NS7 2.2 Training Guide G A 151873

950A151873 (Rev.
G)
NORAN System 7 Version 2.2
NORANSystem 7
Training Guide
5225 Verona Road

Madison, WI 53711 USA
Customer Support: 800-642-6538 (USA) or +1 608 273 5015 (worldwide)
Corporate: 608-276-6100 (USA)
E-mail: us.techsupport.analyze@thermofisher.com
World Wide Web: http://www.thermo.com
Revision history
Revision Revision date Principal changes Software version
A September 2002 First publication System SIX 1.1
B February 2004 Revised edition System SIX 1.4
C July 2004 Revised edition; added Feature Sizing System SIX 1.5
D March 2005 Revised eddition; added X-Phase, Spectral System SIX 1.6
Match, System SIX 1.7
E January 2007 Revised edition System SIX II 2.0
F August 2007 Revised edition - Build 31 System SIX II 2.0
G November 2008 Revised edition System 7 2.2
© 2008 Thermo Fisher Scientific. All rights reserved.
Syste SIX and System 7 are trademarks of Thermo Fisher Scientific.

Fat Spot is a trademark of Thermo NORAN/Thermo Electron Corporation.
Table of Contents
Chapter 1
Tour of System 7 Software Interface . . . . . . . . . . . . . . . . . .1
Overview of System 7 Capabilities . . . . . . . . . . . . . . . 1
Software Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Starting System 7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Arranging the Screen. . . . . . . . . . . . . . . . . . . . . . . . . . 4
Saving Your Rearranged Screen. . . . . . . . . . . . . . . . . 5
Overview Of The Menus . . . . . . . . . . . . . . . . . . . . . . . 6
Overview Of The Toolbars. . . . . . . . . . . . . . . . . . . . . . 9
Chapter 2
Project Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13
Project Explorer Window . . . . . . . . . . . . . . . . . . . . . . . 14
Creating a New Project . . . . . . . . . . . . . . . . . . . . . . . . 15
Opening a Project . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Creating a New Template . . . . . . . . . . . . . . . . . . . . . . 16
Resetting a Project . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Importing Files From Another Project . . . . . . . . . . . . . 16
Searching for a Project . . . . . . . . . . . . . . . . . . . . . . . . 17
Chapter 3
Spectrum Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19
Pre-analysis Considerations . . . . . . . . . . . . . . . . . . . . 19
Selecting Spectrum Mode . . . . . . . . . . . . . . . . . . . . . . 20
General Spectral Acquisition Procedures . . . . . . . . . . 22
Spectral Acquisition Setup. . . . . . . . . . . . . . . . . . . . . . 23
Acquisition Setup Considerations . . . . . . . . . . . . . . . . 25
Microscope Properties. . . . . . . . . . . . . . . . . . . . . . . . . 27
Detector Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Adjusting Spectral Display. . . . . . . . . . . . . . . . . . . . . . 30
Qualitative Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Using SpectraCheck After Identification . . . . . . . . . . . 45
Comparing Spectra . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
TABLE OF CONTENTS i
TABLE OF CONTENTS Quantitative Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . .48
Specifying Quant output . . . . . . . . . . . . . . . . . . . . . . . .53
Quantification With Standards. . . . . . . . . . . . . . . . . . . .55
Quantification For STEM/TEM Analysis . . . . . . . . . . . .62
Additional Tools in Spectrum Mode . . . . . . . . . . . . . . .67
Calibrating Fine Gain . . . . . . . . . . . . . . . . . . . . . . . . . .73
Adjusting Configurations . . . . . . . . . . . . . . . . . . . . . . . .75
Chapter 4
Electron Imaging Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Imaging Mode Interface . . . . . . . . . . . . . . . . . . . . . . . .79
Setting Imaging Acquisition Properties . . . . . . . . . . . . .80
Acquiring An Electron Image. . . . . . . . . . . . . . . . . . . . .80
Post Acquisition Processing . . . . . . . . . . . . . . . . . . . . .81
Managing Image Files . . . . . . . . . . . . . . . . . . . . . . . . . .83
Chapter 5
Point and Shoot Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Setting Point and Shoot Acquisition Properties. . . . . . .86
Performing a Point and Shoot Acquisition. . . . . . . . . . .86
Chapter 6
Spectral Imaging Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Setting Acquisition Properties . . . . . . . . . . . . . . . . . . . .90
Extraction Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .93
Extracting data from a polygon . . . . . . . . . . . . . . . . . . .93
Extracting data from a rectangle . . . . . . . . . . . . . . . . . .94
Extracting data from a spot . . . . . . . . . . . . . . . . . . . . . .95
Extracting linescan data . . . . . . . . . . . . . . . . . . . . . . . .96
Extracting Multiple Spectra . . . . . . . . . . . . . . . . . . . . . .101
Spectral Imaging X-ray Mapping . . . . . . . . . . . . . . . . . .101
Analyzing X-ray Maps . . . . . . . . . . . . . . . . . . . . . . . . . .103
Extracting Additional Data Types . . . . . . . . . . . . . . . . .106
Compass Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .111
Chapter 7
3D Visualization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
Selecting Color Schemes . . . . . . . . . . . . . . . . . . . . . . .119
II NORAN SYSTEM 7 TRAINING GUIDE

Clipping the data outside the color range . . . . . . . . . . 120 TABLE OF CONTENTS
Selecting a cursor style for the 3-D image. . . . . . . . . . 121
Smoothing the 3-D image . . . . . . . . . . . . . . . . . . . . . . 121
Setting the opacity of the 3-D image . . . . . . . . . . . . . . 121
Displaying an outline box. . . . . . . . . . . . . . . . . . . . . . . 122
Chapter 8
Linescan Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .123
Setting Linescan Acquisition Properties . . . . . . . . . . . 123
Setting Up Linescan Elements . . . . . . . . . . . . . . . . . . 124
Acquiring a Linescan . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Analyzing a Linescan. . . . . . . . . . . . . . . . . . . . . . . . . . 125
Saving Linescan Files . . . . . . . . . . . . . . . . . . . . . . . . . 126
Export as *.csv Files . . . . . . . . . . . . . . . . . . . . . . . . . . 126
Opening Linescan Files . . . . . . . . . . . . . . . . . . . . . . . . 126
Chapter 9
Creating Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .127
Setting Up a Printer Report . . . . . . . . . . . . . . . . . . . . . 127
Previewing and Printing Reports . . . . . . . . . . . . . . . . . 129
Copying Items to Third-party Programs. . . . . . . . . . . . 130
Chapter 10
Spectral Match . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .131
Creating a Database . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Creating a Match Database. . . . . . . . . . . . . . . . . . . . . 134
Using Spectral Match . . . . . . . . . . . . . . . . . . . . . . . . . 136
Spectral Match Parameters . . . . . . . . . . . . . . . . . . . . . 137
Chapter 11
Feature Sizing and Chemical Typing . . . . . . . . . . . . . . . . . .139
Feature Sizing Setup Mode . . . . . . . . . . . . . . . . . . . . . 139
Running A Particle Analysis . . . . . . . . . . . . . . . . . . . . 152
Chemical Typing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
Running Chemical Typing . . . . . . . . . . . . . . . . . . . . . . 162
Advanced Feature and Chemistry Filtering . . . . . . . . . 163
TABLE OF CONTENTS iii

TABLE OF CONTENTS
IV NORAN SYSTEM 7 TRAINING GUIDE

CHAPTER
1
Tour of System 7
Software Interface
Overview of System 7 Capabilities
NORAN System 7 is a combination of a high-performance X-ray energy-
dispersive detector and supporting electronics, and controlling software that is
installed on a dedicated computer. System 7 detectors can be connected to a
variety of electron microscopes - Scanning (SEM), Transmission (TEM) and
Scanning Transmission (STEM). Thermo Fisher Scientific offers several
models of detectors with various ultra-thin windows, resolutions, and cooling
options:
• Liquid nitrogen cooled X-ray (SiLi) detector

• SuperDry II electrically cooled X-ray (SiLi) detector
• UltraDry electrically cooled Silicon Drift Detector
• NORVAR and PleXus ultra-thin windows
The basic System 7 (Model 102) allows you to acquire, analyze, quantify, and
create reports of X-ray spectra. With additional electronics and software
packages, System 7 (Model 202) adds electron imaging, spectral imaging, and
linescan data acquisition capabilities (with release of version 2, the only method
of collecting X-ray maps is via spectral imaging). Additional capabilities may be
added to System 7 (Model 302) through optional software packages. System 7
supports the following optional software modules:
• Compass: a statistical analysis of components.
• Direct To Phase option includes Compass, Phase Analysis (XPhase) and
Spectral Match to automatically create Phase Maps during a Spectral
Imaging acquisition and match them to known materials.
• Analysis Automation: after defining the desired parameters, this option
lets you automatically perform repetitive acquisitions on large scale analy-
ses without the need for user intervention or input (requires stage control).
CHAPTER 1: TOUR OF SYSTEM 7 SOFTWARE INTERFACE 1

• Drift Compensation option automatically corrects for sample drift during
acquisitions.
• Feature Sizing and Chemical Typing software measures morphological
parameters of particles or features in a sample as well as determining their
chemical makeup.
• Spectral Match: this option allows comparing unknown spectra with identi-
fied spectra from a spectral database.
Additional Options:
• Single Keyboard, Single Mouse (SKSM) - allows control of both micro-
scope and System 7 from a single mouse and single keyboard.
• Electron Microscope Column Integration - for integrating microscope
parameters with System 7 applications.
• Electron Microscope Stage Control - software for controlling microscope
stage movement from System 7applications.
• WDS Automation and Analysis - software for integrating wavelength-dis-
persive spectrometer acquisitions and analysis with System 7 EDS acquisi-
tions (requires MagnaRay spectrometer).
• Dual Detector Option - Two detectors controlled by one front end.
Software Overview
The NORAN System 7 provides complete microanalysis acquisition, analysis,
reporting, and file management. System 7 features a common, multi-pane user
interface containing a wide assortment of analytical views and controls. All
microanalyses functions are accessed from this single, multi-pane interface.
All commands are initiated through Main Menu entries with submenus. The
most common commands can also be accessed by clicking toolbar buttons.
Each analytical mode has a unique toolbar with appropriate buttons associated
with that mode. Some toolbars, such as the Acquisition Toolbar, are common to
all modes. As you switch analytical modes, the set of toolbars changes to reflect
the various functions preformed in that mode. For each mode, once set,
toolbars remain in the same location and use the same icon set. General,
program-wide operations, such as controlling acquisition and microscope
parameters and managing data layout, are accomplished through dialog boxes.
2 NORAN SYSTEM 7 TRAINING GUIDE

System 7 can automatically identify, label peaks and quantify data during or
after spectral acquisitions. Manual identification may be performed using KLM
markers, X-ray line search, or by selecting elements from a periodic table.
Data are saved and managed within projects. As you switch modes, the
project’s files for that mode are displayed in the File List view. Data files are in
industry standard formats - TIFF for images, EMSA for spectra. X-ray maps are
saved in TIFF format.
Image Cursor Info
Menus Windows Control

Button
Tool Bars
Analysis Mapping Cursor

Modes Information
Image Mapping View

View
Navigation Coordinated
Pane Cursors
Base File
Name
Spectrum View
File List
View
Analysis
Controls
Pane
Status Bar
System 7 Spectral Imaging Mode with Associated Panes

Starting System 7 Starting System 7
Running System 7 from the Windows Start menu:
1. Click Start >All Programs > Thermo Scientific> NSS>NSS.
2. When System 7 starts, Project Explorer is automatically opened (you may
also get an EDS bias on prompt after closing Project Explorer).
3. Select a project, or create a new project, and click OK.
Because System 7 requires an active project for data storage, NS7 automati-
cally starts the Project Explorer window prompting to either select an existing
project or create a new project before continuing (see Chapter 2 for information
on Project Explorer). After closing Project Explorer you may get a prompt
window to turn on the detector bias voltage (overrides the temperature sensor
time out) if the front end has been restarted. System 7 then opens in the last
analysis mode that was accessed.
Arranging the Screen

The System 7 screen is highly customizeable. You can arrange the window
panes (containing Analytical views) and move toolbars for convenience.
Note: System 7 is designed for a screen resolution of 1152 X 864.
For best viewing, change the screen resolution and maximize the System 7
interface window.
Changing the size of window panes

Note: Each mode has separate window pane settings.
Resizing left/right panes
Move the mouse pointer over the vertical pane border until the
cursor changes to right and left arrows. Click and drag the pane
border right or left.
Resizing top/bottom panes

Move the mouse pointer over the horizontal pane border until the
cursor changes to up and down arrows. Click and drag the pane
border up or down.
Resizing all panes

Move the mouse pointer over the intersection of the horizontal
and vertical panes until the cursor changes to 4-way arrows.
Click and drag the pane borders up or down, right or left.

Rearranging toolbars Saving Your Rearranged
You can move toolbars to various locations on the screen. Screen
To move a toolbar, click on or near the left edge of the toolbar (called the
control bar). Click and drag the toolbar by the control bar to a new location. You
can position a toolbar on the left, right, or bottom edge of the System 7 window.
Spectrum Toolbar
Positioned on the right edge of the Spectrum View window.
Click on the left edge of a toolbar (control bar) and drag it to
reposition it.
Control Bar (moves toolbars)
Toolbars can float over the System 7 window as a separate window. To create
a floating toolbar, either drag it over a main portion of the window or double-
click the left edge (control bar) of the toolbar. To return a floating toolbar to its
original position, double-click the toolbar’s title bar. The toolbar snaps back to
its last parked position.
Restoring toolbars
It is possible to remove a toolbar from the window by floating a toolbar and then
closing it instead of returning it to a parked position. To restore toolbars after
closing, select View from the System 7 menu options, and select Restore
Toolbars from the drop down menu selections. Toolbars that were closed will
now be restored and available.
Saving Your Rearranged Screen

When you exit System 7, all of the coordinates for window pane sizes and
toolbar positions are saved. The next time you open NS7, the screen is
arranged as it was when you last exited System 7.

Overview Of The Menus Overview Of The Menus
Menus and functions will change with analysis mode for convenience and are
made active only when applicable.
Menu Selection Function
File Project Explorer.. Opens the Project Explorer dialog box to

open, create, or edit a project and its
contained files.
Close Project Closes the current project.
Create Creates a new template from the current

Template... project.
System Security Password protects service screens from

unauthorized user changes to system
parameters.
Open... Opens the dialog box to select a file to

open (not projects).
Close Closes the current file.
Save Saves the current file under its current

name.
Save Map File Opens the Save As dialog box to save an

SI map set. You can enter a different
name for the map set and save it.
Export Image as Exports an image as a Comma Separated

CSV Value file.
Page Setup... Opens a tabbed series of dialog boxes to

define how the data will be printed.
Print Preview Displays the pages as they will appear

printed.
Print Prints the current selection or report.
Export to Word Copies the current data, opens Microsoft

Word, and pastes the data into a new
Word document.
Export to Power Copies the current data, opens Microsoft

Point Power Point, and pastes the data into a
new Power Point slide.

Menu Selection Function Overview Of The Menus
File Compress SI File Opens Dialog box to select and compress

a Spectral Imaging file(s).
Exit Closes System 7 software.
Edit Undo Undoes the previous act.
Cut Cuts the selected data, when available.
Copy Copies the selected data, when available,

to the clipboard.
Copy To.. Saves selected window pane in JPEG

format (*.jpg) to a selected folder.
Paste Pastes the copied or cut data.
Erase All Points In Point and Shoot Mode, erases all points
on the image (before acquisition).
Acquisition Displays the Acquisition Properties dialog

Properties... box.
Microscope Displays the Microscope Parameters

Parameters... dialog box.
Properties... Displays the Properties tabs for all views

available on the screen.
Reset Project Restores the project to the template’s

settings.
Language Selects language for displays
View Restore Toolbar Restores all Toolbars that have been

closed.
Status Bar Toggles the status bar on/off. To select

the fields to display, open the Microscope
Parameters and Status Bar Selection
dialog box.
Drift Diagnostics Displays dialog window of drift

compensation information.

Overview Of The Menus Menu Selection Function
Spectrum sizing functions These commands coordinate with the

Spectral toolbar functions to change the
Spectral View.
Remove Escape Remove Escape peaks from acquired

Peaks spectrum
Remove Sum Remove Sum peaks from acquired

Peaks spectrum
Identify Runs the Identification algorithm on the

current spectrum.
Quantify Runs the quantification algorithm on the

current spectrum.
Match Runs Spectral Matching routine
Decrease/ Displays the KLM lines for the next

Increase Z element lower or higher on the periodic
table from selected element.
Search Down/Up Searches for elements with KLM lines

near the energy cursor location.
Label Peak Adds one peak label for the selected

element whose KLM line is closest to the
cursor.
Unlabel Peak Deletes selected peak label.
Show / Hide KLMs Toggles the display of the KLM markers.
Show/Hide Cursor Toggles the display of the cursor
Element X-Ray Displays selected element and line energy

Lines values. Also allows to change values.
Reference Add or subtract element reference peaks

Subtract/Add from acquired spectrum peaks.
Image extraction tools: Coordinates with the Extraction Toolbar.

Select a shape to extract from the image.
Intensity Toggles intensity cursor on or off
Ruler Toggles the measuring tool on or off.
Legend On/Off Toggles the image legend on or off.

Menu Selection Function Overview Of The Toolbars
All Overlays Off Removes all map overlays from the

image.
Batch Create Montage Creates a montage of images collected

Processing with Analysis Automation
Quant Analysis Performs a quantification analysis on a

series of selected spectra.
Linescan Analysis Reanalyzes a linescan data set (data are

processed using the parameters setup on
the Processing tab: Automatic group)
Point & Shoot Reanalyzes a P&S data set using the

Analysis processing parameters
Specials Special reports and data acquisition

parameters for special applications.
Linescan Export as *.csv Saves X-ray or extracted linescan data to

file in comma separated value format.
Help Help Topics Displays the help file.
What’s This? Cursor changes to a question mark to

learn about an item (item help).
About NSS Displays software versions.
Overview Of The Toolbars

Tool Tips
To view a button’s tool tip (description/function), move the mouse pointer over
the button on the System 7 display for one second.

Overview Of The Main Toolbar
Toolbars Contains buttons for general functions such as opening and saving files,
copying, printing, and opening the help file.
Project Save Paste Print Export to Power

Explorer Preview Point
Help
Cut Copy Print Export to About

Word
Analysis Toolbar
Contains buttons for qualitative and quantitative analysis.
WDS Scan
Identification
Quantify Spectral Match
Acquisition Toolbar
Contains buttons for acquisition operations, including starting, stopping,
pausing, and aborting. Also includes buttons for Acquisition Properties and
Microscope Parameters.
Acquire Averaged Microscope
Image Stop Abort
Parameters
Start Acquisition Acquisition

Enable Drift Pause
Properties
Compensation

Extraction Toolbar Overview Of The Toolbars
Contains buttons for extracting spectral data and maps from a Spectral Imaging
reference image. Also contains a button for turning on and off the image
intensity cursor.
Image Image
Intensity Ruler
Polygon Cursor
Linescan
Extract by
Image
Intensities
Rectangular Fat Spot Extract Maps
Spectrum Toolbar
Contains buttons for adjusting the scale and range of the Spectrum display.
Scroll Scroll
Right Down
Expand
Apply y-log
Full Scale
Spectrum
Scroll Max Vertical

Compress Scroll Up Scale
Left
Spectrum ID Toolbar
Contains buttons for controlling searching, displaying KLM lines and peak
labels.
Search Elements Label Peaks Show KLM

Lower
Scroll KLM
Markers Down
Cursor On/Off
Scroll KLM Markers Search Elements Remove Labels

Up Higher

Overview Of The Point and Shoot Toolbar
Toolbars Contains buttons for acquisitions and analysis in Point and Shoot Mode.
Rectangular area Circular area

Toggle between single or Image Intensity
multiple spot mode Cursor
Polygone area
Scan area
Review shape Similar intensity area
Compass/Phase Toolbar
Contains buttons to toggle from maps to Compass components and extracting
phases.
Manually Determine Phases
from Maps
Toggle between
compass and x- Automatically Determine
Phases from Maps
ray maps
Toggle between Toggle between Manually Determine Phases from

compass and x-ray maps Phases and Components
(depressed for compass) Components
Automatically Determine
Phases from Compass
components

CHAPTER
2
Project Management
Project concept
A project is essentially a folder created by the user for storing and organizing
Noran System 7 data. In addition, a project includes various parameters -
element lists, identification configuration, quantification data and acquisition
properties. The initial parameters are stored in a “template” which is selected
when a project is created. The template parameters are updated when various
parameters are changed during use. Acquired data are stored, along with their
acquisition properties, within a project using a base file name(s). Each project
can consist of several subprojects.
When a project is opened, or created, a temporary folder is also created. Newly

acquired data are copied into the current project’s temporary folder and inherit
the project’s settings. A project’s temporary file is closed only when the project
is closed. When manually saving new data (menu File >Save), System 7
moves the file from the temporary folder to the project folder using the base
name, appended with acquisition number, as the file name. This permanently
saves the file.
When you close a project, System 7 will automatically ask if you want to save
the acquired or altered file(s) within the current project. If you choose to save
the data within the project, the file(s) is moved from the project's temporary
folder to the main project folder. The temporary folder is then removed along
with any non-selected data. If NS7 is closed, or electrical power is lost, without
first closing a project, the temporary folder and all contained data are main-
tained. If you are working with data stored in the temporary folder (not yet
saved to a project) and experience a power failure, the data will be in the
temporary folder when you restart System 7. Thus, all acquired data are never
lost due to accidentally closing System 7 or by power failures.
CHAPTER 2: PROJECT MANAGEMENT 13

Project Explorer Window Project Explorer Window
As mentioned above, projects are essentially folders and can be manipulated
through Windows Explorer. However, they contain additional information that is
unique to System 7. Thus, it is best to perform data and file manipulations using
System 7 Project Explorer, not through Windows Explorer.
The menu items File and Edit commands are coordinated with the toolbar func-
tions. The Properties tab contains information about the project, and the
Explorer tab allows for individual file manipulations.
Copy a Project or Rename Project or

Folder Folder
Create New Project Delete Project or

Folder
Create New Folder Paste Project or

Folder
Properties Tab
Project folders are marked

in green.
3.

