image depth will be set to the maximum value for the image depth (8 bit images = 255, 16 bit images = 65535).


[counter]

The following keywords define the counter-timer channel input defaults.

beamchannel = true

autostretch = on

count time = 0.1

max = 9

maxelm = 8

ch1 = "Beam"

ch2 = "Si"

ch3 = "Fe"

ch4 = "Ca"

ch5 = "Al"

ch6 = "1"

ch7 = "2"

ch8 = "3"

ch9 = "4"

en1 = off

en2 = off

en3 = off

en4 = off

en5 = off

en6 = off

en7 = off

en8 = off

en9 = off

bits1 = 16

bits2 = 16

bits3 = 16

bits4 = 16

bits5 = 16

bits6 = 16

bits7 = 16

bits8 = 16

bits9 = 16

Beamchannel = this entry specifies if the first channel on the counter inputs is a beam current input. If true, then the program will offset the "elmfile" text strings by one channel. For the counter-timer inputs this is normally true. Default = false.

Autostretch = this entry specifies if a linear palette stretch should be applied automatically to the image acquisition by default. The entry must be one of the following choices : "on", "ON", "off" or "OFF". The enabled values can be enclosed in double quotes or not. The default is on.

Count Time = the "count time" entry defines the default count time used by MicroImage for counter input image acquisition in seconds. The count time is the actual count time that the program will acquire pulse count data for each pixel for each image frame acquisition. The default is 0.1.

Valid "count time" values must be from 0.01 to 1,000,000 and can be modified in 0.01 increments.

Max = use this entry to specify the maximum number of pulse counter input channels in the microprobe system. Pulse counter inputs may include any digital signal which switches between 0 to 5 volts. Examples include x-ray PHA signals. The default is 1. All input channels greater than the "max" value, will be disabled and unavailable to the user. "Max" should be less than or equal to the number of counter-timer channels available (including the beam channel).

MaxElm = use this entry to specify the maximum number of labels to read from the .ELM file specified by the "ElmFile" keyword (usually C:\Program Files\Probe for Windows\Probewin.elm). This value must be less than or equal to the number of spectrometer channels (or lines) found in the .ELM file. If the keyword is missing, the default is calculated as "MaxElm" = "Max" - "BeamChannel".

MaxEDS = use this entry to specify the maximum number of labels to read from the .EDS file specified by the "EDSFile" keyword (usually C:\Program Files\Probe for Windows\Probewin.eds). This value must be less than or equal to the number of digital EDS ROI channels (or lines) found in the .EDS file. If the keyword is missing, the default is calculated as "MaxEDS" = "Max" - "MaxElm" - "BeamChannel".

Ch[n] = use the Ch[n] (for channel) entries to indicate the default name of the pulse counter input channel as it should appear in the image window.  If "beamchannel" is true then the first channel is reserved for beam current measurements on aperture beam current microprobes.

Note that the name of the digital input and pulse counter input channels can be the same and will in fact normally be the same, since they are loaded in real time from the PROBEWIN.ELM file (if it was specified in the [software] section above). MicroImage will automatically append an "_d" to digital channel names and an "_c" for pulse counter input names, to differentiate the digital inputs from the pulse counter inputs in the window names. The default is "Counter[n]".

The character [n] in Ch[n] should be from 1 to "max" and there should be a unique entry for each valid channel.  For example : if the first digital input channel is for tunable spectrometer #1, specify the channel name by using the string ch1= "Spec1" or ch1="Sp1" or whatever is preferred. Spaces in the channel name will be converted to underscores.

In addition, the name can be edited and changed from the Counter Inputs dialog box while the program is running. The channel string name must be enclosed in double quotes.

En[n] = the En[n] (for enabled) entry is used to indicate if the channel is selected or not by default when the program is started. The character [n] in En[n] should be from 1 to "max" and the entry must be one of the following choices : "on", "ON", "off" or "OFF". The enabled values can be enclosed in double quotes or not. The default is off.

Bits[n] = use the Bits[n] (for bits per pixel) entry to specify the default image depth for each channel image. The character [n] in Bits[n] should be from 1 to "max" and the only valid choices are 8 or 16. Use "8" to specify an image depth of 8 bits per pixel (256 possible pixel values) or "16" to specify an image depth of 16 bits per pixel (65535 possible pixel values). The default is 16 to allow 16 bit image depth.

X-ray images acquired using digital inputs can only increment a pixel value at most by 1 count for each image frame acquisition, unless pixel averaging is used. Therefore, without pixel averaging, it would require at least (and usually much more than) 256 image frames to be acquired before an 8 bit image will overflow.

Pixel values that overflow the image depth will be set to the maximum value for the image depth (8 bit images = 255, 16 bit images = 65535).


[stage x]

Each motorized stage axis must have it's own section defined. Only the x and y stage axes are supported by MicroImage. Both must be defined here in the MICROIMAGE.INI file for stage control to operate correctly.

axis name = "X Axis"

span = 10

encoder ratio = 3333.3333

low limit = 5

high limit = 610

backlash = .001

axis name = the axis name. The default is none.

span = the default stage scan setup width in stage units. The default is 1% of the stage axis range.

encoder ratio = the controller encoder ratio.  The default is 1.0.

low limit = the motor low limit in real stage units.  The default is 1.0

high limit = the motor high limit in real stage units.  The default is 1.0

backlash = the X axis backlash jog in stage units. Note that the direction of the backlash operation is dependent on the Stage X Polarity flag in the [software] section above. That is, the backlash is always performed when moving in a direction opposite to that specified by the Stage X polarity flag. For no backlash on the X axis set this value to 0.0 (the default).


[stage y]

Each motorized stage axis must have it's own section defined. Only the x and y stage axes are supported by MicroImage. Both must be defined here in the MICROIMAGE.INI file for stage control to operate correctly.

axis name = "Y Axis"

span = 10

encoder ratio = 3333.3333

low limit = 5

high limit = 600

backlash = .001

axis name = the axis name. The default is none.

span = the default stage scan setup width in stage units. The default is 1% of the stage axis range.

encoder ratio = the controller encoder ratio.  The default is 1.0.

low limit = the motor low limit in real stage units.  The default is 1.0

high limit = the motor high limit in real stage units.  The default is 1.0

backlash = the Y axis backlash jog in stage units. Note that the direction of the backlash operation is dependent on the Stage Y Polarity flag in the [software] section above. That is, the backlash is always performed when moving in a direction opposite to that specified by the Stage Y polarity flag. For no backlash on the Y axis set this value to 0.0 (the default).


Glossary of Terms

ANALOG

ASCII

AVERAGE

CLASSIFY

COUNTER

DIGITAL

FALSE COLOR

GRID

HISTOGRAM

IMAGE DEPTH

P/B

PALETTE

PHA

PIXEL VALUE

TIFF

WDS


ANALOG

MicroImage can input several different data signal types such as analog, digital and counter pulses. Analog signals are characterized by a smoothly varying voltage which must be converted using a analog-to-digital converter before the image can be displayed or processed. MicroImage supports 16 bit A/D acquisition boards.


ASCII

(American Standard Code for Information Interchange) A set of 256 electronic codes that most computers use to represent letters, numerical digits, special characters and other symbols. Only the first 128 of these codes are standardized; the remaining 128 are defined by the computer or printer manufacturer.

A file is said to be an ASCII file when it can be simply typed out on the computer screen or printed to any line or parallel printer without using special software.


AVERAGE

Also known as the mean or arithmetic mean. The average is calculated by simply dividing the sum by the number of values. The calculation is shown below.

where : 	X 	are the values to be averaged

n	is the number of values to be averaged


CLASSIFY

MicroImage includes a sophisticated procedure for determining the modal abundance of various regions in a related set of images (often referred to as spectral bands). By correlating corresponding pixels from a related set of images, these phase regions can be colored for visual interpretation and the number of pixels in each quantified. See the Classify menu item under the Advanced menu.


COUNTER

MicroImage can input several different data signal types such as analog, digital and counter pulses. Counter signals are really digital signals that are accumulated using a timed digital pulse counter instead of a simple digital I/O channel. This results in a much faster data input rate capable of producing images of even very weak signals. On the other hand the count time required per pixel is significantly longer than for a simple digital I/O input image acquisition.

Use the counter inputs for low resolution low level signals such as minor or trace elements and the digital I/O inputs for high resolution high level signals from major element concentrations.


DIGITAL

MicroImage can input several different data signal types such as analog, digital and counter pulses. Digital signals are characterized by discreet signal levels, typically 0 to 5 volts. These signals can be read by simply scanning the digital I/O inputs. This results in a rapid data input rate capable of producing high resolution images. On the other hand, because only a single digital count is processed per frame acquisition, the sensitivity is very low, requiring many frame averages to produce even minor statistical significance. Compare to counter inputs.