Creating a New Project Creating a New Project
Follow the steps below to create a new project:

1. Click the Project Explorer button or use the NS7 Main menu: File >
Project Explorer to open the Project Explorer window.
2. Click on (highlight) the folder you want to contain the project.
3. From Project Explorer File menu, select New Project, or click the Create
a new project button.This will create a folder, which will be green, and
name the folder “New Project”.
4. Rename the folder: Highlight the “New Project” folder (left click on the file
name) and right mouse click. From the displayed submenu select
Rename and type in the desired name.
5. Enter project information in the Properties pane. Click OK to save the
entered information, activate the project and close the Project Explorer
window.
Field Name Description
Author Enter an author’s name.
Key words Select or enter any key words you want associated
with the project. Key words are searchable.
Client Select or enter the client name.
Due Date Select or enter the due date.
Project Template Select the project template from those existing in the
NS7 Project Templates directory.
Notes Enter any relevant notes.
Opening a Project
Follow the steps below to open an existing project:
1. Click the Project Explorer button (or from the File menu, select
Project Explorer).
If any other projects are currently open, System 7 prompts you to save or
discard the data.

Creating a New Template 2. Select the project folder. Project folders are marked in green.
• If you know the project’s location, navigate to the folder, click on it, and
click OK.
• If you do not know the project’s location, right-click on the parent folder
and select Project Search from the submenu. Enter a keyword. Click
OK. The project folder(s) that include that keyword are marked with a
red tag. To open one of the project folders, click on the folder and click
OK.
• The name of the active project appears in the System 7 title bar.
Creating a New Template

Follow the steps below to save the current project settings as a new template:
1. From the File menu, select Create Template from Project.
2. Use the default folder to save the new template.
Note: Only those templates stored in the NS7 Project Templates
directory will be visible when you create a new project. Default
location: C:\program files\Thermo Scientific\NS7\project
templates\
3. Enter the name of the new template.
4. Click Save.
The acquisition properties, periodic table settings including the history, and the
spectrum processing setup are saved in the template. The new template is
stored with a .tnp extension.
Resetting a Project
Resetting a project restores the template settings for that project.
To reset a project, open the Edit menu and select Reset Project.
Any changes to the settings are returned to the settings for the original template
file used for the project.
Note: If the template settings have changed during the time between when the project
was created and the time the project was reset, the project will be reset to the
original template’s current settings.
Importing Files From Another Project

To import a file into the current project:

1. Go to the mode that corresponds to the file type. Searching for a Project
2. From the File menu, select Open.
3. In the Open box, navigate to the project containing the file.
4. Click on the file.
5. Click Open.
The data are copied into the current project's temporary folder and inherit the
current project's settings.
When you close the project, System 7 will prompt to save this file with the
current project. If you choose to save the file with the project, the file is moved
from the temporary folder to the main project folder.
Searching for a Project

You can search project folders to find key words associated with one or more
projects containing the key word.
1. Click the Project Explorer button (or from the File menu, select
Project Explorer).
2. Right-click on a folder. Projects at or below this folder will be searched.
3. Select Project Search.
4. Enter a key word. Click OK.
5. Folders containing the key word you searched are marked with a red tab.

Searching for a Project

CHAPTER
3
Spectrum Mode
This chapter discusses the System 7 Spectrum mode and its associated
components. An in-depth look at the tools for setup, acquisition, qualitative
analysis, quantitative analysis, and energy calibration is included. These tools
are common for any analysis mode that includes a spectrum, such as Point-
and-Shoot and Spectral Imaging. Before discussing the Spectrum mode, there
are some general concepts to consider before performing any microanalysis.
Pre-analysis Considerations
Sample preparation, microscope operating conditions, and detector geometry
all have an effect on the accuracy of EDS analyses. This section provides
general guidelines to consider before performing an analysis.
Sample preparation
The first step with any analysis is sample preparation. It is highly recommended
that samples are flat, well polished, and electrically conductive. If the sample is
not flat and polished, be aware that some topography may affect the line of
sight to the detector. A conductive coating should be applied to samples that
are not electrically conductive, or use variable pressure if you have this type of
SEM. When you apply a conductive coating you are putting an element into the
spectrum, such as carbon or gold, that may not be present in the sample.
Elements of the coating material must be noted and accounted for if a quanti-
tative analysis is to be performed.The thinnest useful coating of carbon is best
for the majority of samples. Be aware that coatings with high atomic number
materials will absorb x-rays of low atomic number elements within the sample.
Geometry and microscope considerations

The sample should be placed in the microscope at the optimal working distance
defined by the detector installation documentation. The working distance is
usually indicated on the microscope as WD or focus. Use the stage Z controls
to raise or lower the sample surface to the optimal working distance for your
detector.
The detector should be fully inserted prior to any acquisition. The insertion
position is determined and set during installation. The position of the detector
CHAPTER 3: SPECTRUM MODE 19

Selecting Spectrum affects the efficiency of x-ray collection. Certain conditions may preclude the full
Mode insertion of the detector. When this occurs there is a chance for stray x-rays
from areas not associated with the sample to be detected.
The microscope accelerating voltage determines the energy range of x-rays that
are fluoresced and the rate of excitation from a sample. Estimate the highest
order of element lines of interest and set the accelerating voltage 1.5 to 2 times
higher (over voltage) than the energy of that line. For example, if you are trying
to analyze the Copper Kα line (8.047 keV), the minimum accelerating voltage to
use would be 13 kV. Microscope probe current, spot size, or aperture settings
should be used to optimize the rate of x-ray excitation to achieve a pulse
processor dead time percentage between 20 and 30. The chances of inducing
spectral artifacts will increase as dead time values increase. If you operate at
lower dead times you may need to acquire for a longer time period to get suffi-
cient x-ray counts for statistically good analyses.
Selecting Spectrum Mode

In the System 7 Navigation Pane, click on the Spectrum icon. System 7 will
display the Spectrum mode and all associated controls for EDS microanalysis.
Spectrum Mode Icon Spectrum Label Detector selection

button - with dual
detector option
Spectrum Display/
View Pane
Analysis Control Pane Information Pane
There are 3 main Window Panes associated with Spectrum Mode: Spectrum
Display Pane, Analysis Control Pane and the Information Pane.

Analysis control pane Selecting Spectrum Mode
The Analysis Control Pane has 5 or, with optional software, 6 tabs for
controlling spectrum analysis.
Tab Functions
Element Setup Displays identification results, allows selecting or
excluding elements for analysis, selecting elements
to view KLM markers.
Quant Results Displays results of quantification analysis .
Parameters displayed are selected from the main
menu Edit > Properties > Quant Results tab.
Analysis Setup Setting parameters for identification sensitivity, type
of matrix correction and quant fit methods.
Processing Allows toggle on/off auto ID, auto quant, auto
extract for Spectral Imaging and selection of
quantification for x-ray maps and linescans.
Compare Selection of spectra, synthesized spectrum, and
Information background for comparitive overlay views of a base
spectrum.
Analysis Automation Optional software package. Setup for multipoint
automatic analyses
Information pane
The Information Pane has 6 tabs which present information about the displayed
spectrum.
Tab Functions
Attributes Displays acquisition information about the acquired
spectrum. Details button provides additional
information. These attributes are stored with the
spectrum.
Notes Allows adding additional notes and information
about the displayed spectrum. These are stored
with the spectrum.
Detector Status Displays information about the detector.
Standards Available when using quant with standards.
Displays information about the standards used in
the project.
Match Results Displays results from Spectral Match.
Region Tool Displays mathematical results from regions of
interest in a spectrum.

General Spectral General Spectral Acquisition Procedures
Acquisition Procedures
This section provides a short list of step by step procedures for a spectral acqui-
sition, element identification and quantification.
1. Prepare sample, set up the microscope at the EDS detector optimal
working distance and obtain a good electron image of an area of interest
on the sample.
2. Fully insert the detector.
3. Start System 7.
4. Project Explorer will open. Select, or create, a project. Close Project
Explorer
5. Click Spectrum mode icon in the navigation pane.
6. Click on the Microscope Parameters button and enter the
Accelerating Voltage and Magnification from the microscope in the
appropriate edit boxes (if you have Column Automation, these values will
be automatically updated).
7. Set up acquisition:
• Click the Acquisition Properties button. On the EDS tab, select 100
(seconds) from the pull down list in the Live Time Limit section in the
Termination Criteria group. Leave other termination settings at defaults.
• In the Energy Range group, select Auto in the Low Energy Cutoff edit
box, and Auto in the Max keV edit box.
• In the Pulse Processor group, select Auto in the Time Constant edit box.
• Click OK to save these acquisition parameters and close the Acquisition
Properties window.
8. Adjust the beam current, (spot size or condensor) on the microscope to
obtain a detect rate of 2,000 - 2,500 counts, or a dead time of between
25% - 30%. For UltraDry detectors, the count rate will be higher (on bottom
right pane, click on Detector Status tab to observe dead time, stores,
etc.).
9. Enter a name for the spectrum in the Base Name edit box. This is also the
spectrum label and file name. The default name is “Base.”
10.Click the Go button to begin spectrum acquisition. You can stop an

acquisition by clicking on the stop button. The data are saved.
• To pause the acquisition, click the Pause button
• Click the Abort button to stop the acquisition. The data will not be
saved.
11.Acquire until Time Limit termination. The green rate bar in the Status Bar
at the bottom of the System 7 window indicates the time remaining for an

acquisition. After ending, the Go button will return to active status (turns Spectral Acquisition Setup
black).
12.Click on the Identification button to identify elements. If Auto ID is

active, element identification will be processed automatically.
13.To quantify the identified elements, click the Quantification button.

Quant results are displayed in the Quant Results tab in the Analysis
Controls pane (bottom left pane).
Spectral Acquisition Setup

This section discusses the tools associated with the System 7 spectral acqui-
sition. These tools are common to all analyses which involve spectra.
Setting acquisition parameters

To access the Acquisition Properties dialog window, click the Acquisition
Properties button or open through the menu Edit > Acquisition Properties.
This dialog box is common to all acquisition parameters and is in tabbed format.
The tabs allow selection of the mode for the parameters you want to set. The
tabs are: EDS, Imaging, Spectral Imaging, Linescan and, optionally, Drift
Compensation. For spectral acquisitions, the EDS tab is used.
Acquisition Properties - EDS tab Acquisition Properties - EDS tab

Single Detector Dual Detector Option

Spectral Acquisition On the EDS tab window, edit the properties as desired. Click the OK button to
Setup save the parameters and close the dialog window.
Field Description
Termination Criteria
Live Time Limit The duration of the acquisition in live time seconds. A
general rule for spectral acquisition is 100 seconds of
live time collection at 25-30% dead time using the 50
usec time constant.
Max Peak Terminates the acquisition when the vertical full-scale

Counts of any channel in the spectrum reaches this value.
Element Enter atomic symbol for an element to define the

energy region.
Line Select the x-ray line for the element of interest to define
the region of interest.
Max Counts Terminates the acquisition when the integral counts in

the selected region of interest reaches this value.
User Defined Allows the user to redefine the low and high eV values
for the region of interest. Max Counts terminates the
acquisition. If all termination limits are set, the first
reached limit will terminate the acquisition.
Energy Range
Low energy X-ray counts below this energy are ignored during an
cutoff EDS acquisition. This cutoff eliminates the “noise” peak
in the low energy region. Auto adjusts the energy value
according to the Pulse Processor Time Constant. Each
time constant has a unique noise level.
Max keV X-rays of energy up to this limit are included in the EDS
acquisition. Typically, 20 keV will include an x-ray line
from all elements using a scanning electron
microscope. For TEM, 40 keV is appropriate. Auto
changes the energy limit according to the microscope
kV.
Pulse Processor
Time Constant Select a time constant. Rate 8 has the worst resolution;
Rate 2 or 3 has the best resolution. Rate 3 or 4 is a
general, all-purpose time constant. Auto adjusts the
time constant to keep the dead time between 30% and
50%. Depends on the beam current and accelerating
voltage.

Field Description Acquisition Setup
Considerations
WDS
Check box Acquire WDS elements simultaneously for comparative

quantitative analysis. This is only available on systems
with MagnaRay WDS installed with System 7.
Beam Current Measurement
Check box Measure beam current before acquisition. Must have

optional software and hardware.
Acquisition Setup Considerations

Termination criteria
Essentially, there are two criteria for terminating an acquisition: by time or by
counts. Termination by counts can be by three methods: 1) maximum peak
counts. That is, if any channel in a spectrum reaches the specified number of
counts, the acquisition is terminated; 2) region of interest by element line; or, 3)
region of interest defined by the user. In the region of interest selection, if the
total number of counts within that region reaches the specified number, the
acquisition is terminated.
If values, other than 0 or blank, are entered in the termination section, the first
reached criterion will terminate the acquisition (zero equates to infinite).
Generally, spectral acquisitions are terminated by time. The length of time

should be sufficient to acquire a statistically valid spectrum. That is, there
should be sufficient counts in a peak to achieve a counting error of less than
1%. As a rule of thumb, a peak with 5,000 counts in the center channel (full-
scale) will have about 1% error. The length of acquisition time depends on the
number of stores per second. Stores rate is dependent on beam current and
the pulse processor time constant. Using a time constant of 50000 nsec and a
beam current to achieve between 25-30 % dead time, the count rate will be
about 2,000 stores per sec. At this store rate, an acquisition time of 100 sec will
yield a spectrum with about 4500 full-scale counts. Thus, using the 50000 nsec
time constant, beam current to obtain 25% dead time, and counting for 120 sec
will yield a good spectrum.

Acquisition Setup Energy range
Considerations Within the Energy Range group there are 2 selections - Low Energy Cutoff (ev)
and Max keV.
The Low Energy cutoff clips the energy display range from 0 eV to the value
entered in the edit box (clips off the noise peak). The Auto selection will adjust
the cutoff value depending on the estimated noise at a given pulse processor
time constant. Generally a value of 100 to 120 will eliminate the noise peak at
the low energy range for most time constants.
The Max keV energy range selection determines the number of channels allo-
cated in memory (each channel represents 10 eV). For example, if a maximum
keV range of 10 keV is selected, 1024 channels of memory will be allocated. At
this range any peak greater than 10.240 keV will not be saved nor displayed.
Generally, the accelerating voltage in an SEM is limited to 30 KV. At this voltage

the highest energy x-ray line that can be fluoresced and displayed would be Mo
Kα line at about 17.4 keV. Thus, on an SEM, the maximum keV range would be
20 keV; whereas, on a TEM at 200 KV, 80 keV range would be appropriate.
In selecting the maximum range, the pull down menu gives the following
choices: Auto, 5, 10, 20, 40, and 80 keV. The Auto selection will automatically
adjust the maximum range to the accelerating voltage of the microscope. If the
accelerating voltage is not entered correctly, the range may be incorrect. Fixing
the maximum range to 20 keV for an SEM will provide consistent spectra for
comparison.
Pulse processor
The pulse processor time constant is the time allowed for the pulse processor to
estimate the energy of an x-ray. The longer the time, the better the estimate of
the energy. The better the estimate, the higher the resolution of the peak.
However, the longer the time constant, the higher the dead time for a given
count rate. For high resolution spectra (long time constant), this translates into a
lower count rate and a longer time to acquire a statistically valid spectrum.
For high resolution (extreme) detectors, there are 10 fixed time constants plus
the Auto selection. Non-extreme detectors have 9 fixed time contants plus the
Auto choice. All fixed rates have estimated through-puts (counts per second).
When selecting a time constant, consideration must be given to the resolution of

the spectrum and the length of time it takes to acquire the spectrum. Generally,

select the longest time constant and acquire at a lower count rate to obtain a Microscope Properties
high resolution spectrum. For general samples, a faster time constant (Rate3-
35000 nsec) can be used to increase throughput which shortens acquisition
times but will still yield a good spectrum. For UltraDry detectors, a time constant
of Rate5 will yield good spectra.
Care should be taken when using the Auto selection. System 7 will adjust the
time constant to achieve between 30% and 50% dead time. At high beam
currents, the time constant will be shorter and spectral resolution will degrade.
Microscope Properties
For any analysis, the accelerating voltage of the microscope must be known by
System 7. Various parameters, including the accelerating voltage, are entered
in the Microscope Properties window. To open the Microscope Properties and
Status Bar Selection dialog box, click on the Microscope Properties
button, or from the main menu Edit > Microscope Properties. Enter the accel-
erating voltage in the edit box. This dialog box also allows for displaying various
parameters on the status bar. If optional Column Automation software is
purchased, these parameters are updated automatically.
The Microscope Parameters can be automatically displayed at the start of an

acquisition by checking the check box “Display On Acquisition Start.”
In any analysis mode, the status of various paramaters can be monitored on the
Status Bar. Those parameters you wish to display on the Status Bar are
selected in the Microscope Properties and Status Bar Selection dialog box.The

selected parameters are displayed on the Status Bar at the bottom of the
System 7 window.
Note: To toggle the Status Bar off or on, use menu View > Status Bar
Magnification Dead Time Time Constant
Accelerating Working Distance Stores Rate

Voltage
Detector Status
In Spectrum mode, the bottom right pane (Information Pane) provides infor-
mation about the acquired spectrum, allows additional information about the
acquired spectrum to be noted, status of the detector, and, if using analysis with
standards, provides information about the standards in use. The Detector
Status tab provides information about the condition of the detector and events
occurring with an acquisition.

The information displayed by the Detector Status tab is divided into two groups, Detector Status
PHA (Pulse Height Analyzer) and Current Times. In addition, a histogram of the
noise level (Zero) may be displayed and special applications software may be
launched through the Advanced Status Button. The chart below describes the
information displayed.
Group Description
PHA
Detects The number of x-rays entering the crystal per

second
Converts Number of x-rays converted to pulses per

second.
Stores Number of x-rays that are converted, pass

through the discrimminators and are entered into
the spectrum per second.
Time Constant The current pulse processor time constant.
Zero FWHM The full width half max measure of the zero peak
(the noise peak). Zero FWHM indicates the level
of random noise in the system. Small FWHM
indicates a “quiet” detector system. This gives
some indication of the system resolution.
Current Times
Dead Time The current dead time.
Live Time Displays the accumulating Live Time for the

current acquisition.
Remaining Time Shows the remaining Live Time for the current
acquisition. With no acquisition, displays the
duration of acquisition set in Acquisition
Properties: Live Time Limit.
Show Zero Histogram Displays a histogram of the noise peak. There is

(Check box) always a noise peak present, even when no
acquisiton is running.
Advanced Status Launches the FrontEnd Status applications

(Button) software.

Adjusting Spectral Displaying the zero histogram also displays the Vertical Full-Scale (VFS) of the
Display zero peak. Along with Zero FWHM, VFS provides indications of the overall
system performance.
Adjusting Spectral Display

Changing the appearance of spectral display
Following a spectrum acquisition, the appearance of a spectrum, such as back-
ground color, can be changed to suit various needs.
1. Move mouse pointer into the spectrum display and right click (brings up
Spectrum Properties window) or Main Menu > Edit > Properties, Spectrum
tab.
2. Click on the check boxes to select the desired display from the Spectrum
tab.
3. To change color of the background, cursor or spectrum, click on the
corresponding colored button and select a color from the color pallet.
4. Click the Apply button to make changes immediately.
5. Click OK to close the window.
Spectrum
Properties
Spectrum Tab
Click on colored
boxes to change
colors

Sizing the spectrum Adjusting Spectral Display
You can change the size and range of the spectrum using the mouse, toolbar,
or the number keypad.
Spectrum Toolbar Full View Expand Scroll Right Scroll Log y-scale
Down
Use these buttons to adjust the
spectrum range
Most of these functions conincide with
mouse and keypad functions
Scroll Left Compress Scroll Up Full Verticle Scale
Function Keypad method

Full Spectrum Home (7)
Scroll left Num lock + Left arrow (4)
Scroll right Num lock + Right arrow (6)
Expand Page Up
Compress Page Down
Full vertical spectrum End (1)
Increase vertical scale Num lock + up arrow (8)
Decrease vertical scale Num lock + down arrow (2)
Expanding the spectrum

From near the low energy range, click on the spectrum, hold tthe left mouse
button down and drag right to expand the spectrum.
Place the energy cursor near the energy range of interest and click the Expand
Spectrum button on the Analysis Toolbar. The spectrum will expand and
keep the cursor near the center of view.
Compressing the spectrum

To reduce the magnification of the spectrum and show a greater energy range,
click the Compress Spectrum button on the Spectrum Toolbar, or with the
mouse pointer in the spectrum, double click the left mouse button
Scrolling the spectrum

After the spectrum is expanded, drag left or right to scroll through the spectrum
horizontally, or up and down to scroll vertically.

Adjusting Spectral Or click the Scroll Left/Scroll Right or Scroll Up/Scroll Down buttons on the
Display Spectrum Toolbar.
Zooming in on a peak
To zoom in on a portion of the spectrum, hold down the Ctrl or Shift key and
drag the mouse pointer across the peak.
Applying a log scale

Click the Log button to toggle the spectrum between a logarithmic and
linear vertical scale for the intensity values.
Restoring the full spectrum view

Use one of the following methods to restore the spectrum to full view:
• Click the Full Spectrum button on the Spectrum Toolbar.
• Double-click the mouse on the Spectrum View.
• Press Home on the keypad.

Adjusting Spectral Display
Magnified portion of the spectrum

To return the X and Y axes to their
original scales, click the Full
Spectrum button.
Spectrum restored to its full range
Managing spectral files

After you acquire a spectrum—either from an acquisition or from a Spectral
Imaging extraction—you can change the label of the spectrum, add notepad
text, or read and edit the attributes of that spectrum. Elements can be identified
and labeled automatically or manually.
Changing File Name/Label of a spectrum

The default name and label of a spectrum is the Base File Name entered in the
Base name edit box (left hand, lower pane) and is automatically applied to an
acquired spectrum. Subsequent spectra will have the same base name
appended with the acquisition number until the Base File Name is changed. To
change the file name and the label of an acquired spectrum, double left click on
the spectrum label at the top of the spectrum in Spectrum view to bring up an
edit window. Enter a new file name and click OK. The spectrum file name will
be changed and the label will be updated to reflect that new name. If the name
is left blank, or If the new name is the same as an existing file, an error
message will be displayed.

Adjusting Spectral
Display
Changes File name
Changing spectrum label only

The best way to change just the label is through the Attributes dialog window.
Click on the Attributes tab and click Details button to open the attributes dialog
window.You can change the name in the Label edit box and when you close the
window, the label will be updated on the spectrum but the file name will not be
changed. To remove the label, use the details button to delete the label. This
method should be used when you want to print a spectrum without a label.
When you reopen the spectrum, the label will revert to the original file name.
Edit Label Box
Attributes tab - Details button
Adding note text

To add additional notes regarding the spectrum, click the Notes tab in the infor-
mation pane. Enter the text in the notepad area. Notepad text is saved with the
spectrum. To save notes with an prior spectrum use Main Menu: File: Save to
save immediately.

Opening spectral files Adjusting Spectral Display
Files opened in Spectrum Mode are handled as standard spectral files. These
files can be those acquired with System 7 or spectral files from a third-party
EDS system in EMSA file format.
To open a file within a project:
1. Open the project and go to Spectrum Mode.
2. Click on the spectral file in the File List view.
To open a file outside the current project in Spectrum Mode:
2. In the Open box, navigate to the folder (Project) containing the file.
4. Click Open.
The file is imported into the project’s temporary directory. When you close
the project, System 7 asks if you want to save the file to the project folder
or discard it. The temporary directory is only emptied when you close the
project.
Saving a spectrum
Acquired spectra in Spectrum Mode are stored automatically in the temporary
folder (associated with the open project) with the .emsa file extension. The user
will be prompted when a project is closed, or a new project is opened, if the new
files should be saved.
To manually save a spectrum:

1. Display the desired spectrum
2. From the File menu, select Save.
3. The file will be moved from the temporary fold to the project folder. The file
name will be the same as the original name. To change the name before
saving, use the Changing File Name/Label procedure as described
above.

Qualitative Analysis Qualitative Analysis
Qualitative analysis is the identification of elements which make up a specimen
by recognizing the characteristic x-ray energy peaks associated with those
elements in an x-ray spectrum. Qualitative analyses may be performed
manually or automatically. There are a number of tools in System 7 which aid
identification of elements in a sample. This section provides an overview of the
two methods, guidelines to perform an accurate analysis, and general quali-
tative analysis procedures.
Automatic qualitative analysis can be defined by allowing the application

software to identify the spectral peaks found in a spectrum. The Identify Peaks
Automatically program uses peak shape and location of the peaks for identifi-
cation. Manual inspection of the automatic results is always recommended,
especially to incorporate any prior knowledge of the sample and resolve uncer-
tainties due to overlapped peaks. The manual peak identification software tools
allow the operator to identify the spectral peaks using KLM markers that locate
the lines for each element. The manual peak identification software is explained
in detail later in this section.
To perform an accurate qualitative analysis you should have a basic working

knowledge of events in the atom and how to use that theory to interpret the
information in the spectrum. The following points can be used as a guideline to
assist in performing a more accurate qualitative analysis:
• Acquire spectral data long enough to achieve sufficient counts for a
good statistical analysis. General rule is at least 100 seconds at 25 to 30
percent dead time at the longest time constant.
• Verify calibration of the peak centroid.
• Use caution when identifying rare elements. Scandium or Promethium
for example.
• Use caution when identifying less likely elements such as Bromine or
Tantalum.
• Be aware that spectral artifacts may be present in the spectrum due to
operating conditions.
• Be aware that some peak energies are shared by more than one
element. That fact, and the inherent resolving power of the EDS
detector, will result in the overlap of energy peaks in the spectrum.
Specifying identification sensitivity

1. In Spectrum mode, click on the Analysis Setup Tab (Analysis Controls
Pane).

2. In the Ident Sensitivity edit box, enter a number between 1 and 100. The Qualitative Analysis
lower the number, the higher the sensitivity.
This value determines how large a peak must be before it is detected. The
larger the value, the larger a peak must be to be detected by the peak
identification algorithm. A larger value reduces the number of element
labels on the spectrum. The default value is 5, which produces good
results.
Analysis Setup tab
Set Identify sensitivity for Auto ID
Other parameters are used for

Quantification
Setting automatic spectral processing

The spectral Processing parameters define how the spectrum is handled after it
is acquired.
1. Click the Processing tab in the Analysis Controls pane to select the
automatic processing parameters.
2. In the Spectrum Processing group toggle off/on to have Sum Peaks and/
or Escape Peaks removed automatically.
3. In the Spectrum Results group, click on the desired icon to toggle on/off to
automatically process spectra.
Note: If no Auto processing parameters are active, you must click the buttons in the
Analysis Toolbar or use the menu items to process the spectrum.

Qualitative Analysis Auto ID
If Auto ID is active, System 7 identifies spectral peaks during an acquisition with
a final ID at the end of the acquisition
Auto Quant
When Auto Quant is active, System 7 calculates the quant information and
displays it in the Quant Results tab. If Auto Quant is active, Auto ID must be
active.
Auto Match (Optional Software)

If Auto Match is toggled on, System 7 will perform an automatic spectral match
after acquisition or when the autoID button is clicked. Results will be displayed
in the Match Results tab in the Information Pane.
Automatic group settings

These settings are used with Spectral Imaging and X-ray LineScan and will be
discussed under their respective sections.
Note: The spectrum’s peak markers and appearance are specified in the Spectrum
Properties dialog box.
Processing tab
Here you can specify whether or not

identification and analysis to automati-
cally take place after the spectrum is
acquired.

Identifying elements automatically Qualitative Analysis
1. Click the Identify button in the Analysis Toolbar.
System 7 scans for all elements on the periodic table except for those
marked as Excluded.
Manual element selection - Element Setup tab

The Element Setup tab in the Analysis Controls pane allows selection of
elements for identification and also those elements used for quantification.
Following a peak identification, System 7 creates a list of possible elements in
the Element Setup periodic table. You can refine these results to search for or
identify specific elements or exclude other elements.
Note: The Element Setup periodic table does not change when you switch analysis
modes. This enables you to analyze a spectrum in one mode, then switch to
another mode and use the same identification results.
Edits to the Element Setup periodic table are stored in the project template.
Element Setup periodic table

The identification results are
displayed in this table. You also can
manually specify which elements to
identify and which to exclude.
SpectraCheck Chi-Squared value.
Excluding elements from analysis

To exclude an element from any analysis:
1. In the Element Setup periodic table, right-click on the element you want
excluded.

Qualitative Analysis 2. Select Excluded. The element symbol appears lined dark gray.
3. You can also left click and toggle through the choices.
By default H, He, Li, the Nobel gases, the Lanthanide and Actinide elements are
excluded. The L, A, and n boxes toggle between exclude/inactive elements
within the respective groups. When you click on one of the L, A, or n buttons in
the periodic table, the elements in that group are toggled according to these
rules:
• If an element was excluded before, it changes to Inactive.
• If an element was anything other than excluded, it becomes excluded.
Clearing identification results

The Clear button has two different functions.
• To clear the identification results from the spectrum currently displayed,
make sure the History button is NOT checked, and click Clear.
• To clear all identification results from every file in the project and the current
spectrum, check the History box then click Clear.
Viewing Identification History

The History displays the identification results from every spectrum within the
project. Check the History box to view the cumulative identification results for
the open project.
Identifying elements manually

To specify an element's status, right-click on the element and select the status
from the submenu. You may also left-click on the element repeatedly until it is
the corresponding color of the status you want to apply.
Label Color Meaning

Inactive light gray The element was not identified.
(default)
Identified bright green The element was identified in the sample.
Excluded lined dark User-selected option; the element is not
gray included in any identification.
Always lined User-selected option; select this option
Identified magenta before analysis to pre-determine the
presence of a particular element.
Selected red outline The selected element.

Label Color Meaning Qualitative Analysis
Possible orange The element could be in the sample but
was not confirmed during auto peak ID.
Near cyan outline These elements have KLM lines close to
the spectrum’s energy cursor; changes as
the user moves the cursor.
Identifying possible elements

System 7 displays lines that locate each peak in the spectrum when KLM
markers are hidden. The automatic peak identification function labels each
peak that System 7 identifies. Use these markers as a starting point for manual
peak identification. The Spectrum ID Toolbar contains the tools for peak labels
and KLM lines.
System 7 provides several aids in locating an element at a peak including peak
ID lines, KLM markers and automatic labels.
To view a list of possible elements, place the energy cursor on the peak. Those
elements with a K, L or M energy level near the energy cursor position are high-
lighted in cyan in the Element Setup periodic table. You can change any of
them to Identified if they match the element you are seeking.
Some knowledge of the sample and other element peaks is useful in deter-
mining which elements should be identified manually.
Viewing KLM markers

There are two ways to view the KLM markers.
The first is on the Spectrum ID Toolbar:
• Click the KLM Lines button . The KLM lines appear on the spectrum for
the selected element (you must select an element). From here you can
click other elements or scroll through the periodic table using the arrow
keys.
The second is in the Spectrum Properties box and allows for more customi-
zation:
1. Right-click in the spectrum view pane.
2. In the Spectrum Properties box, click the KLM Page tab.
3. Check the Show KLMs box. Here you can adjust the types and range of
lines you want displayed. Click OK to close the window.
4. In the Element Setup periodic table, click on the element. The KLM
markers appear in the spectrum.

Qualitative Analysis Adjusting the number of KLM lines displayed
To adjust the number of KLM marker lines appearing on the spectrum, go to the
spectrum properties box.
1. Right-click on the Spectrum view, or use menu Edit > Properties.
2. In the Spectrum Properties window click on the KLM Page tab.
3. In the Include Shells edit box pull down, select the number of shells to
display. Best choice is All
4. In the Include Order edit box pull down, select the number of orders to
display. Best choice is All
5. To adjust the number of lines appearing, change the number in the
Intensity Above box. Best choice is All.
KLM Page Tab
The bottom left corner of the Spectral Display Pane shows the symbol of current
element that has its KLM markers displayed.
Scrolling KLM markers with keyboard arrow keys

KLM markers are scrollable from the arrow keys on your keyboard.
The Next Element and Previous Element buttons scroll KLM markers by atomic
number. You can also use the Left and Right arrow keys.
The Element Search Up and Element Search Down buttons use the energy
reading at the energy cursor to search System 7’s database of element lines
and displays candidate KLM markers for each element found. You can also use
the up arrow key and down arrow key.

A low-toned beep signals that you have reached the end or the beginning of the Qualitative Analysis
possible elements.
Searching for KLM lines on the spectrum

You can place the energy cursor on the spectrum and then search for elements
that have KLM lines higher or lower than that point on the spectrum.
To search for KLM lines:
1. Click on the spectrum to place the energy cursor at a point of interest.
2. Click an Element Search button, either up or down.
A high pitched beep means System 7 found another element near the cursor.
The element is outlined in red or red dashes in the periodic table and its KLM
lines are shown on the spectrum. The elements with KLM lines near the cursor
are outlined in the periodic table in cyan.
A low pitched buzz means you have reached the end of the periodic table from
that cursor point.
KLM lines displayed for

Tungsten
Press the KLM markers
button to turn on the KLM
markers.
The atomic symbol for the
element with its KLM lines
displayed appears in the
lower left corner of the
Spectral View.
Scroll KLM Search KLM Markers

Markers Down Elements Lower ON/Off
Energy Cursor
On/Off
Scroll KLM Search Element label

Markers Up Elements Higher
Add and Delete
Use the Left/Right arrow keys or the Scroll
KLM markers buttons to scroll by atomic
number.
Use the Up/Down arrow keys or the Search
Elements buttons to scroll by peak elements

Qualitative Analysis Labeling peaks
After you have manually identified a peak, you might want to label it on the
spectrum for reference and reports. All peak labeling commands are found in
the Spectrum Properties dialog window. The menu contains commands for
deleting and adding labels to peaks at the current mouse pointer position.
Spectrum Properties Peak Page
Right-click on the Spectrum View

and click the Peak Page Tab
Here you can select the peak label

format, color and font
Managing peak label appearance

To manage peak labels, right-click on the Spectrum View to access the
Spectrum Properties window. Click the Peak Page tab.
You can choose to show short peak labels (element symbol only) or long peak
labels (element symbol and KLM lines). You can also change the font and color
of peak labels.
Note: Selecting None for Peak ID Labels turns off all Peak ID labeling. If you try to
label an individual peak it will not appear on the spectrum.
To change the font or color of the labels, click the label graphic appearing at
Peak Label Font. Other spectrum appearance controls (such as the spectrum
background) are found on the Spectrum tab.
You can also specify whether you want peak labels to appear during or after the
acquisition. Auto ID on the Spectral Processing tab in the Analysis pane must
be active for the Label Peaks function to apply.
Deleting peak labels

To delete all the peak labels for one element, right-click on the element in the
periodic table and select Inactive from the submenu. That element’s labels are
removed from the spectrum. To delete a single peak label, click on the peak
label so it is outlined. Press the Delete key on the keyboard or click the remove

label button in the Elements buttonbar. The element label at that peak is Using SpectraCheck After
removed. Identification
Adding peak labels

You can label elements for reference and reports. You can label all of the
element’s peaks or just a single peak.
To label an individual peak, select the element from the Element Setup (labels
all peaks), then delete individual peak labels as described above.
To label all peaks for a particular element, right-click on the element in the
periodic table and select Identified.
X-ray line overlaps

To view possible overlaps for an element, left click on the desired element label
and double left click to bring up a pull-down list box. Click on the down arrow to
view a list of possible elements which overlap.
Labeling a peak
Labeling all peaks for one element
Right-click on the element in the Element Setup
periodic table and select Identified.
Double left click on the element label to bring up

an element pull-down box. Click on the down
arrow to view list of possible elements.
Using SpectraCheck After Identification

After identifying all the peaks in a spectrum, an additional aid in conformation of
correct identification is SpectraCheck. SpectraCheck is toggled between
active and inactive on the Compare Information tab in the Analysis Controls
pane. The synthetic spectrum in the compare information: spectrum pane must
be checked and Overlay checked for the Chi-squared function to be active.
With SpectraCheck active, a theoretical model of a spectrum is generated and
compaired to the base spectrum. A Chi-squared statistic is then run on the
synthetic spectrum and the acquired spectrum. The resultant Chi- squared
value is displayed in the Analysis Pane, Element Setup tab. Generally, a value
of less than 10 indicates a reasonable fit. The closer the Chi-squared value is to
zero, the better the fit.

To activate
SpectraCheck, toggle
SpectrCheck to
active. Check box on
synthetic spectrum,
check button overlap
on
SpectraCheck toggle
active/inactive
Comparing Spectra
You can compare two or more spectra in the Spectrum Mode.
1. Open a project and go to Spectrum Mode.
2. Load a spectrum. This is the base spectrum.
3. Click the Compare Information tab in the bottom left pane.
4. In the Spectrum section, check one or more spectra to compare against
the base spectrum. With Spectra Check active you can also select a
synthetic, background, or residual spectrum:
• Synthetic – Based on the elements identified in the periodic table, System 7
calculates how the spectrum should appear and generates this synthetic
spectrum.
• Background – The synthetic background spectrum.
• Residual – The peaks of the elements defined in the periodic table used for
generating the synthetic spectrum are removed from the spectrum to create
a residual spectrum. This spectrum shows what peaks were not accounted
for in the original spectrum.
Note: A theoretical model of the background shape and spectrum can be created if
the approximate mass of the sample, the energy of the excitation electrons, the
geometry of the system, and detector characteristics are known. Generation

and comparison of synthetic models will provide visual evidence of the
accuracy of the identified elements list and possible suitability of the sample for
quantification.
5. In the Method section, select Overlap.