Use the digital inputs for high resolution high level signals such as major concentration elements and the counter inputs for low resolution low level signals from minor or trace element concentrations.


FALSE COLOR

The process of colorizing pixel values using either ranges or interpolated color schemes to visually enhance certain image characteristics.


GRID

(Grid File) A file format used by SURFER (Golden Software) to store data with 3 coordinates of information (X, Y and Z). The file is a binary file with no structure and may be read from FORTRAN, C or Pascal. A grid file always has the extension ".GRD". The format is as follows :

cdum	a 4 byte string containing the characters 'DSBB'

ixgrid, iygrid	two integer*2 values containing the grid density

xmin, xmax	two real*8 values containing the X data min and max

ymin, ymax	two real*8 values containing the Y data min and max

zmin, zmax	two real*8 values containing the Z data min and max

data	ixgrid * iygrid real*4 values containing the Z data values


HISTOGRAM

A graphical method for representing the numerical distribution pixel value. Typically, the x-axis is used to plot the pixel values and the y-axis is used to plot the number of pixels of each value.


IMAGE DEPTH

MicroImage can acquire both 8 and 16 bit images. The 8 or 16 refers to the image depth or bits per pixel of the image. Images with 8 bits per pixel can have pixel values ranging from 0 to 255. Images with 16 bits per pixel, can have pixel values ranging from 0 to 65535.

However, both image types are displayed with a maximum 256 colors and output to disk as TIFF or PCX image files is also limited to 256 colors. In order to preserve the actual 16 bit image data, use the GRID (*.GRD) file output type. This file type is compatible with SURFER for DOS or SURFER for Windows software for display of contour or 3-D surface plots using a REAL*4 or floating point data type.


P/B

Peak to Background Ratio. A measure of the sensitivity of the analysis. To improve your detection limit, you will want to increase the peak to background ratio. This can be accomplished by using the analyzing crystal with the highest theta available (for example run K Kα on LiF rather than PET) and using lower noise flow detectors rather than sealed detectors. The P/B is calculated as :

where : 	is the background corrected peak intensity

is the background continuum intensity


PALETTE

The colors selected to represent the numerical pixel value of the image. Also known as a "look up table" (LUT). MicroImage is supplied with several palette options, Red, Green, Blue, Grey and Full. Using the full palette, the user can represent the numerical pixel values with a large variety of false color schemes including Thermal (Black-Red-Yellow-White), Rainbow (Red-Orange-Yellow-Green-Blue-Violet) and BlueRed (Blue-Red) or user defined from the False Color menu.


PHA

(Pulse Height Analyzer).  This is the electronics used to convert the analog signal from the detector pre-amp into digitized pulses for input to the x-ray counter scalers. Used to filter low energy noise and high energy interferences from the signal. Because Probe for Windows utilizes a sophisticated interference correction, it is best to use a "loose" PHA filter to avoid energy shift effects in the analysis, rather than try to eliminate interferences with the PHA settings.


PIXEL VALUE

The data value of a pixel. Typically 0 to 255 for 8 bit images (one byte per pixel) or 0 to 65535 for 16 bit images (two bytes per pixel).


TIFF

(Tagged Image File Format) An image file format consisting of rasterized pixel color information. MicroImage uses the TIFF file format because it is almost universally supported.

To include registration of the TIFF image, MicroImage has two private TIFF tags to define the x-y and z image registration in real world units. For example, the TIFF image size may be 256 x 256 pixels, but the real world size may be from 24020 to 24120 um in X stage units and 32435 to 32535 um in Y stage units. That is, 100 x 100 um in size. The TIFF color information may range 0-255 color values but the real world units (in the case of an analog image) may range from 2.4 to 5.6 volts or from 34.45 to 38.6 weight % (in the case of a quantitative image). This information is stored directly in the TIFF image.

Be aware that other image processing programs will not be able to utilize or even save this image registration information since it is not part of the public TIFF standard.

For more information on accessing these private TIFF tags, please contact Advanced MicroBeam.


WDS

(Wavelength Dispersive Spectrometry) X-ray analysis based on Bragg's law of x-ray diffraction.

where :	is the order of the x-ray (1st, 2nd, etc.)

is the wavelength in angstroms

is the analyzing crystal 2d spacing in angstroms

is the angle of diffraction