6. Normalize options adjust the selected spectra to the factor you select; the
normalize options do not affect the base spectrum.
Normalize options are:
• None — No normalization is applied.
• Livetime — Uses the livetime of the overlapped spectrum with respect
to the livetime of the base spectrum to create a multiplier that
normalizes the spectral data of the overlapped spectrum. This simulates
the same amount of acquisition time for the overlapped spectrum as the
base spectrum.
• Element — Adjusts the overlapped spectra to the height of the base
spectrum, based on the element peak selected. The peak or line
chosen is based on accelerating voltage and the energy range of the
spectrum.
• Multiplier — Value used to scale all overlapped spectra.
• Range — Allows you to select an energy range to create multipliers with
respect to the same region in the overlapped spectrum and the base
spectrum. The overlapped spectrum is scaled by the multiplier value
relative to the base spectra. When you select Range, two range cursors
appear in the Spectral View, appearing as dashed vertical lines. Move
each cursor to create the region.
Steel spectrum with Braze

overlaid
Range normalize cursors

Quantitative Analysis Quantitative Analysis
Quantitative analysis determines the chemical composition of a sample. The
quantitative analysis software calculates the relative concentrations of chemical
elements in the sample from the relative x-ray counts and applying matrix
corrections. The matrix correction adjusts for atomic number, absorption, and
secondary fluorescence effects.
This section will provide guidelines to perform an accurate analysis, and a
general quantitative analysis procedure.
Overview of the quantitative process

1. After acquiring a spectrum, perform an element identification. Verify that
the element list is accurate.
2. The process is initiated by clicking on the Quant button.
3. The bacground is removed by either a “top hat filter” or gaussian model.
4. The net x-ray counts in each peak is determined.
5. A matrix is constructed of simultaneous equations with the element
concentration as unknowns.
6. The matrix correction is calculated through iteration.
7. Element concentrations are calculated by multiplying a theoretical K-ratio
by the matrix correction.
8. The data are normalized to 100% and the results are reported.
Specifying element lines to use

System 7 identifies which lines are used for quantitative analysis based on the
element and the accelerating voltage. If you choose to use a different line, click
on the Lines Utilized drop-down boxes in the Element Setup periodic table and
select from the list of possible lines. Some elements might only have one
selection. Usually the dominant line is used for quant. However, if a line is too
close to the accelerating voltage, the Quant lines selection will use a line lower
in energy for quant data.
To exclude an element from quantitative results when it is identified as present
in the sample (i.e., elements used for coatings), select that element, and select-
Absent in the Lines Utilized, Quant box in the Element Setup tab.
Note: These changes are permanent and applied to future analyses in the current
project until the History is cleared.

Quantitative Analysis
Overvoltage
On the Analysis Setup tab, select the Overvoltage amount. Typically, the accel-
erating voltage should be 1.5 to 2 time greater than the highest x-ray energy
line. This value is used by System 7 to select a dominent x-ray line.
Selecting quant fit method

On the Analysis Setup tab, select the Quant Fit method.
• Filter Fit (default) applies a digital top hat filter to remove the background.
Select either With or Without Standards.
• Gaussian Fit uses Gaussian functions to calculate and subtract a theoreti-
cal background. Select either With or Without Standards.
If either fit method is selected “With Standards” the Standards tab must be used
to specify which standard spectra are to be referenced. See below for adding
standards.
Note: Usually rinning a quantitative analysis without standards is sufficient to meet

the needs of most analyses.

Quantitative Analysis Selecting a matrix correction
On the Analysis Setup tab, if you use matrix correction, you can select a calcu-
lation method.
• Proza adjusts the theoretical reference spectrum for average atomic num-
ber (Z), absorption (A), and fluorescence (F) factors. These factors influ-
ence spectrum differences between elements in pure form and elements in

composition. Used in SEM applications, especially for light elements in a
heavy matrix.
• ZAF adjusts the theoretical reference spectrum for average atomic number
(Z), absorption (A), and fluorescence (F). These factors influence spectrum
differences between elements in pure form and elements in composition.
Used in metallurgical SEM applications.
• Cliff-Lorimer (MBTS) without absorption provides metallurgical and biologi-
cal thin section corrections based on relative elemental K factors (cliff-
Lorimer factors). Correction assumes there is no absorption. Used in TEM/
STEM applications.
• Cliff-Lorimer (MBTS) with absorption is the same as MBTS but corrects for
absorption in thicker samples.

Typical quantitative analysis routine Quantitative Analysis
1. Acquire a spectrum for a sufficient amount of time to allow for a good
statistical analysis.
A general rule is 100 seconds of livetime at 25 to 30 percent deadtime.
2. Perform an identification to mark the correct elements for your sample in
the Element Setup periodic table.
Note: The results of the qualitative analysis will have a great impact on
the accuracy of the quantitative analysis.
If necessary, click the Identify button to run the automatic

identification program, or perform a manual peak identification and mark
the elements on the Element Setup periodic table.
3. On the Analysis Setup tab, select Quant fit method and matrix correction
best suited for your sample.
4. From the Edit menu, select Properties. In the Properties window, click the
Quant Results tab. Check the items you want to appear in the quantitative
analysis results. Click OK.
5. To run the analysis, click the Quantify button .
6. When System 7 completes the analysis, click the Quant Results tab in the
Analysis controls pane to view the results.
The lower the Chi-squared value, the better the fit. A perfect fit is 0; as a
general rule, a Chi-squared value under 10 is good.
Rerunning a quantitative analysis

1. Edit the Element Setup periodic table as desired and click the Quantify
button on the Analysis Toolbar.
The Quant Results tab display changes to reflect the new quantitative analysis.
Rerun an analysis any time you change the Element Setup periodic table, or
when you add or delete quant results parameters.
Cliff-Lorimer and ratioed elements (TEM)

If you use one of the Cliff-Lorimer matrix correction methods, the K-factor must
be automatically calculated, or entered manually.
1. Select the element you want to ratio in the Element Setup periodic table
and click the Advanced button.
2. Check the Is Ratio Element box. This normalizes the k-factor for that
element to 1.

Quantitative Analysis
Fixing a weight percentage

1. On the Element Setup periodic table, click the element for which you want
to define the weight and click the Advanced button.
2. Click the Fixed button and enter a weight percentage.
When a percentage is entered, the program will fix the element percentage
to this value and take that into account when calculating the quantitative
results for other elements.
If you select Calculated, System 7 calculates the percentage.
Adjusting for oxides, bromides, carbides and

nitrides
To specify a compound formula:
1. On the Element Setup periodic table, select the element and click the
Advanced button.
2. Click the Use Compound check box.
3. Select the correct compound from the list box.
Note: To specify compounds for all elements, click the Analysis Setup
tab and check the Use Compounds for All Elements box. If this
box is checked, System 7 uses compounds regardless of whether
or not you check the Use compound box on the Advanced dialog
box.

Specifying Quant output Specifying Quant output
There are a number of parameters that are calculated during the Quantification
routine. To select which parameters you want displayed with the quant results
use the Quant Results tab on the Properties window.
1. From the Main Menu: Edit: select Properties.
2. Select the Quant Results tab on the properties window.
3. Select the parameters you want displayed. These parameters are
displayed in the Quant Results tab in the Analysis Controls pane.
4. An s by the element indicates stoichiometry
5. Click OK to close window.
• Normalization, Total Weight%: The default is 100%. If you know the com-
position of the sample, you can type in a Total Wt% value. Generally, for
standardless analysis, normalize to 100% is the standard value.
• Output X-ray Lines: All will show the x-ray lines that are displayed in the
spectrum. For example, All will list the Ka and La for Cu in the quant results
tab. However, only the dominent line will be used for quant. In this example
the Cu Ka will have a quant value and the La will have no value. Matrix
Only will only display the x-ray line used for quantification. In the example

Specifying Quant output above, only the Cu Ka will be displayed in the Quant Results tab. Matrix
Only cuts down on the number of entries in the Quant Results tab and
makes for cleaner Quant Results display.
• Output Precision, Decimal Places: Because of the inherent error in EDS, 1
decimal place is warrented. However, you can use 2 or 3 if your protocols
require.
• Output Precision, Errors: The choices are 1, 2 or 3 Sigma. One sigma is

about 68% confidence, 2 Sigma is about 95% confidence and 3 Sigma is
about 99% confidence. For example, if the Wt% of an element is 10.0%
with a 2 Sigma error of +/- 1.0% then we are 95% confident that the true
wt% of the element lies somewhere between 9.0 and 11.0 Wt%.

Select all the parameters you want displayed by the check boxes next to the Quantification With
parameter. Click the Quant button to complete the analysis. The results are Standards
displayed on the Quant Results tab in the Analysis Controls pane.
Quantification With Standards

Generally, running a quantitative analysis without standards (standardless
analysis) is sufficiently accurate to meet the needs of most analyses. However,
you may prefer to use standards. In some instances, analyses with standards
can be more accurate since the standard and the sample are collected under
the same conditions. Before running a quantification with standards, you must
first create a standard and then enter into a standards database.
To use Quant with Standards, select a Quant Fit Method with standards on the
Analysis Setup tab (Analysis Controls pane). The tab labeled Standards (Infor-
mation pane) is used to enter the standards that will be used for the quant. You
can build a set of standards (standards library) and store them for later use, or
you can use the standards immediately. Be aware that you must know the
beam current (not specimen current) to use Quant with standards. The beam
current may vary between standard and sample acquisitions, but you must
know the beam current in both instances. You can create standards from pure
element or mixed element (multi-element) samples.
Creating standards
Before creating your standards, use the following guidelines to make the
standard as accurate as possible.
• Use a standard that is flat and well polished. If the standard is non-
conductive, coat with a thin (<5 nm) layer of Carbon - just enough to
keep from charging (or use variable pressure microscope).
• The standard should be well characterized with known weight percents.
A “traceable” (NIST) standard is preferable.
• Count for sufficient length of time to obtain minimually 10,000 integrated
counts. Ten thousand counts results in a 1 Sigma error of 1%.
• Use the longest fixed pulse processor time constant rather than Auto.
Adjust the beam current to get a dead time of about 25 - 30%.
• Collect the unknown sample under the same conditions as you
collected the standard. That is the same working distance (should be at
optimal working distance), detector fully inserted, and same beam
current. The exception is that the beam current can vary because
System 7 adjusts for beam intensity differences (the standards are
calculated in counts/second/nA of current).

Quantification With Use the following procedures to create a standards database:
Standards
Collect a spectrum of the standard

1. Place the standard in the microscope at optimal working distance. Obtain
a good electron image of an area on the sample. Use an accelerating
voltage that will be used on the unknown sample (remember overvoltage).
2. Start up System 7 and click on the Spectrum mode icon in the Navigation
pane.
3. Open the project in which you want to create the standards. The
standards database(s) can be stored in a project, or you can create the
standards libraries anywhere.
4. Setup the Acquisition Parameters. Use the longest fixed pulse processor
time constant (extreme or slow) to get the highest resolution.
5. Adjust the beam current to get about 25% dead time (this will be a low
count rate, long time acquisition for highest resolution with fewest spectral
artifacts).
6. Measure the beam current using a Faraday Cup, preferably on the sample
block, or an insertable Faraday Cup if the microscope is equiped with one.
7. Open the Microscope Parameters dialog box and enter the correct values
for Accelerating Voltage, Magnification, Beam Current, Working Distance
and EDS Slide Position.
8. Click on the Start button and acquire spectrum of the standard. Aim
for about 10,000 vertical full-scale counts.
9. In the Analysis Controls pane, select the Element Setup tab and select
(green with red outline) the element for which you want to create a
standard.
10.Click on the Standards tab in the Information pane.
11.Click on Add Standards button. This will display the Add Standards dialog
box.
12.Click on the New Standard button. This will display the New Standard
window.
13.The Element symbol and the Line used will be added from the Setup
Element periodic table. If the entries are incorrect, go to the Setup
Elements tab and change the Element and Quant Line entry.
14.Enter an identifying name in the Standard Name edit box.
15.Adjust the keV range by typing in the edit boxes, or adjusting the range
cursors in the spectrum view. The defaults work well.

16.Click OK when all parameters are added. For pure standards leave the Quantification With
Multi Element Standard box and the Standardless Reference box Standards

Quantification With
Standards
unchecked. This will close the New Standard window and put the new
standard into the Add Standards dialog window.
17.Add more standards to the Standards Database list if desired. You can
create a database with many standards, or just one standard.
18.For convenience, add all element standards you expect to find in the
unknown.
If your standard has more than one element (multi element standard) check the
Multi Element Standard box.
Select the Concentration Data Type from the pulldown menu. This will display a
multi element data section. Enter the known values for the data type. You will
need to do repeat these steps for each element in the standard, entering one at
a time.

Quantification With
Standards
To use a standard
To activate a standard, or standards, use the following procedures:
Creating a Database for use

1. On the Add Standards window (Standards tab; Add Standards button)
Highlight the standard to use and click on the Add Selected button in the
Add Standards dialog window. This will put the standard in the lower box
“Standards In Use.” To use all, click on Add All button. The standards will
be moved into the Standards in Use (lower) box.

Quantification With 2. Click OK to close the Add Standards window and move the selections into
Standards the Standards in Use box in the Standards tab.
3. On the Analysis Setup tab, Quant Method edit box, select either Filter with
Standards or Gaussian with Standards.
4. Click on the Quantify Spectrum button to run a Quant with Standards.
5. Click on the Quant Results tab in the Analysis Controls pane to view the
results.

Quantification With
Standards
Quant with Standards
Saving a standards list

After selecting and adding available standards to the Standards in Use box, you
can save this list to use again.
1. After adding the standards in the Add Standards window, click on the
Save button.
2. In the Save As window, enter a name for the standards list. You can
navigate to a folder (default is the current Project). Click Save button to
save.

Quantification For STEM/ Using saved standards lists
TEM Analysis 1. Click on the Add Standards button in the Standards tab to bring up the Add
Standards window.
2. Click on the Load button in the Add Standards window. Select from the
standards (*.stn) files and load the file containing the standards you wish
to use. The list will be loaded into the Add Standards > Standard Database
window.
When using an analysis with standards, it is recommended to use Normalize

Wt% in the Properties: Quant Results (see above under Specifying Quant
results). Generally, when using with standards, no normilization is used.
However, displaying normalization when using standards gives additional infor-
mation as to the accuracy of the quant.
Quantification For STEM/TEM Analysis

Cliff-Lorimer (MBTS) corrections
Typically, samples for TEM or STEM are thinner than the x-ray generation
(interaction) volume. Under these conditions, the complex ZAF corrections can
be replaced by the Cliff-Lorimer simplification, in which a “K-factor” charac-
terizes the relationship between elements. However, similar to the ZAF correc-
tions, Cliff-Lorimer correction requires a K-factor for each element that is being
quantified.
Defining K-factors
There are 2 ways to enter/define K-factors: manually calculate and enter the
values, or automatically calculate and enter the values through System 7
software.
Manual method
To manually calculate K-factors you need to acquire a spectrum of a sample
with known concentrations (i.e. a NIST or similarly well characterized standard)
using the same acquisition parameters as the unknown - beam current, acceler-
ating voltage, count rate, etc. After spectral acquisition, a quant must be run to
obtain the net intensities for the reference element and the desired element.
Typically, Si is used as the reference element. Not all standards will have all the
elements, including the reference, of interest. You can calculate the K-factor for
an element against the reference using an intermediate K-factor using a
different reference element.

To calculate K-factors, use the following mathematical equation: Quantification For STEM/
TEM Analysis
K-factor = (Ca / Cref) * (Iref / Ia)
where Ca = concentration of element a
Cref = concentration of reference element (usually Si)
Iref = Intensity of reference element
Ia = Intensity of element a
Concentrations can be in Wt% or Atom%, but must be known.
1. Acquire a spectrum of the standard under the same acquisition

parameters as the sample to be analyzed
2. Click on the Analysis Setup tab and select a Quant Method, either filter
without standards or Guassian without standards.
3. In the Quant Results tab - Main Menu: Edit: Properties - include Intensity
and Intensity error. This is really the only parameter needed for
calculating K-factors.
4. Click on the Element Setup tab and select the elements and lines in the
Periodic Table for the elements in the standard.
5. Click on the Quant button to generate the Intensities of the
elements.

Quantification For STEM/ In the above example, Si will be used as the reference. The matrix correction
TEM Analysis was Proza and the Quant Fit Method was Filter without Standards. The
following values will be used for calculating K-factors (from the certification
sheet):
Si concentration = 64.52 Wt%
Fe concentration = 8.01 Wt%
The K-factor for the reference Si = 1

K-factor for Fe = (8.01/64.52) * (5697.5/4067.6) Intensities from Quant results
= 0.12421 * 1.407
K-factor = 0.1738
Enter into the Standards: New Standard

1. On Element Setup tab, select Fe
2. On Analysis Setup tab, Correction Method, select Cliff-Lorimer w/o
absorbance.
3. In the Information Pane, click on Standards tab.
4. Click on Add Standard button.
5. On the New Standard window, enter the beam current, K-factor and
reference element. Uncheck “From Current Spectrum.”
6. Click OK to add to the Standards Database.

7. From the Standards Database, select the Fe K-factor just created and Quantification For STEM/
click on the Add Selected button to place into “Standards In Use” group. TEM Analysis
Automatic calculations of K-factors

In this example, Si will be used as the reference. The matrix correction was
Cliff-Lorimer w/o absorbance and the Quant Fit Method was Filter without Stan-
dards.
Si concentration = 64.52 Wt%
Fe concentration = 8.01 Wt%
Mg concentration = 27.47 Wt%
This example uses the mult-element standard used as an example above.

1. Acquire spectrum of the standard as above.
2. On the Analysis Setup tab, select the matrix correction as Cliff-Lorimer
and the Quant Fit method as Filter without Standards.
3. In the Element Setup tab, select Si (this will be the reference).
4. In the Information Pane, select Standards tab and click on Add Standard
button.
5. In the Add Standards window, click on New Standard button. This brings
up the New Standard window.
6. Select Multi Element Standard and in the Concentration Data Type, select
the type of data. In this case select weight %.
7. Select From Current Spectrum.
8. In the Multi Element boxes, enter Si from the pull down periodic table. The
first element entered is the reference.
9. Enter all elements in the spectrum and their corresponding Wt% values.
10.Adjust the energy range bars to just include the Si peak.
11.Click OK to calculate the K-factor (Si as the reference is 1) and add to
Standards Database window.
12.On the Element Setup tab, select the next element (in this example, Mg).
13.Click on New Standard button in the Add Standards window.
14.Adjust the energy range bars to just include the Mg peak.
15.Click OK to add to Standards Database window.
16.Repeat for remaining elements.

Quantification For STEM/
TEM Analysis
Adjust energy
range
17.After adding all elements, select all the elements just added in the
Standards Database (Add Standards window) and add to the Standards in
Use (select and click on Add Selected button).
18.Click OK to add to the Standards in Use on the Standards tab.
The elements with calculated K-factors are now in the Standards in Use on the
Standards tab (Information Pane).

Additional Tools in
Spectrum Mode
Additional Tools in Spectrum Mode

Reference Subtract/Add...
To activate the Reference Subtract/Add function the spectrum must first be
quantified. From the Main Menu Spectrum select Reference Subtract/Add from
the submenu. This will bring up another window with the elements in the
spectrum listed. Select the desired element/x-ray line (check box) and click on
the Add or Subtract radio button. Click on Apply or OK and the spectrum will be
processed in accordance with the selections.

Additional Tools in
Spectrum Mode
Creating user reference spectra

System 7 has three sets of reference spectra embedded in the software. The
set of references used depends upon the resolution of the detector. Detectors
are divided into 3 types. During installation, the service engineer selects the
type of detector that is installed. This in turn selects the reference set. Because
of slight differences in detectors and electronics, it is advisable to create a
reference set using your system.
Reference spectra are saved into a database in a similar fashion as Standards
described above.
• It is best to use pure elements whenever possible.
• Use the accelerating voltage that is routinely used.
• Use a long pulse processor time constant.
• Use a dead time of between 25% and 30%.
• Acquire long enough to get at least 10,000 counts verticle full scale in the
major peak.

To create a reference spectrum, acquire, or open, the spectrum of choice. Additional Tools in
• Select the element in the Element Setup tab. Spectrum Mode
• Select the Standards tab in the Information Pane.
• On the Standards tab, click on the Add Standard button. This brings up the
Add Standards window.
• In the Add Standards window, click on New Standard button to bring up the
New Standard window.
• Select the x-ray line to use.

• Click on the Use As Standardless Reference check box.
• Leave the Proza and ZAF Calib. Factor at defaults (1)
• Click OK to save.
• References are saved in the C:\NS7 Libraries\StandardlessReferences
folder.
If user references are available, System 7 will use the user references first. If
user references are not available for an element, NS7 will use the supplied
references. To verify that the user references are a good fit, acquire a spectrum
of a sample that contains the element and use the Reference Add/Subtract as
described above.

Additional Tools in Element x-ray lines
Spectrum Mode This is a handy tool to use instead of a slide rule. From the Main Menu
Spectrum click on Element x-ray lines from the submenu to quickly reference
the energy of an element and x-ray line. To select an element, click on the pull
down arrow next to the element. This will bring up a small periodic table to
select an element. From the pull down menu next to the line series, select the
desired line. You can also edit a selected line and change the energy and
intensity.
Batch processing
You can quantify a number of spectra and save the results as a .csv (comma
separated values) file which can be opened in a spread sheet application, such
as Microsoft Excel, for further mathematical analysis.
To batch process spectra, Sum Peak removal, Escape Peak removal, Auto ID
and Auto quant must be ON. From the Main Menu Batch Processing, select
Quant Analysis from the submenu. A Select Files... window will be displayed.
While holding the Ctrl or Shift key (same function as in Windows operating
system), left click on the spectral files you want processed.
After selecting files to process, click on Open button to begin processing. A File
Save.... window will open. Enter a file name for the .csv file.

Additional Tools in
Spectrum Mode

Additional Tools in Region tool
Spectrum Mode The region tool is used to extract peak counts or rate data in a spectrum. In
addition, mathematical manipulations can be performed on element data in a
spectrum. You can add, subtract, multiply or divide peak counts or peak rates of
elements in a spectrum. You can determine the net and gross counts of a single
peak or determine a ratio (divide) of two elements in a spectrum.
Click on the Region Tool tab in the Information Pane. To select elements, click
on the pull down arrow in the Elements selection and select the element from
the periodic table. Also select the x-ray line from the pull down arrow next to
Lines. Select the math function from the pull down arrow. Select None if you just
want peak counts. Click on the radio button next the the data type you wish
(Counts or Rate). You can change the eV range of the peak region in the User
Region Range edit boxes. Click on the plus (+) button and add the elements and
math operation into the Region Operations window. Results will be displayed.
To remove a prior operation, highlight the operation in the Region Operations
window and click on the minus (-) button.

Calibrating Fine Gain Calibrating Fine Gain
The Fine Gain calibration makes final corrections to peak position. This
procedure should be used if peak positions are not correct.
1. Select the Service Mode tab and click on the EDS Calibration Icon.
2. Click the Auto tab in lower left corner of the EDS Calibration mode to
display the Fine Gain calibration settings.
3. Put a clean Manganese (you can use any element, but Mn is the industry
standard) sample in the microscope.
• Minimum accelerating voltage of 15KV.
4. In the Setup section of the window, select Mn as the Atomic Symbol, K as
the Line, and 30 for Maximum Iterations using the pull down selections.
5. Select a Time Constant from the drop down selections.
6. Click the Play to start the automatic calibration.

• A spectral acquisition will start.
7. An Automatic Calibration prompt will appear. Place the energy cursor
near the centroid of the Mn Kα peak in the display and click the OK button
to continue with the calibration.

Calibrating Fine Gain
• The program will move the peak selected to the energy value of
Manganese that was selected in step 4.
8. A Prompt will appear stating Calibration completed successfully. Click the

OK button to finish.
• The new Fine Gain setting and the Calibration Date will be updated in
the status section in the right hand section of the Auto tab.
9. Repeat steps 4 - 8 to calibrate the Fine Gain for all available Time
Constants.

Adjusting Configurations Adjusting Configurations
1. Select the Service Mode selections and switch to the Instrument

Configuration mode from the System 7 Service selections.
• Click the Instrument Configuration icon in the left hand navigation pane.
The Instrument Configuration mode is displayed.
NS7 Instrument
Configuration mode.
2. Type desired name in the Instrument name section.

3. In the Update attributes section, select the desired time (Before, During,
or After the start of any acquisition) to update the attribute parameters.
Note: Column and Stage automation is needed to update the column
and stage attributes automatically.
4. In the Image input names section, keep the default names for the two
inputs.
• SEI is a secondary electron image and BEI is backscattered electron
image.

Adjusting Configurations 5. In the MCS section, keep the Input Enable box unchecked and the Name
field blank unless a WDS spectrometer is available.
• MCS is Multi Channel Scaler. A check mark in the Enable box will
enable the MCS Input. The Name field is available to type in a name for
the MCS Input. This is only used when a WDS spectrometer is added.
6. In the Hardware Communications section, verify that 90.0.0.50 is the IP
Address. Keep the Sync Port and Async Port at default values (5001 and
5002).
• The IP Address refers to the Internet Protocol Address of the NORAN
System 7 chassis.
7. In the EDS Detector section, enter the appropriate values to describe the
installed detector.
• Detector name: Type a name to be used for the detector.
• Extreme Detector: Check the box if the detector is 129 eV resolution.
This will add the Extreme Time Constant setting (100 microseconds).
• Azimuth Angle: Horizontal angle, in degrees, between the EDS detector
and the direction of stage tilt. Refer to the detector drawing for the angle
information. These values are used for matrix correction if the stage is
tilted during EDS acquisition.
• Incline Angle: Angle, in degrees, at which the EDS detector is mounted
on the microscope. Refer to the detector drawing for the angle
information. Typically, the detector is a “high angle takeoff” and is limited
by the microscope construction.
• Initial slide position: Position, in mm, of the EDS detector slide when the
detector is fully inserted. Refer to the detector drawing for desired
position. Input actual value.
• Intersection distance: Vertical distance, in mm, from the microscope pole
piece to the EDS detector crystal center line. Refer to the detector
drawing for distance information. This is the optimal working distance
with the detector fully inserted.
• Crystal Tilt: Angle, in degrees, at which the EDS detector’s crystal is
mounted. Refer to detector drawing for angle information.
• Crystal Area: The area, in square mm, of the EDS detector’s crystal.
Refer to detector specification sheet for area information.
• Crystal Material and Thickness: Select the crystal type from the drop
down list and verify the proper thickness, in mm, is specified. Refer to
detector specification sheet and default values provided below.

Adjusting Configurations
• Contact layer Material and Thickness: Select the proper contact
material from the drop down list and verify or type the proper thickness
in microns. Material is based on the crystal material. Refer to the default
values provided below.
• Dead Layer Thickness: Type the thickness, in microns, of the detector
dead layer. Based on crystal material. Refer to default values below.
Typically 0.1 microns.
• Window Material and Thickness: Select the proper window material
from the drop down list and verify or type the proper Thickness for the
selection. Refer to the detector specification sheet for material and the
default values below for thickness.
• Window coating Material and Thickness: Select the proper window
coating material from the drop down list and verify or type the proper
coating thickness in microns. Refer to default values below.
• Contamination Material and Thickness: Select the type of contamination
from the drop down list and enter the thickness of the contamination, in
microns. For new detectors or for clean detectors, the values should be
None and zero.
NORVAR PleXus Quantum Diamond Parylene Aluminum Beryllium

Window Thickness
0.3 0.3 0.26 0.4 0.1 0.1 7.5
(um)
Window Coating
Aluminum Aluminum Aluminum Aluminum Aluminum None None
Material
Window Coating
0.04 0.02 0.016 0.015 0.015 0.0 0.0
Thickness (um)
8. Click the Apply button in the lower right hand corner to apply the changes.
Saving configurations
1. From the Instrument Configuration mode, click the Save button (or
from the File menu, select Save)
• A Save As window will appear.

Adjusting Configurations 2. Navigate to the desired directory.
3. Type in desired filename.
4. Click the Save button.
• The Instrument Configuration, EDS Calibration, and Image Calibrations
are saved to a file with the extension .nsscfg.
Note: Original installation calibrations are normally stored as install.nsscfg and placed
in the C:\Install Calibration folder.
Restoring saved configurations

This procedure will restore values for Instrument Configuration, EDS Cali-
bration, and Image Calibration that was previously saved as a NORAN System
7 Configuration (*.nsscfg) in the event of a DPP board replacement, hard drive
replacement, or hard drive re-format.
1. Run System 7 from the Windows Start menu.
• Start > Programs > Thermo Scientific> NSS> NSS.
2. Switch to the Instrument Configuration mode from the System 7 Service
selections.
• Click the Instrument Configuration icon in the left hand navigation pane.
The Instrument Configuration mode is displayed.
3. From the Instrument Configuration mode, Select the File menu and select
Open from the pull down menu.
• An Open window will appear.
4. Navigate to the directory in which a calibration file is saved.
5. Highlight the .nsscfg file and click the Open button.
Note: Original installation calibrations are normally stored as install*.nsscfg and
placed in the C:\Install Calibration folder.

CHAPTER
4
Electron Imaging Mode

This chapter discusses the System 7 Electron Imaging mode, which
allows you to acquire, save, and load electron image files. The images are
saved in the standard .TIF file format. The Imaging mode also provides an
image ruler for measuring objects in the image. Guidelines for setting up
and acquiring images from a scanning electron microscope are provided.
With optional stage and column integration modules and the optional
module Analysis Automation, you can also acquire and create a single
image (montage) from multiple images
Imaging Mode Interface

In the imaging mode, all the necessary tools for collecting images,
processing and file manipulations are presented in the imaging panes.
Column and Stage

information tab
Pixel and Frame

information tab
Notepad area
Analysis Automation
setup tab (optional
software module)
CHAPTER 4: ELECTRON IMAGING MODE 79

Setting Imaging Setting Imaging Acquisition Properties
Acquisition Properties
To set the acquisition properties for electron imaging:
1. Click the Acquisition Properties button .
2. Click the Imaging tab. Set values as desired. Values are described in
the following table.
Field Description
The size of the image in pixels. A higher resolution

Resolution provides greater image detail and increases
acquisition time.
A long frame time increases the acquisition time

and reduces image noise. A shorter frame time can
Frame Time result in blurred and streaked images. Optimum
values depend on microscope and detector type.
System 7 will determine the time if set to Fastest.
The length of time the beam is placed at each pixel

location. A longer dwell time reduces image noise
Dwell Time and increases the acquisition time. A shorter dwell
time might cause a blurred or streaked image.
The number of frames to be acquired or averaged.

A frame is one complete scan from the upper left
corner to the lower right corner of the map. For
Number of Frames beam-sensitive samples, increase the number of
frames and decrease the dwell time. When this field
is set to 0, the acquisition must be manually
stopped by clicking the Stop or Abort buttons.
Acquisition Time System 7 estimates the total acquisition time.
Selects the channel from which the image data is

Use Input boxes
acquired. Typically uses input 1.
Acquiring An Electron Image

Prior to the acquisition, make sure all acquisition properties are properly set.
1. Switch to Electron Imaging Mode.
2. Click the Acquire Averaged Electron Image button on the

Acquisition Toolbar to acquire an averaged electron image. Or, click
the Start button to acquire a live electron image.

3. Either wait until the acquisition terminates according to the criteria set Post Acquisition
up in the Imaging Acquisition Properties dialog box, or click the Stop Processing
button on the Acquisition Toolbar.
• To pause the acquisition, click the Pause button on the
Acquisition Toolbar. Click the Acquire Image button to resume.
• Click the Abort button to stop the acquisition at the end of the
current line. The data are not saved.
Post Acquisition Processing

There are a limited number of image processing tools in System 7. For full
image processing and analysis, use third-party image analysis software.
With optional software module Feature Sizing particles and features in an
image can be sized, counted and a number of parameters extracted.
Contrast and brightness

To adjust the image’s contrast and brightness, right-click on the image and
bring up the General Properties window and select the Image View tab..
Adjust the Contrast and Brightness slider bars.
Overlay transparancy
factor for Spectral
Imaging mode.
Brightness and
Contrast slider bars
Micron marker in manual brightness
location check and contrast mode.
box
Auto brightness
and contrast
Hot pixel
supression mode
Image View tab in

General Properties

You can also select the auto mode of brightness and contrast adjustments.
The Hot pixel supression mode will eliminate those random noise pixels
which are at maximun brightness in an effort to bring the overall image
brightness to an average level. For example, the image brightness may be
a lower level. There may be one pixel which is at maximum brightness. This
makes the image appear dark or black with one pixel full white. By elimi-
nating this pixel, the overall brightness will be brought up, making the image
of average brightness.
Micron marker bar

Checking the box for Micron bar in header will display the micron bar in
the header above the image, just below the image label. The default is
unchecked and the micron bar is displayed in the lower right corner of the
image.
Ruler
Click on the Ruler button in the Extraction tool bar to display the ruler
line in the image. Left clicking and draging on either end of the ruler line will
lengthen or shorten the line. Left click and draging the middle of the line will
move the entire line. The length of the line is displayed with the line.
Ruler line

Managing Image Files Managing Image Files
Changing file name/label

To label the image:
1. Double click on the image title at the top of the Image View.
2. Enter the new label. Click OK. (This will also change the file name)
Note: If you change the image label, a new image file is created with the label as
the filename.
Saving image files

Files saved in Image Mode are stored with a .TIF file extension. By default,
all images are saved in the current project directory.
Opening image files

Files opened in Electron Imaging Mode are handled as standard image
files.
1. Open the project and go to Electron Imaging Mode.
2. Click on the image file in the File List View.
The image appears in the Image View.
To open a file outside the current project:
2. In the Open box, navigate to the directory containing the file.
4. Click Open.
The file is imported into the project’s temporary directory. When you
close the project, System 7 asks if you want to save the file to the
project folder or discard it. The temporary directory is emptied when
you close the project.
Batch processing
In imaging mode, a series of images can be stitched together to create one
larger image (Montage). However, the images must be collected through
the optional software mode Analysis Automation.

Managing Image Files

CHAPTER
5
Point and Shoot Mode

This chapter discusses the System 7 Point and Shoot mode which allows
you to acquire spectra from user-defined points or areas on a reference
electron image. Guidelines for setting up and acquiring data are provided.
Point and Shoot has two acquisition modes: Immediate and Batch
(multiple). In the immediate mode, spectral acquisition begins immediately
after defining the point or area. The batch mode allows for a series of points
or areas to be defined then begin an automated sequence of spectral acqui-
sitions. Also you can use the P&S Select tab in the analysis controls pane to
specify which points and areas to display on the image. You can also use
the tab to select for deletion a point or area that has not yet been acquired.
Spectrum
View
Image View
Point and Shoot Mode Interface
CHAPTER 5: POINT AND SHOOT MODE 85

Setting Point and Shoot
Acquisition Properties
Point and Shoot Select Tab
Setting Point and Shoot Acquisition Properties

1. Click the Acquisition Properties button and setup both Imaging
and EDS acquisition parameters.
• On the Acquisition Properties window, select the EDS tab and set
the parameters for spectral acquisition. Set the parameters as you
would for a single acquisition for the sample.
• On the Imaging tab in the Acquisition Properties window, set the
acquisition parameters for a good reference image.
Performing a Point and Shoot Acquisition

You can either start with an existing image or acquire a new image. To
acquire the new image, click the Acquire An Averaged Electron Image
button. You can do two different styles of Point & Shoot acquisitions, imme-
diate or batch, using a mixture of five different shapes (point, rectangle,
irregular, Fat Spot and polygon). An immediate acquisition begins when you
click a new point or area. In a batch acquisition you select a batch of points
or areas and then acquire data. For best image registration, use shorter

acquisition times. Spectral analysis works the same way in this mode as in Performing a Point and
other modes. Shoot Acquisition
Immediate Acquisition
Button Depressed
Batch Acquisition
Button NOT Depressed
Review Location
Point and Shoot Tool Bar
Immediate individual acquisitions

1. Click the Immediate Acquisition button on the Point and Shoot
Toolbar and leave DEPRESSED.
2. Select the type of acquisition: point or area
scan Fat Spot
rectangular area (circular
area)
scan polygone
area
selects point select area by

(spot) mode image intensity
3. Click on the image at the location where you want to begin the
acquisition. In spot mode, acquisition starts when you click the point.
For area modes, acquisition begins when you complete selecting the
area.
4. Wait for acquisition to complete, or you can move the spot/area to a
new location before the acquisition completes. The new location will
have the same number as the original.
5. To add another point, click a new location.
Note: System 7 begins a new acquisition at each new cursor position under
the base name appended with point number.
Batch acquisitions
1. Click the Batch Acquisition button on the Point and Shoot
Toolbar. Leave the button NOT depressed.
CHAPTER 5: POINT AND SHOOT MODE 87

Performing a Point and 2. Select the type of acquisition. You can mix spots with areas. Each
Shoot Acquisition spot/area will be numbered sequentially.
3. Click on the image to mark the locations you want to acquire. For
areas, adjust the size of the area.
4. When you are finished marking locations, click Start . button.

System 7 acquires each spectrum individually. You can edit the
locations from the P&S Select tab in the Analysis Controls pane.
Reviewing data locations

1. Click the Review button .
2. Click on the point you want to view. The spectrum from that location/
area will be displayed in the Spectrum View pane. The spectrum
name is the number of the point. The spectrum can be analyzed using
the same functions as in Spectrum Mode.
Saving individual spectra from a P&S file

A Point and Shoot file has the reference image, the points locations and
numbers, and the respective spectra from the points. To save an individual
spectrum from a selected point, a copy of the spectrum must be separated
from the P&S file.
1. Switch to the Point and Shoot mode and select the desired file.
2. Using the review button, select the desired point and display the
spectrum in the Spectrum View pane.
3. Click on the Spectrum mode icon (switch to the Spectrum mode). The
selected Point and Shoot spectrum will be displayed in the Spectrum
mode. Click the Save button or from Main Menu File > Save. A copy
of the spectrum will be saved in the Spectrum Mode.
Batch processing
After acquiring spectra from a number of points or areas, you can quantify
all spectra in the P&S file at one time rather than manually quantifying one
at a time. When exporting to a report, the data are organized in such a way
that they can be further analyzed, such as calculating average Wt%.

CHAPTER
6
Spectral Imaging Mode

Spectral Imaging acquires a data set of dead time corrected spectra at
every point (pixel) in the reference electron image. Once acquired and
stored, you can reanalyze the data and generate a spectrum for qualitative
and quantitative analysis of the entire image or selected areas, create a set
of x-ray maps, create linescans, and print reports.
System 7 Spectral Imaging mode Interface
CHAPTER 6: SPECTRAL IMAGING MODE 89

Setting Acquisition Spectral Imaging is the only mode for collecting x-ray maps. Also, Compass
Properties (component analysis) is an integral part of Spectral Imaging. You can
create component maps through Compass.
In level 300 (model 302) and higher you can also acquire phase maps
during an acquisition (Direct to Phase option).
Setting Acquisition Properties

Refer to Chapter 4 for setting image acquisition properties.
To set the mapping acquisition properties for the data set:
1. Click the Acquisition Properties button .
2. Click the Spectral Imaging tab.

Setting Acquisition
Properties
Field Description
The size of the map image in pixels. A larger

Resolution resolution provides greater image detail but
increases acquisition time. 256 is a good choice.
A long frame time increases the acquisition time

and reduces image noise. A shorter frame time
can result in blurred and streaked images.
Frame Time
Optimum values depend on microscope and
detector type. NSS automatically calculates the
dwell time from the frame time.
The length of time the beam is placed at each

pixel location. A longer dwell time reduces image
noise and increases the acquisition time. A
shorter dwell time might cause a blurred or
Dwell Time
streaked image. The dwell time is set through the
frame time. Minimum dwell time should be about
4-5 times longer than the pulse processor time
constant. The shortest dwell time is 50 usec.
The number of frames to be acquired or

averaged. Infinite means you must manually stop
the acquisition by pressing Stop or Abort. A frame
Number of Frames is one complete scan from the upper left corner to
the lower right corner of the map. For beam-
sensitive samples, increase the number of frames
and decrease the dwell time.
Acquisition Time System 7 estimates the total acquisition time.
Avg. Counts per Pixel The acquisition will terminate when the total x-ray
Limit counts in a pixel reaches this value
Element Map Vertical The acquisition will terminate when the vertical
full scale of the accumulated spectrum reaches
Full Scale
this value
If you select an element and x-ray line, the

acquisition will terminate when the counts in any
Element Line
channel within the element line peak reaches this
value
Acquire a gray level image at the same time as

the maps. This image defaults to single color and
Acquire Video
is displayed in the map view pane at the same
(Check Box) resolution as the maps

Setting Acquisition Acquiring a Data Set
Properties
Spectral Imaging files are acquired using the settings in the EDS, Imaging
and Spectral Imaging tabs of the Acquisition Properties. Prior to the acqui-
sition, make sure all acquisition properties and microscope parameters are
set. Use short time constant and high counts rates for good results within a
reasonable time.
1. Go to Spectral Imaging Mode.
2. Acquire Reference Image. Click the Acquire Image button in the

Acquisition Toolbar. Wait until the image acquisition is complete.
• To pause the acquisition, click the Pause button on the
Acquisition Toolbar. The Image Acquisition pauses at the
completion of the current frame. Click Start to resume.
• To immediately stop the acquisition, click the Stop button on the
Acquisition Toolbar. The Image Acquisition stops at the completion
of the current frame.
• Click the Abort button to stop the acquisition at the end of the
current line. The data are not saved.
The electron image will be collected from the microscope based on
the parameters set in the acquisition properties Imaging tab. The
electron image is used as the reference for the data set to be acquired
in the next step.
3. Acquire x-ray data. Click the Start button on the Acquisition

Toolbar to begin data acquisition.
4. Wait until the acquisition is complete, or click the Stop button when
desired data has been collected.
The cumulative spectrum from all pixels appears in the Spectral View
pane. If Auto ID is enabled, an AutoID is performed periodically during
the acquisition and x-ray maps are added to the display.
Note: When the acquisition is complete, the data set is automatically stored in the
temporary directory and is ready for analysis. From here you can perform
extractions to view spectral information or create maps and linescans. If
you save the file to a project, you can exit the System 7 interface and return
to your data set at any time.
During an acquisition you can switch to Compass mode and acquire
component maps (302 model). The component maps will be updated and
displayed periodically during the acquisition. You can also switch back to x-
ray maps. Click on the Compass button to switch.

Extraction Tools Extraction Tools
Once the Spectral Imaging data set is acquired, you can extract spectral
data from areas of the electron image for spectral analysis.
The Extraction Toolbar contains buttons to specify an area of the electron
image for analysis. To preform and auto extraction, click the Auto Extract
ON in the Processing tab.
Rectangle Fat Spot Extract maps

(circle)
“Magic Wand”
Polygon Extraction by Image
Intensities
Linescan Image
Intensity Ruler
Cursor
Extracting data from a polygon

Polygon extraction allows you to draw multiple unique shapes on the image
for analysis.
Note: Turn OFF the image intensity cursor before beginning the extraction. Click
on the Image Intensity Cursor button to toggle off or on.
1. Click the Polygon extraction button .
2. Click on the image at the point where you want to begin your shape.
Draw a closed shape.
Note: To draw straight lines, click on the corners of the shape rather than
holding down the mouse button and drawing.
3. Right-click on the shape to close and fill it. This begins the extraction.
Drawing a Polygon Extraction

Click the starting point of the shape and trace the area to be extracted.
For Straight lines, click on the corners of the shape.
Right-click in the middle of the shape to fill it.

Extracting data from a When you draw the area, the cumulative spectrum is extracted. The identifi-
rectangle cation and analysis depend on the Spectral Processing settings.
Note: To remove an existing shape, click the polygon extraction button. The
shape disappears when the extraction button is not active. Click the
extraction button again to draw a new shape.
Note: To draw multiple shapes, hold down Ctrl while drawing.
Extracting data from a rectangle

With the Rectangle Extraction tool, you can extract spectra from a
rectangular shaped region.
Note: Turn off the image intensity cursor before beginning the extraction.
1. Click the Rectangular Extraction button.
2. Click and drag a rectangular area over the electron image.
Start at any corner of the rectangle and drag towards the opposite
corner. To delete the shape and redraw the area, drag a new
rectangle over the image.
Drawing a rectangle over the image with the

rectangular extraction tool.
Click on any corner and drag to the opposite corner.
To extract from the entire image, click the maximize
button (small square in upper right corner of the rect-
angle)
When the area is drawn and the left mouse button is released the cumu-
lative spectrum from all contained pixels is created. The spectrum
appearance and the identification depend on the Spectral Processing
settings. X-ray maps are extracted from the entire image.
• The rectangle can be moved to another location. Move the mouse
pointer into the rectange and it will change to a 4-way arrow. Hold
the left mouse button and drag the rectangle.

Extracting data from a
• You can resize an existing rectangle by moving the mouse pointer to spot
a corner or side of the rectangle. The mouse pointer will change to a
2-way arrow. Click and drag the corner or side to resize the
rectangle.
• Extracting from entire image. The rectangle has a small square near
the upper right corner. Clicking on the square will expand the
rectangle to fill the entire image. Clicking again will reduce the
rectange to its original size.
Extracting data from a spot

Fat Spot™ extraction procedures are similar to rectangular extractions but
are circular.
1. To change the size of the “Fat Spot”, right-click on the Image View.
Click the Image Extract tab.
2. Enter a radius (in % of image) for the spot size. Click OK.

3. Click the Fat Spot extraction button .
4. Place the mouse pointer where you want to extract and left click to set
the center of the spot.
Note: To remove an existing shape, place a new shape over the image.
Fat Spot
When you place the spot, the cumulative spectrum is extracted. The
appearance of the spectrum and the identification depend on the Spectral
Processing settings.
Extracting linescan data

Linescan extraction allows you to investigate and analyze the elemental
transitions from region to region on the sample. You can specify the
direction and width of the extracted area.
1. In the Element Setup periodic table, mark the elements to include in
the linescan as Identified.
Note: If you are unsure whether or not to display an element, include it in the
initial linescan. You can exclude elements that are not of interest later.
2. Right-click on the image. Click the Image Extract tab.
3. In the Line group enter a Thickness value (in % of image).
4. Enter the Number of Points to show in the linescan. Click OK.
5. Click the Linescan extraction button .

6. Click on the start of the line and drag to the end of the line. Extracting linescan
7. Linescan data appears in the top right pane. data
Adjusting linescan appearance

You can modify the linescan display by several means:
• Elements displayed are selected prior to an extraction or collection. To
remove an element from the analysis, right-click the element in the
periodic table. Select Inactive. Re-extract is necessary.
• To change the appearance of the linescan data, right-click on the lines-
can view.
In the Graph Properties dialog box, you can change from plane line to
with symbols, and title of the linescan. You can also apply a grid or cur-
sor to the linescan..
Analyzing linescans
The electron image and the linescan data use the image intensity cursor. As
you move one cursor, the other cursor moves as well. Click the image
intensity cursor button in the Extraction Toolbar to activate the cursor

Extracting linescan
data
Coordinated cursors
The spectrum from the point at the cursor location is displayed in the
spectrum pane (lower right pant). You can also change the results param-
eters to Wt%, Atom%, K ratio or Net Counts. Click on the Processing tab in
the Control pane and from the pull down menu in the Automatic group
select the analysis parameter you want. Redraw the line to extract and
process the data.
To overlay a data set for an element on the line, click on the desired elment
in the linescan data display.

Extracting linescan
data
To change the element data overlay, right click on the image and select the
Linescan Overlay tab in the General Properties window. You can choose to
have the overlay on the linescan or at the bottom of the image. For multiple
elements, you can choose to have them stacked or overlayed and also
scaled separately.
Saving extracted linescan data

To save the extracted linescan data:
1. Select the main menu Linescan > Export as *.csv (the linescan
graph pane must be the active pane).
2. In the Save As dialog box, file name edit box, enter a name for the file.
3. Click OK to save the data. The data are saved as a Comma
Separated Value file.
Opening a *.csv data file

Open a spread sheet applications program, such as Microsoft Excel.
1. In the spread sheet program, select main menu File > Open.

Extracting linescan 2. In the File Open dialog box, File of Type edit box, select Text Files.
data 3. Navigate to the folder which contains the *.csv file and select the file.
4. Click OK.
Extracting “Magic Wand” data

Magic wand selects an irregularly shaped area on the reference image
based on grey-level intensity values. Similar to a polygon, but uses inten-
sities, within specified values, to define the area. Much easier than hand
drawing a polygon.
1. Select the “Magic Wand” tool from the extraction toolbar.
Extraction by
Intensities
“Magic Wand”
2. Selecting the magic wand tool will open the Image Intensity Selection
window.
3. In the Cursor Diameter edit box, enter the size of the cursor as a
percentage of the image, or size in microns. If in microns, check the
Diameter in Microns check box. The cursor diameter is the size or
number of pixels around the mouse pointer that will be evaluated.
4. On the Similarity slide bar, adjust the percent similarity in intensity to
include in the selected area. If the area selected appears spotty or
does not include all the area of interest, decrease the percent
similarity. A lower percent will include more pixels.

5. In the Smoothing edit box, select the number of passes for a Extracting Multiple
smoothing function. One or two passes will decrease the noisey pixels Spectra
around the mouse pointer which decreases the pixelation of the area.
6. Check the Spectrum auto extract check box to automatically extract
the spectrum after intensity area is selected. If unchecked, the Extract
Spectrum button will be displayed
95% similarity 95% similarity 85% similarity

0 smooth 2 smooth 2 smooth
Extracting Multiple Spectra

To compare spectra from multiple extraction regions, each spectrum file
must be manually saved to the project folder. Spectral comparison is then
performed in Spectrum Mode.
To gather additional spectra from one acquisition, perform another
extraction, and switch to Spectrum mode. Rename the spectrum and select
Save for each spectrum you want compare.
Spectral Imaging X-ray Mapping

Creating x-ray maps
To create the x-ray maps for a Spectral Imaging data set.
1. Open or acquire the Spectral Imaging data set.
2. Perform an extraction.

Spectral Imaging X-ray 3. Click the Identify button to identify the elements in the spectrum.
Mapping The results appear in the periodic table.
4. Mark the elements you want included as Identified. Make the elements
Inactive that you do not wish to be mapped.
5. Click the Extract Maps button in the Extraction Toolbar. The new
map set is created in the upper right pane.
Automatic extraction
Spectral identification and extracting x-ray maps may be performed auto-
matically.
1. Click on the Processing tab in the Analysis Control pane.
2. In the Results group, toggle AutoID to active.
3. In the Automatic group, toggle Auto Extract to active.
• When preforming an extraction, spectra will be automatically
extracted and an auto ID processed. After auto ID, x-ray maps will
be automatically extracted for the elements in the auto ID list.
After performing the initial extraction, you can add or remove elements from
the map display.
To add or remove elements from the maps, mark the elements in the
periodic table as Identified or Inactive. Click the Extract Maps button.
The new maps appear in the Maps pane.

Specifying energy ranges and lines Analyzing X-ray Maps
System 7 automatically identifies which lines are used for mapping based
on the element and the accelerating voltage in the microscope parameters.
If you choose to use a different line, click on the Lines Utilized drop-down
boxes in the Element Setup periodic table and select from the list of
possible lines. Some elements might only have one selection.
Mapping Energy Range field in the periodic table identifies the range of
energies that you want included in the element’s map. If the default energy
range is too wide or the range overlaps some other identified element’s
mapping range, enter an adjusted range that yields more specific and
accurate maps.
These changes are permanent and applied to future analyses in the current
project until the History is cleared.
Analyzing X-ray Maps

Image intensity cursor
System 7 includes a coordinated image intensity cursor for analysis of the
x-ray map set. When you place the image intensity cursor on the electron
image or any of the x-ray maps, the coordinated cursors move to the same
point on the image and all maps.
When you move the cursor to a new point, readouts for the cursor’s X-Y
position (in pixels) and intensity appear above the electron image and to the
right of the x-ray maps (example: x:177 y:76 i:94).
Click the image intensity cursor button in the Extraction Toolbar to turn
it on or off.
The default color for the image and x-ray maps cursors is red. To change
the color, right-click on the image and select a different cursor color in the
General Properties Image View tab.
Note: Both the image intensity cursor and the Spectral Imaging extraction cursor
can be toggled on and off. If both the extraction cursor and the image
intensity cursor are visible, the mouse controls the image intensity cursor.
To use the extraction cursor, turn the image intensity cursor off by clicking
on its button in the Extraction Toolbar.
Map overlay on image

To overlay the element map on the image, click the element label.
To adjust the SEM image visibility, right-click on the image and modify the
transparency percentage in the Image View tab.

Analyzing X-ray Maps Map intensity and color
Intensity values for the x-ray map elements and the image’s greylevel
values are shown in the upper right corner of each map and image. To
adjust the brightness or contrast, right-click on the image or map and adjust
the brightness and contrast slider bars.
General Properties Image View tab
Use the Contrast and Brightness slider bars to adjust
the image. Map color and other properties are
adjusted from the Map Properties
To change the color of an element, right-click on the element’s map. On the

Map Properties dialog box, select the new color. All color changes are
stored in your program settings for consistency.
Map Properties
Move the mouse to the desired map
and right click to bring up the Map
Properties dialog box
Use the Map Color drop down arrow
selections to change the color of the
map.
Brightness and contrast can also be
adjusted in the manual mode

Contour coloring maps Analyzing X-ray Maps
Maps can also be colored by a contour method. Within the contour there
are three modes of coloring: 1) outline, 2) fill, and 3) outline+fill. In addition,
the contours can have a number of gradations.
To contour color maps:
1. Move the mouse to the desired map and right click. This will bring up
the Map Properties dialog box.
2. In the Image Properties group, Mode pull down, select Contour. This
will activate the Contour Properties group.
3. Select the type of contour coloring desired.
4. Click Apply to impliment the contour mode.
5. You can change the color of the contour in the Image group, Map
color.
Selecting Contour will activate the

Contour Properties group. Select
the type and gradations desired
Map Properties
Select Contour
Map
Contour
Outline + Fill
gray color

Extracting Additional Extracting Additional Data Types
Data Types
In addition to analyzing x-ray maps by intensity (x-ray counts), the maps
can be analyzed by weight%, atomic%, k-ratio or net counts (background
corrected, which cleans up noisy maps).
Use the following steps to extract additional data from an SI file:
1. Click on the Spectral Imaging icon in the navigation pane and load the
desired SI file (if not already loaded).
2. Extract data from SI file as described above.
3. Click on the Processing tab and in the Automatic section, select the
type of data from the pulldown menu in the Maps/LS Data Type edit
box.
4. In the Kernal Size box select Auto.
5. In the Quant Map Detail box select the detail you desire. Low detail is
the fastest and High takes the longest time to process.
6. In the Filter Fit Type select either low or high precision
7. Click on the Extract Map Images button to start the processing.
8. After extracting the data, click on the Image Intensity Cursor
button in the Extraction Toolbar. Move the cursor to read the data at
the cursor location.
Opening Spectral Imaging files

If the file is in the current project, click on the file in the File List View. Or,
select Open and navigate to the .si file.
Compressing Spectral Imaging files

To reduce the size of the SI file:
1. Main Menu> File and select Compress SI.
2. Select one or more SI files in the same directory to compress.
3. Click OK. A progress dialog box appears. Compression time might
take several minutes per file.
The selected files are drastically reduced in size. The menu option is
disabled if an SI file is currently open or if an acquisition is in progress.

Saving Maps Extracting Additional
Data Types
After extracting or processing x-ray maps, the set of maps can be saved as
well as individual maps. From the Main Menu > File, select Save Map File.
All maps will be saved with the SI file name and with the type of processing
with the extention .map. A prompt window will appear with the added delim-
iters. In addition, each map will be save as a .TIF file. For example:
482SRM_Counts.map, and 482SRM_Cu_K_Map.tif. The individual maps
can be opened in the Electron Image mode. They will appear in the File List
View
SI file name Processing Type
Additional Tools
Extract/Maximal Button
When extracting spectra from an SI file, you can select to extract the
Maximal peak counts using any extraction tool. The button at the top of the
reference image toggles between Extract which presents total x-ray counts
from the entire extraction area or Maximal which remembers the maximum
counts for each channel in the area. The Maximal option aids in finding
small concentrations of an element, or small, localized areas of an element
which would otherwise be lost in the total background.

Extracting Additional
Data Types

Data Types
Single Pixel Extraction

To extract from a single pixel, use the Rectangle extraction tool. Move the
mouse pointer to the desired location and single left click. You may have to
move the existing rectangle to some other location in a similar fashion as
changing the rectangle. The single pixel rectangle will be represented as a
yellow cross.

Data Types
Single Pixel

Compass Tool Compass Tool
Compass, now an integral component of Spectral Imaging mode, extracts

compositionally distinct phases from a Spectral Image data set. This tool
uses an advanced statistical analysis algorithm to determine principal
components in the reference image. This is a completely statistical determi-
nation with no user input.
The statistic is analysis of co-variance. However the data set is a 3 dimen-

sional array (pixel location, element x-ray line, and x-ray counts/wt%) and,
thus, is a matrix with matrix mathematics (uses Eigenvectors).
Using compass
1. Acquire a Spectral Imaging data set, or open an existing Spectral
Imaging file.
2. Click on the Compass button in the Compass tool bar (the button will
be depressed and the Maps button will change to Components)
3. Click on the Map Extraction button in the Extraction tool bar.
When Compass has processed the data, the component maps are
displayed in the top right pane of the Spectral Imaging interface window.
Each component map represents one unique component in the sample.
The first component consists of those elements with the smallest co-
variance. The second map consists of those elements with the next largest
co-variance, and so forth.
The spectrum displayed in the spectrum pane (lower right pane) is, by
default, the spectrum of the first component (the map labeled C1). To
display the spectrum from other components, click on the map image.
To change the color of the map, right click on the map and change the color
in the Map Properties, Map Color tab. You can configure the Component
maps the same way as x-ray maps.

Compass Tool To change the method of Compass analysis use the Compass properties
tab in the Properties window - Main Menu Edit > Properties.
In the Method group, select either Spectral or Area as the method of

comparison. Spectral method arrays those components based on spectral
differences. Area method arrays components based on the percentage
area covered on the reference image.
Select a Background correction of either Calculation based on data set or

an Internal Model.
Use the Low Energy Cuttoff (eV) to eliminate the noise peak if present in the
data set.
Set the number of Components you want displayed. Generally use the Auto
(0) choice when first analyzing an unknown data set. You can then lower
the number. This combines components with close co-variance.

Phase Extraction Compass Tool
Phases can be compiled from either x-ray maps or principal components.
From x-ray maps, the elements considered in phase calculations can be
selected before extracting phases. From principal components, the number
of components also can be selected.
Phases from X-ray Maps

1. Acquire a Spectral Imaging data set, or open an existing file
2. Extract x-ray maps (be sure the Compass button is not depressed)

Compass Tool 3. On the Phase Analysis tab (Controls pane) select the elements to
include in the phase analysis (default is all).
4. Click on the Auto button in the Compass tool bar.
5. The pases will be extracted based on the elements selected. The

phase maps will be automatically overlayed on the reference image.
6. The Phase Analysis tab will display the phases and the element
combinations. The spectrum from Phase 1 will be displayed in the
Spectrum pane.

7. Click on the phase maps to display the spectrum associated with that Compass Tool
phase.
8. Combine phases by selecting the phases to combine in the Phase
Analysis pane. Select a phase (highlight) then hold the Ctrl key and
select another phase to combine with. You can select more than one.
9. In the Combine Phases group pulldown, select the phase to combine
into (default is the first phase selected.
10.Click on the Combine button and the phases will be re-displayed with
the combined phases.
Phase Extraction from Components

Extraction of phases from Compass components is performed in a similar
fashion as with maps.
1. Extract Compass components from a Spectral Imaging file as
described above. Click on the Auto button to extract phases. The
phases will be overlayed on the reference image automatically. The
spectrum from the first phase (Phase 1) will be displayed in the
spectrum pane.

Compass Tool 2. Phases from Compass components can be combined in a similar
fashion as with phases in x-ray maps (see above under Phases from
x-ray Maps)
Phase Extraction Properties

The method of phase extraction from either x-ray maps or Compass compo-
nents is controlled by the Phase tab on the Properties window - Main Menu
Edit > Properties > Phase tab.
You can select to extract phases by either maximum intensities in a pixel of

the x-ray lines or by the co-variance of relative concentrations of the
elements in the entire image (XPhase).

CHAPTER
7
3D Visualization
3-D Visualization mode lets you view a three-dimensional representation of
various types of map data. First use the appropriate mode to display the
desired type of data, and then switch to 3-D Visualization mode to view and
manipulate a 3-D image. For example, if you have displayed x-ray map data
using Spectral Imaging mode, you can view a 3-D image of the distribution
of x-ray count values for an element over the measured sample surface.
CHAPTER 7: 3D VISUALIZATION 117

When you click the element symbol in the upper-left corner of the element’s
map display box, the 3-D image for the element is generated and displayed.
Changing the appearance of 3-D
To change the appearance of the 3-D view use the general Properties
window - Main Menu Edit> Properties. The first tab is the 3-D properties.
Select the properties you want to change, and click Apply then OK to see
the changes.
Option What the Option Displays

A warped, interpolated surface showing values at different
Show Surface locations on the sample. This is a conversion of the
contour display (see the description of Contour below) to a
three-dimensional form that makes it easier to see the
values across the sample.

Black lines running along the intersecting edges of the Selecting Color
Wireframe imaginary planes of the surface plot (see the description of Schemes
Show Surface above) but without the planes themselves
displayed.
Contour lines representing constant values. If Show
Surface is selected, the contour lines are black. If Show
Contour Surface is not selected, the values are indicated by colors
defined in the color bar. These lines are similar to the
contour lines of a geographical relief map that indicate
constant elevation.
Profile lines representing constant Y-axis values. If Show
Profile Surface is selected, the profile lines are black. If Show
(Waterfall) Surface is not selected, the Z (vertical axis) values are
indicated by colors defined in the color bar.
Combine A three-dimensional gray scale image in which the grays
Electron match those in the electron image. Values are indicated by
Image peak heights (Z values) rather than by colors.
Selecting Color Schemes

Specify a color scheme for the 3-D image by selecting an option in the Color
Scheme box on the 3-D Visualization tab of the Properties dialog box
(available through Properties in the Edit menu). The table below describes
how each option represents values.
Color Description
Scheme
Uses shades of gray along a gradient to represent

values. This option is useful for printing 3-D images on a
black-and-white or gray-scale printer. Since the values
change as the gray shades become darker, it is easy to
identify areas of relative low and high value on the
Gray Scale printed image. If you print a 3-D image on the same
printer, however, the darkness of the resulting printed
gray shades will not necessarily correlate with the
values. A color that represents a high value, for example,
may appear as a light gray on paper. This option is also
useful for seeing contrast in the display of data.

Clipping the data Rainbow Uses a gradient of blended rainbow colors to represent
outside the color range values.
Banded Uses bands of colors, rather than a gradient of blended

colors, to represent values.
Blue To Red Uses blended colors from blue to red to represent

values.
The color bar below the Color Scheme box shows the colors used in the 3-
D image. The scale below the color bar indicates the values of the colors.
The vertical bars on the color bar indicate the limits of the value range
currently used for the colors in the 3-D image. You can change this range
by horizontally dragging the vertical bars. This in turn changes the distri-
bution of the colors.
If one or both of the vertical bars have been moved away from the ends of
the color bar, you can drag the portion between the vertical bars to the left
or right. To specify a different color scheme for the data, select the desired
option in the Color Scheme box.
Clipping the data outside the color range

Select Clip Data Outside Color Range on the 3-D Visualization tab of the
Properties dialog box if you want data outside the range specified by the
color bar not to be displayed in the 3-D image. This results in the display of
only the data in the range of interest.
ved away from the ends of the color bar, you can drag the portion between
the vertical bars to the left or right. To specify a different color scheme for
the data, select the desired option in the Color Scheme box.
You can rotate the 3-D image in any direction to see the data from different
angles. Simply drag the image in the direction you want to rotate it; the
image rotates as you move the mouse. Release the mouse button when
you have displayed the desired view of the data. If you release the mouse
button while the mouse is moving (and the image is still rotating), the image
will continue to rotate. This can help you study the shape of the data from all
sides.
To move the image to a new location within the pane, hold down the Shift
key and drag the image.

To enlarge or shrink the image, drag vertically across it with the right mouse Selecting a cursor
button held down. style for the 3-D image
• Note: Just as you can in Spectral Imaging and some other modes, you
can right-click the image pane to set the brightness, contrast and other
properties of the image.
Selecting a cursor style for the 3-D image

Specify a cursor style for the 3-D image by selecting an option in the Cursor
Style box on the 3-D Visualization tab of the Properties dialog box (available
through Properties in the Edit menu). The table below describes the
available styles.
Cursor Description
Style
Wireframe Outlines of three imaginary orthogonal (perpendicular)

Planes planes intersect at the cursor location. Perpendicular
lines that pass through that location appear as well.
3-D Cross Three-dimensional cross hairs appear at the cursor

location.
Extended Perpendicular lines pass through the cursor location and

Cross Hairs extension lines that connect those lines to the axes.
Smoothing the 3-D image

Select an option in the Smoothing box on the 3-D Visualization tab of the
Properties dialog box if you want the 3-D image to have smoother edges
and more blended color transitions. Mesh smoothing has a greater effect on
peak heights than does shading (Gouraud) smoothing.
Setting the opacity of the 3-D image

Use Show Surface on the 3-D Visualization tab of the Properties dialog box
to set the opacity of the 3-D image. Drag the small vertical bar below
Opacity % to the left or right. Reducing the opacity lets you see peak
shapes through other, closer peaks as though they were translucent.

Displaying an outline Displaying an outline box
box
Select Show Outline Box on the 3-D Visualization tab of the Properties
dialog box (available through Properties in the Edit menu) if you want the
outer limits of the 3-D image to be indicated by lines that form a bounding
box around the image.

CHAPTER
8
Linescan Mode
System 7’s Linescan Mode allows you to acquire an electron image and
linescan data. After the acquisition, analyze the linescan using the image
intensity cursor. You can save and load standard linescans in this mode
(with qualifications, as described in this section).
Note: Prior to a linescan acquisition, you must have knowledge of the sample’s
elements. This can be learned from a Spectral Imaging data set or Spectral
acquisition. If you already know the elements of interest you can mark them
on the periodic table.
Setting Linescan Acquisition Properties

To set up acquisition properties for the linescan:
1. Click the Acquisition Properties button on the Acquisition Toolbar.
2. Click the Linescan tab.
Field Description
These appear as data points in the linescan. The

Number of Points in general rule is to include at least one point per
Scan
micron.
Number of Scans The number of times the electron beam scans the
line.
The length of time the beam is placed at each

Dwell Time per Pixel
pixel location.
CHAPTER 8: LINESCAN MODE 123

Setting Up Linescan
Field Description
Elements
System 7 estimates the total acquisition time in
Acquisition Time
seconds.
System 7 estimates the total length of time per

Total Line Time
line in seconds.
Acquire video linescan data concurrently with

Acquire Video
region of interest data.
Acquire a new spectrum at each linescan point.

Save Spectra These spectra are saved to the Temp folder until
you save them to the project or delete them.
Setting Up Linescan Elements

There are several methods for specifying elements to include in the
linescan:
• Identification following analysis of a Spectral Imaging data set.
• Identification following a Spectrum or Point and Shoot Mode
acquisition and analysis.
• With Auto ID active, peak identification will run automatically and add
the elements.
• By directly marking elements in the Element Setup periodic table.
The goal of any of these methods is to complete the Element Setup periodic
table.
Note: The periodic table does not change when you switch analysis modes in
System 7. The elements you have identified are used to create the
linescan.
Acquiring a Linescan
Once the elements and acquisition properties have been defined:
1. Switch to Linescan Mode.
2. If you have not already acquired an image, click the Acquire Image
button .
3. Once the image is acquired, click on the image and draw the line
across the image.
4. Click on the Go button. The linescan acquisition will start and
data will appear in the linescan view.

Analyzing a Linescan
5. Either wait until the acquisition terminates according to the criteria set
up in the Linescan Acquisition Properties dialog box, or click the Stop
button on the Acquisition Toolbar.
To pause the acquisition, click the Pause button on the

Acquisition Toolbar. Click the Start button to resume.
Analyzing a Linescan
Once the linescan is acquired, the data appears in the top right view.
Image Intensity Element count values Linescan Cursor

Cursor
Linescan Mode
To analyze the linescan, click and drag either the image intensity cursor or
the Linescan cursor. The cursors are coordinated to move to the same
point.
CHAPTER 8: LINESCAN MODE 125

Saving Linescan Files Count values for each displayed element are shown below the linescan
graph, with colors and symbols to used delineate each element.
To remove or add elements from the graph, mark the elements on the
Element Setup periodic table as Identified or Excluded. (You cannot add an
element that was not previously acquired.)
To change the appearance of the linescan graph, right-click on the linescan.
In the Graph Properties box you can specify the linescan's title, color, and
display.
Linescan element data can be overlayed on the linescan in the image the
same as with Spectral Imaging Linescan extraction.
Saving Linescan Files

Files saved in Linescan Mode are stored as linescan files with a .lscan file
extension.
When you close a project, System 7 displays a list of files that have been
modified in the current session. Uncheck those files you DO NOT want
saved. Click OK to save the changes; click Cancel to close the Save box
and return to the project without saving any changes. You can change the
label in the same fashion as discussed in Spectrum Mode (Chapter 3)
Export as *.csv Files

Linescan data can be exported in the same fashion as extracted linescans
in Spectral Imaging Mode (Chapter 6)
Opening Linescan Files

1. Open the project and go to Linescan Mode.
2. Click on the linescan file in the file list view.
To open a file outside the current project:
2. In the Open box, navigate to the directory containing the file.
3. Click on the file and click Open.
The file is imported into the current project’s temporary directory. The
temporary directory is emptied when you close the project.

CHAPTER
9
Creating Reports
System 7 provides two methods for creating reports:
• Printer report generation
• Copy and paste reporting
Printer report generation is automatically set up in System 7. You can
customize the items you want to appear in the report and preview the report
before printing.
Copy and paste reporting uses a third party word processing, spread-
sheet, or page layout program to create the report. System 7 includes a
copy function that transfers the material in the current view into the
Windows clipboard for use by another program.
Setting Up a Printer Report

System 7 uses a Printer Page Setup dialog box to control the appearance
of the Printer Report. To access the dialog box, open the File menu and
select Page Setup.
This dialog box contains eight tabs for customizing the report.
Page Setup Dialog Box

In this box you can enter the report title and
company name and specify the page layout.
The different tabs refer to the different types of
data you can include in the report.
CHAPTER: 9: CREATING REPORTS 127

Setting Up a Printer Header — Manages the appearance text appearing on each report page,
Report and page numbering (use Margins tab to change font):
• User Name, Company Name, Title — These fields appear on each
page of the report.
• Pagination — Set to On if you want to print the current page number
and total page numbers: Page 1 of x.
• Logo — Specify a BMP file shown on every page.
• Logo Position — Enter the size of the logo as a percentage of the page
width.
Margins — Set the report margins and font used in Header/Footer.
Spectra — Determine System 7 spectral items appearing in the report.
• Type — Select Overlayed or Discreet. Check the Quant box if you want
Quant results printed with the report.
• Layout — If you checked Discreet for type, select the page layout for
the spectra.
• Quant Results — If you checked Quant Results, select the results you
want included. Click the Adv button and check the fields you want
included.
• B&W — Forces the spectrum into black and white for printing.
Point and Shoot — Determines the Point and Shoot items in the report.
• Layout — Select the page layout.
• Options — Check the items you want included in the report. Check the
Quant box if you want Quant results printed with the report.
• Quant Results — If you checked Quant Results in Options, select the
results you want included. Click the Adv button and check the fields
you want included.
• B&W — Forces the views into black and white for printing.
Compass — Determines the size of the image and spectrum, and image
information to appear on the report.
• Options — Check the items you want included in the report. Check the
Quant box if you want Quant results printed with the report.

Spectral Imaging — Determines the size of the image and spectrum, and Previewing and
image information to appear on the report. Printing Reports
• Options — Check the items you want included in the report.
• B&W — Forces the image and maps into black and white for printing.
Linescan — Determines the appearance of the linescan and the infor-
mation to appear on the report.
Images — Determines the size of the image and spectrum, and image
information to appear on the report.
• B&W — Forces the image into black and white for printing.
Phases — Determines the size of the image and associated spectrum of
phases
• B&W — Forces the image into black and white for printing.
Feature Sizing Results — Determines the appearance of the feature
sizing and the data on the report.
Previewing and Printing Reports

You can preview the report before sending it to the printer by clicking the
Print Preview button on the Main Toolbar (or from the File menu, select
Print Preview).
If the report is acceptable, send it to the printer from the preview by clicking
Print.
To print the report from the main System 7 screen, click the Print button
on the Main Toolbar (or from the File menu, select Print).
CHAPTER: 9: CREATING REPORTS 129

Copying Items to Copying Items to Third-party Programs
Third-party Programs
System 7 can copy any of the analysis and results views to the Windows
clipboard for use in third-party programs, such as Microsoft Excel or Power-
Point.
To export to Microsoft Word:
1. Click on the view you want to copy.
The selected view is outlined in yellow.
2. Click Export to Word . System 7 opens Word and pastes the

selected material, or you can Export to Power Point .
To copy material to a different third-party program.
1. Start the third-party program. Switch back to the System 7 window.
2. Click on the view you want to copy.
If the currently selected view is a spectrum, map, image, or linescan, it
is outlined with a yellow box.
3. Click the Copy button on the Main Toolbar. This places the
current view into the Windows Clipboard.
4. Switch to the third-party program (using Windows taskbar, Alt-tab, or
other method to switch programs).
5. In the third-party program, use Edit > Paste or Ctrl-V to paste the
copied material.
Edit the third-party document as needed.
6. To copy additional items, switch back to System 7 and select the next
view. Repeat the process above.

CHAPTER
10
Spectral Match
With Spectral Match optional software an unknown sample spectrum can be
searched against a database of previously identified spectra for quick identifi-
cation.
Before using spectral match, a database must first be created. From a large
spectral database, smaller databases may be created.
Creating a Database
Use Database Manager to manage spectral databases, including creating
them, adding spectra to them and organizing them into groups.
On the Analysis Setup tab click on the database browse button to open the
database manager.
CHAPTER 10: SPECTRAL MATCH 131

Creating a Database With the database manager you can add to the larger database from which you
create a subset of spectra to build, or create a new, a searchable database.
To begin you must first add, make available, spectral files for a match database.
(the match database is by default located in the C:\NSS Libraries\Matchdata-
bases folder, but you can put them anywhere). You can make available files
from a spectrum that is currently displayed (From Spectrum), or you can import
a spectrum from any project, or you can manually add a file, or you can add
from a CSV file of an analyzed spectrum.
From Spectrum: Open a spectral file in Spectrum mode. Click on From
Spectrum button. The infromation from the displayed spectrum will be added to
the available match files pull down box in the Database Manager.
Import: Clicking on the import button will bring up an Open window which you
can browse other projects or folders to import a spectrum and add to the
Available Match Files folder.
Manual: You can manually enter elements and composition to create a Match
file. Click on the Manual button to open a form for entering data. Enter the
elements and data type in the boxes. Then click Define for Match, then Close.
The file will be in the Available Match Files.

Creating a Database
From CSV: You can also enter spectral data into the Available Files from CSV
files. CSV files can be created directly through Batch Processing in Spectrum
mode. These files can then be used to create Available Files for Match. Click on
the From CSV button to open the Create Simulated Spectrum from CSV files
window. Select the desired file. Click on the Define for Match button to enter
into the Available Files pulldown box.

Creating a Match
Database
Creating a Match Database

After making spectra available for match, you can select a subset of available
spectra for specific use, or you can use them all.
1. Click on the Match Database browse button on the Analysis Setup tab.
2. In the Database Manager window, move the mouse to the Current
Database edit box and left click.
3. Type in a name for the database. The Create Database button will now be
active.

4. Click on the Create Database button. This will create a database with the Creating a Match Database
file name you typed in.
5. In the Available Match Files pulldown box, highlight the files you want to
add to the current database. Hold the Shift Key or CTRL Key to select
more than one file.
6. Click on the Add To Database button to move the selected files into the
Currently in Database box.
7. Click Close button to save the database. This database is now the active
database for Spectral Match.
Changing a Database
You can create a number of databases for convenient use. To activate a
database, click on the Match Database browse button in the Analysis Setup
tab.

Using Spectral Match In the Database Manager, click on the pulldown arrow in the Current Database
edit box. Select the desired database and click Close. This is now the active
database.
Using Spectral Match

After selecting and activating a Match database you can run spectral match
automatically or manually.
Manual match
1. Acquire or open a Spectrum
2. Click on the Spectral Match button in the Analysis
Toolbar.
3. Click on the Match Results tab in the Information pane to view results.

Automatic match Using Spectral Match
1. On the Processing tab in the Controls pane, click on the Auto Match
button in the spectrum results group to toggle on.
2. Spectral Match will be performed when you acquire or open a spectrum.
3. The results are displayed in the Match Results tab in the Information
pane.
In the Match Results tab, the matched spectra are listed in order of the least
Chi-squared value to the highest Chi-squared value. The lowest Chi-squared is
the best fit. A Chi-squared value of 0.0 is a perfect match.
Overlay match spectra

In the Match Results you can overlay the match spectra onto the unknown. The
Show All button will overlay all match spectra. You can also select one at a
time. Click on the box to the left (check box) of the desired spectrum. The Clear
All button will turn off all overlays.
Relabel Unknown button will name the unknown spectrum as “Matched as . . “

and with the name of the selected (highlight the name of the selected spectrum)
match name. Select a Match spectrum and left click the mouse button to select
a spectrum, then click the Relabel Unknown button.

Spectral Match Spectral Match Parameters
Parameters
Set spectral match parameters on the Analysis Setup tab, Match group.
Use Match Cuttoffs (eV) to set the low and high eV range. The defaults are 0
and 10000 (10 keV). These values work for most unknowns.
The number of match spectra is set in the Max. Number of Match Results edit
box. The default is 5 which is usually sufficient. However you can display more if
desired.
Set the maximum Chi-squared value in the Chi-square Cutoff edit box. The
default is 5 which works well for most unknows. However, you may need to
increase this number to include more matches. Generally, a Chi-squared value
of less than 10 may be a reasonable match. The number of background
channels greatly influences the Chi-squared values.
The active database is displayed in the Match Database edit box.

CHAPTER
11
Feature Sizing and

Chemical Typing
Feature Sizing is a System 7 option that lets you measure, count, and
identify particles of interest in a sample. Feature Sizing also includes
Chemical Typing, an advanced tool which allows classification of particles
by matching their quantitative chemical composition to a database of
Chemical Types you create in a Chemical Library.
Feature Sizing Setup Mode

Click on the Feature Sizing tab in the Navigation Pane to access the modes
in Feature Sizing and Chemical Typing. Click on the Setup icon to display
the Feature Sizing panes.
High (blue) and Low (green)

threshold cursors in Video Line
Profile Pane
Intensity line profile along line
High and low threshold cursors
Selected area histogram
CHAPTER 11: FEATURE SIZING AND CHEMICAL TYPING 139

Feature Sizing Setup Acquire Image For Feature Sizing
Mode 1. Select Feature Sizing tab in the Navigation Pane and click on the
Setup icon.
2. Setup microscope with sample at the optimal working distance for the
EDS detector.
3. Adjust microscope settings and obtain a good image of the sample
with features of interest in sharp focus.
Note: Adjust brightness and contrast to get a high contrast image.
Thresholding is much easier with highly contrasting features.
If the sample lends itself, use Backscatter detector (BEI) for
best result.
4. Setup parameters for image acquisition. Click on Acquisition
Properties button and select Imaging tab. Adjust image size and
dwell time for a low noise image.
5. Click on Average Image Acquire button and acquire image into
image pane in Feature Sizing.
Note: You can also acquire an image from Electron Imaging mode
in the Microanalysis Navigation Pane and then switch to
Feature Sizing.
Defining Particles (Thresholding)

To size or define features (particles or phases) to be analyzed, they first
must be segmented from the gray level image; that is, the image is bina-
rized to separate out the features of interest from the overall image. This
process is also referred to as thresholding. Thresholding is carried out by
defining the range of gray level intensity values which contain the intensities
of the desired feature(s) in the image. All pixels within these levels are then
set to 1 (turned on). Those values outside of the selected range are set to
zero (turned off). This process results in a black and white image (binary
image) with the selected features white and all other features black. Noran
System 7 does not display the binary image, but displays the features to
size in red (binary representation).
There are two tools to threshold an image in the System 7 software. (1) the
Video Line Profile intensity cursors, or (2) the Selected Area Histogram
intensity cursors. Both work in conjunction; thus, you can move back and
forth between the two panes to adjust the intensity range to segment just
those features you desire.

Example Using Video Line Profile Feature Sizing Setup
In this example, the image is of particles and has high contrast. Mode
1. Acquire or load the desired image.
2. To resize the Selected Area Box (yellow box in image), move the
mouse to a corner. The mouse will change to a double headed arrow.
Click and drag the corner to the desired size. In this example, the
default size is acceptable
3. To move the Selected Area Box, move the mouse into the box. The
mouse will change to 4-headed cross. Click and drag the box to
desired position. In this example, the default position is acceptable.
4. To move the Line Profile Cursor (horizontal yellow line), move the
mouse to the line. The mouse will change to a double headed arrow.
Click and drag the mouse vertically to desired position. In this
example, the Line Profile Cursor intersects a particle.
5. Adjust threshold. In the Video Line Profile Pane (top right pane), the
intensity histogram of the image along the Line Profile Cursor is
displayed. Move the high and low intensity cursors to desired intensity
range that includes (turn red) the features of interest.
Segmented particles in red
High and
low intensity cursors
Histogram across
line profile
Intensity range (from

cursors) in the Image
Processing group

Feature Sizing Setup Example Using Histogram With Two Phases
Mode This example has two phases. Using the selected area histogram pane
helps distinguish the phases. To add phases, click on the + button in the
Image Processing group (bottom right pane). Additional cursors are
displayed.
In this example, the

selected area
histogram gives
better phase
distinction than the
line profile.
To add an other
phase, click on the +
button in processing
group
Phase 1
Phase 1 and 2

To remove an intensity range, highlight the desired range in the Image Feature Sizing Setup
Processing group and click on the - (minus) button. Mode
Advanced Processing
At times, you may want to modify how features of interest are defined and
processed. There are two additional groups of parameters available which
modify how features are processed. These are Advanced Image
Processing and Advanced Particle Processing. These parameters are
referred to as sieves or filters. The sieves in Feature Sizing are cumulative,
meaning that particles must pass all filter criteria before being stored to the
data file.
Image Processing group
Thresholding intensity
range
Advanced Image
Processing button
Particle Processing group
Chemical Typing on/off
Advanced Particle
Processing button
Processing Pane
Advanced Image Processing

There are two subgroups of sieves under Advanced Imaging Processing:
Guard Region and basic particle Filters.
Guard Region
When features of interest lie on the edge of the image and are not fully
visible, some bias in the results occur because the overall size and shape of
these features cannot be determined. You can select a guard region to
avoid biasing data with partial features.

Feature Sizing Setup
Mode
Advanced Image Processing Group with Guard Region and Basic Filters
None
No guard region is used. All particles are included.
Center of Mass Guard Region

Any particle whose center of mass falls within the defined guard region is
excluded from analysis. This guard region is always a uniform region
around the frame. A rectangle (blue) appears in the image to represent the
guard region boundry. Use this sieve when your frames are not spatially
adjacent and complete coverage of the sample is not required.
Center of Mass
Guard Region
Excluded particle
Included particles

Stereological Guard Region Feature Sizing Setup
Any particle that is within or touches the guard region is excluded from Mode
analysis. The include region is always in the lower right portion of the frame.
This sieve is generally used when you have adjacent frames and you want
maximum sample coverage.
Guard region
Excluded Particle
Stereological Guard region
After selecting a guard region, define its width. You can either type in the
width in the Guard Region edit box, or select a size from the pull down
menu. You can also use the mouse and drag the region delimiting (blue)
line. The % width of the image (frame) is automatically calculated from the
image size.
Setting up a guard region

1. In the Image and Particle Processing pane under the Image
Processing group, click on the Advanced button and select the Guard
Region tab.
2. Select the desired Guard Region.
3. Adjust the size of the guard region, if desired. Enter a number, in
dimensions of the image, in the Guard Region Size edit box, or with
the mouse, drag the delimiting line to the desired position.
4. Click Close to save the selections and close the window.

Feature Sizing Setup Filters
Mode Guard region sieves exclude particles or features from analysis based
solely on their location within the frame. You can further exclude features
based on their size in pixels. Additional Advanced Image Processing
includes filling holes within particles, or separate particles that are touching
other particles.
Remove particles by pixel area

To eleminate particles that are small or noisy pixels, check the box next to
Remove particles with area less than or equal to:. The number of pixels in
the edit box are fixed at 1, 4, 9, and 16.
Fill holes
Runs a dilation filter to fill particles which have holes (voids) inside the
perimeter.
Separate Touching particles

There are four selections to separate touching particles: low, medium, high,
and custom. These selections are erosion/dilation filters with a different
number of passes. Custom separation allows the user to select the number
of passes. The number of erosions should equal the number of dilations or
the particles maybe larger or smaller than original size. Be aware that you
can erode or dilate in unequal numbers of passes.

Mode
Advanced Image Processing - Filters - Custom Separation
Particle Processing
In the particle processing group, there is only one check box and the
Advanced button. The check box turns Chemical Typing on or off. The
Advanced button brings up the Advanced Particle Processing dialog box
which allows control of what you want to measure in the sample, define
parameters used during chemical typing, set particle sieves, manage
spectra and image acquisitions for Extended Acquisitions, and set termi-
nation criteria for automated analysis.

Feature Sizing Setup The various parameters in Advanced Particle Processing dialog box is
Mode divided into five tabs: Morphology, Chemistry, Sieves, Extended Acquisi-
tions, and Termination.
Morphology Tab
Morphology refers to the size, shape and measurements of the particles of
interest. Morphology parameters are divided into two groupings, Particle
and Frame, and Analysis of Subparticles and Saving the locations and
microscope parameters for particles.
Particle parameters group
Parameter Metric Description

Particle area - Number of pixels in the particle
Area area times Pixel Size, in current units squared.
Sum of the distances between centers of

adjacent pixels on the particle perimeter, times
Dimensional perimeter pixel size, in current units. = 0.25 X (perimeter +
SqRoot(perimeter2 - 16 X area)).
circularity Circularity = Perimeter 2/(4πXArea), unitless.
Center of Mass - Average value of particle pixel

Location X X coordinates.
Reference- Coordinate for spectral acquisition at

particle center. Equals center of longest chord on
Y-reference.
Center of Mass - Average value of particle pixel

Y Y coordinates.
Reference - Coordinate for spectral acquisition at

particle center. Equals Y center of mass.
Projection of the particle on the X axis, in current

Feret X units.
Projection of the particle on the Y axis, in current

Y units.
Derived length of fiber/stringer, after it is

Fiber/ length straightened into a rectangle of equal area and
Stringer perimeter, in current units.

Parameter Metric Description Mode
Derived width of a fiber/stringer, after it is
width straightened into a rectangle of equal area and
perimeter, in current units.
aspect ratio = Length/Width, unitless. System 7

Fiber/ aspect ratio will apply parameters best suited to Fiber or
Stringer Stringer analysis.
Angle between the positive X axis and the

maximum particle projection, in degrees.
orientation Clockwise rotation from the X axis is a positive
orientation angle.
Maximum projection (maximum caliper

Projections max dimension) - Largest separation between points
on the particle convex perimeter, in current units.
Minimum projection (minimum caliper

dimension) - Shortest altitude of all triangles
drawn between pixels on the convex perimeter,
min in current units. Triangle bases are defined by
adjacent pixels and peaks be pixels on the
opposite side of particle.
Average of all triangle altitudes drawn between

mean pixels on the convex perimeter, in current units.
Standard Deviation - Standard deviation of all

sdv projections.

Internal perimeter adjacent pixels on the perimeters of particle
inclusions, times pixel size, in current units.
area Area (defined above) of particle inclusion(s).
count Number of discrete inclusions.
Number of pixels inside the particle convex

Convex area perimeter, times pixel size, in current units
squared.
circularity convex perimeter2/(4π X convex area), unitless.
Derived length of particle or fiber, after it is

straightened into a rectangle of equal area and
length perimeter, in current units.
= 0.25 X (convex perimeter + SqRoot(convex
perimeter2 - 16 X convex area)).

perimeter adjacent pixels on the particle convex perimeter,
times pixel size, in current units.

Feature Sizing Setup Frame parameters group
Mode
Parameter Metric Description

The total number of pixels in the frame, time the
Dimensional total area pixel size, in current units squared.
fractional area total area of particles which passed the sieve

covered by and guard region operations/ total area of frame,
particle unitless.
total number of particles which passed the sieve

number
Particles and guard region operations and saved to data
accepted file
number total number of particles which failed the sieve

rejected and guard region operations.
Microscope magnification Magnification value during acquisition
Stage coordinates during acquisition. X, Y, Z,

stage rotation, tilt and bank coordinates.
There are three ancillary parameters in the Morphology tab: Analyze

Subparticles, Return to Particle, and Measurement Units.
Analyze subparticles
Chords are the intersections of test line lengths with groups of pixels that
are turned on in a binarized image (particles). Feature Sizing scans the
image line by line, locates points where horizontal test lines intersect with
particles and then measures the length of each line segment or chord.
Feature sizing automatically determines chord length distributions for
particles.
A particle is composed of a number of smaller subparticles, as determined
by the intersections of the test lines (chords) with the particle. Checking the
Analyze Subparticles box will command System 7 software to run an
analysis on the subparticles of each particle that passes sieve and guard
region operations.
Return to particle
The Return to Particle setting automatically selects Location and Micro-
scope parameters to ensure that System 7 acquires the stage and beam
infomation it needs to visit a particle after analysis is complete. These
parameters provide the information for the “Move To” feature to set the
selected particle in the center of the field of view on the microscope.

Measurement units Running A Particle
This setting allows selection of the measurement units for reporting the Analysis
analyses.
Diagrammatic representation of
some parameters in Particle Sizing
Running A Particle Analysis

To preform a particle analysis, first setup all Sizing parameters, then select
Analysis icon in the navigation pane. Click the Run button to run the
analysis. Results of the analysis are displayed in the upper right and lower
right panes. Each analysis of an image is a frame. You can analyze an
image, change parameters and then analyze again. Each pass would be a
frame. The results of the analysis are stored in a file with the (Base)
Filename and extenstion *.siz.

Running A Particle The upper right pane has three tabs: 1) Histogram; 2) Image, and; 3)
Analysis Spectrum. The histogram is a graphic display of the distribution of all
particles within the frame.
The lower right pane has three tabs: 1) Particles; 2) Frames, and; 3)
Particle Count Summary.
Particles Found and Analyzed
Histogram of
Particle
Analysis
Particle
Analysis
Results
The Particle Results pane four controls at the botton of the pane: 1) Close
button which closes the *.siz file; 2) Move To button which moves the Stage
to the coordinates of the selected particle (highlight a particle then click
Move To button); 3) Apply Filter check box which filters the displayed data
(not the particle analysis filters), and; 4) Setup Filters button which sorts
and filters the displayed data.

Running A Particle
Analysis
Sizing File Control Buttons
Particle Results Pane
To change the displayed results, check the Apply Filters check box. The
filter parameters are setup using the Setup Filters button.
Setup Filters
Select the parameter to
use as the sieve from
the pull down menu.
Enter the low and high

values to filter the
displayed results.
Click on the + button to

add to filter edit box.
Check Apply filters box

to activate the sieve.

Chemical Typing Data display with
filter applied.
Data from display

shown above.
Chemical Typing
Chemical typing is a powerful EDS tool used in conjunction with Feature
Sizing. Features on a sample can be recognized and then chemically
analyzed and categorized into defined types.
The chemistry of sample features can be first “learned” and from the
learned chemistry, the features can be chemically categorized. In addition,
images of the specific features can be acquired and saved and spectra from
a specified chemistry can be acquired and saved.
Setting up for chemical typing

Before running chemical typing, Feature Sizing must be setup and a chem-
istry library created. Next, chemical parameters must be established. Finally
termination criteria are setup. This section describes setting the parameters
for preforming chemical typing on a sample.
Creating a chemical library

When System 7 software was installed, a directry was created for the
libraries that System 7 utilizes for various functions, such as Analysis with
Standards, Spectral Matching and Chemical Typing.
To create a chemical library, select the Chem Lib icon in the Feature Sizing
analysis group in the Navigation Pane. The Chem Lib mode provides for
various chemistry library functions.

Chemical Typing
NSS Libraries directory

and subdirectories
established when
System 7 was installed
Chem Lib Mode in the Feature Sizing group
1. In the Chem Lib mode, select (highlight) the Chem Lib folder.
2. Right click on the Chem Lib folder and select New Library from the
submenu to create a library. This folder will have a green folder
symbol and be named “New Library.”

Chemical Typing 3. Highlight the “New Library” in the upper left Chemical Libraries pane
and right click. Select rename from the Submenu. Type in the desired
name for this new library. The name will appear in the Name edit box
on the Chemical Library tab in the upper right Libraries Information
pane.
4. This chemical library is now available for use in Chemical Typing.
Setting up Chemistry parameters

On a new, unknown sample, the best starting place is to “Learn” the chem-
istry of all particles. Setup for this acquisition is simple.
1. In the Setup mode in Feature Sizing, click on the Chemical Typing
check box. In the Morphology tab be sure to check Return to Particle.
This sets the Reference X and Y of the particles.
2. From the pull down menu in the Particle Processing group select the
Chem Library to use.
Advanced
Particle
Processing
button
Activate Chemical Select the Library to use.

Typing. Check Box

3. Click on the Advanced button in the Particle Processing group. This Chemical Typing
will bring up the Advanced Particle Processing window.
4. On the Advanced Particle Processing window, select the Chemistry
tab.
5. On the Chemistry tab, check the box Learn unknown measured

particles. Leave the learn variance at the default 10% at this time.
6. Uncheck, if checked, Remove background.
7. Select either Classify Element rich or the multi-elements types first
buttons. With unknowns, the Multi-element types first is the better
choice.
8. In the EDS group, Acquisition time, enter the EDS acquisition time.
Generally a short acquisition time will make the analysis go faster. Be
aware of the count rate and pulse processor time constant when
entering an acquisition time.
9. In the Maximum Peak counts edit box, enter a maximum value for
peak counts. If any channel in the spectrum reaches this maximum
count before the acquisition time, the spectral acquisition will
terminate.
10.Select either Raster or Spot mode to acquire the spectrum. In Spot
mode the beam will be directed to the particle center of mass. In
Raster mode, the beam will raster over the shape of the particle.

Running Chemical 11.Check the check box Ignore spectra with insufficient data.
Typing 12.Enter a value in the edit box Spectrum must have max peak counts
>=. If the channel with the highest counts does not equal or exceed
this value, the spectrum is ignored. Generally, if a spectrum does not
have sufficient counts, peaks will be mis-identified which may result in
wrong chemical typing.
Running Chemical Typing

To run chemical typing, feature sizing must be preformed first. Particles will
be identified and analyzed. The center of mass and the shape and location,
along with any other parameters checked, of each particle will saved. The
beam will be directed to the center of mass (in spot acquisition) or rastered
over the particle (in raster acquisition) and the acquired spectrum analyzed.
Each unique spectrum (that is spectra with different chemistries) is saved
with file name “Learned (number).” If two particles have the same chem-
istry, the chemical type will be listed as the same “Learned (number).
1. Acquire an electron image.
2. Setup Feature Sizing parameters. On the Advanced Particle
Processing dialog box, Morphology tab, be sure to check Return to
Particle. This will force System 7 to include the reference location of
each particle to direct the beam for spectral acquisition.
3. Setup Chemical Typing parameters. On the Advanced Particle
Processing dialog box, Chemistry tab, be sure to check Learn
unknown measured particles. Also, be sure the acquisition time is
sufficient to acquire a good spectrum.
4. Click the Go button. The particles will be evaluated and spectra
acquired until all particles which pass the filters (sieves) are analyzed.
5. Results are displayed in the lower right Results pane.
The following figures display the results of two runs on an sample. The first
figure shows an unseccussful run in which the spectral acquisition time and/
or counts were not sufficient to chemically type the particle. The second
figure shows a successful run.

Running Chemical Typing
Results of Feature Sizing with Chemical Typing

Spectra with insufficient data to classify
Result of Feature Sizing with Chemical Typing

Spectra with sufficient data to classify

Advanced Feature and Advanced Feature and Chemistry Filtering
Chemistry Filtering
The above described Feature Sizing with Chemical Typing setup param-
eters are for simple processing. For some samples, advanced criteria for
processing and storing data are required to refine the analyses. In the
Setup mode, Particle Processing, Advanced dialog box, there are three
additional tabs for advanced filtering, saving and termination: 1) Sieves; 2)
Extended Acquisitions, and; 3) Termination.
Sieves
In advanced filtering, particles must pass ALL criteria to be included in
further processing. Virtually any or all morphological, chemistry types or
element concentrations can be used to restrict particle processing.
In this setup only particles that are between 0.5 and 50 square microns
AND (ALL criteria must pass) have a chemical type of Learn 2 will be
processed. All others will be ignored.

Extended acquisitions Advanced Feature and
On the Extended Acquisitions tab you can elect to save images of selected Chemistry Filtering
particles or save spectra from selected particles with any combination of
parameters.
In this setup images of particles that are between 1 and 30 square microns
in size OR (ANY of the critera must pass) have a copper content of 50 wt%
or more OR have a gold content of 50 wt% or more will be acquired and
saved.
In the Acquire and save spectrum group, a spectrum of acquisition param-

eters setup in Spectrum mode will be acquired and saved from particles that
have 60 wt% or more copper OR have 30 wt% or more of gold.

Advanced Feature and Termination
Chemistry Filtering On this tab, you can elect to stop the analysis if certain criteria are met.
These criteria are usually by number of particles and the number of frames
analyzed. Generally, after 100 or so particles have been processed, the
analysis is terminated. The number of particles is usually determined to be
a statistically valid number of particle samples.

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5225 Verona Road

Revision Revision date Principal changes Software version

A September 2002 First publication System SIX 1.1

B February 2004 Revised edition System SIX 1.4

E January 2007 Revised edition System SIX II 2.0

F August 2007 Revised edition - Build 31 System SIX II 2.0

G November 2008 Revised edition System 7 2.2

© 2008 Thermo Fisher Scientific. All rights reserved.

Syste SIX and System 7 are trademarks of Thermo Fisher Scientific.

II NORAN SYSTEM 7 TRAINING GUIDE

TABLE OF CONTENTS iii

IV NORAN SYSTEM 7 TRAINING GUIDE

• Liquid nitrogen cooled X-ray (SiLi) detector

CHAPTER 1: TOUR OF SYSTEM 7 SOFTWARE INTERFACE 1

2 NORAN SYSTEM 7 TRAINING GUIDE

Image Cursor Info

Menus Windows Control

Analysis Mapping Cursor

Image Mapping View

System 7 Spectral Imaging Mode with Associated Panes

CHAPTER 1: TOUR OF SYSTEM 7 SOFTWARE INTERFACE 3

Arranging the Screen

Changing the size of window panes

Resizing top/bottom panes

Resizing all panes

4 NORAN SYSTEM 7 TRAINING GUIDE

Control Bar (moves toolbars)

Saving Your Rearranged Screen

CHAPTER 1: TOUR OF SYSTEM 7 SOFTWARE INTERFACE 5

Menu Selection Function

File Project Explorer.. Opens the Project Explorer dialog box to

Close Project Closes the current project.

Create Creates a new template from the current

System Security Password protects service screens from

Open... Opens the dialog box to select a file to

Close Closes the current file.

Save Saves the current file under its current

Save Map File Opens the Save As dialog box to save an

Export Image as Exports an image as a Comma Separated

Page Setup... Opens a tabbed series of dialog boxes to

Print Preview Displays the pages as they will appear

Print Prints the current selection or report.

Export to Word Copies the current data, opens Microsoft

Export to Power Copies the current data, opens Microsoft

6 NORAN SYSTEM 7 TRAINING GUIDE

File Compress SI File Opens Dialog box to select and compress

Exit Closes System 7 software.

Edit Undo Undoes the previous act.

Cut Cuts the selected data, when available.

Copy Copies the selected data, when available,

Copy To.. Saves selected window pane in JPEG

Paste Pastes the copied or cut data.

Acquisition Displays the Acquisition Properties dialog

Microscope Displays the Microscope Parameters

Properties... Displays the Properties tabs for all views

Reset Project Restores the project to the template’s

Language Selects language for displays

View Restore Toolbar Restores all Toolbars that have been

Status Bar Toggles the status bar on/off. To select

Drift Diagnostics Displays dialog window of drift

CHAPTER 1: TOUR OF SYSTEM 7 SOFTWARE INTERFACE 7

Spectrum sizing functions These commands coordinate with the