Thermo Scientific Apreo Mounting instructions

Apreo
User Operation
Manual
Revision A
Mar-2018

Trademark Acknowledgments
Microsoft® and Windows are registered trademarks of Microsoft Corporation.
This manual was produced using FrameMaker™ document publishing software.
FrameMaker™ and Adobe are registered trademarks of Adobe Systems Incorporated.
Other product and company names mentioned herein may be trademarks of their respective owners.
Copyright © 2018 by Thermo Fisher Scientific Company
The information and materials contained herein are confidential and proprietary to Thermo Fisher Scientific Company.
They are provided for your organization's internal use on a need-to-know basis.
They cannot be duplicated or disseminated for any third party without the express consent of
Thermo Fisher Scientific Company.
Limited Rights
Contractor Name:
Thermo Fisher Scientific
Contractor Address:
5350 NE Dawson Creek Drive, Hillsboro, Oregon 97124, USA
The Government's rights to use, modify, reproduce, release, perform, show, or disclose these technical data
are restricted to those rights specified in:
DFARS 252.227-7015(b)(2), FAR 52.227-14(g)(2) (Alternate II) and FAR 12.211.
Any reproduction of technical data or portions thereof marked with this legend
must also reproduce the markings.
Any person, other than the Government, who has been provided access to such data,
must promptly notify the above named Contractor.
Manufacturer & Technical support
To provide feedback on this document, please submit via
http://www.Thermofisher.com/EM-Sales

CONFIDENTIAL – limited rights User Manual
Revision A Feb 2018
C-i
Table of contents
Chapter 1 System overview
User manuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
Apreo User safety manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
User operation manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
System capabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-2
System performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
Chapter 2 System control
System layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
Other software and hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
Interface elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
Mains switchboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
System states . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
System startup. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
Overnight and Standby . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6
System shutdown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-8
Vacuum system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9
Vacuum status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-10
Vacuum modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
Equipment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-13
Detector types and application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-13
Stages and accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-14
Chapter 3 Software control
Software interface elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Icons. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Tooltips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Pull-down menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Command buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Property editor. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Edit boxes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Radio buttons / Check boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Adjusters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
2D controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Modules. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Dialogs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Tabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Progress bars. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
xT microscope Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
Microscope Control. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
Workspace customization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
Menu bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-9
Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-23
Imaging area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-27
Status bar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-29
Control pages and modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-30
Preferences dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-38
Account Manager application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-49
Accounts control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-49
User Logins and Account Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-51

Table of contents
User Manual CONFIDENTIAL – limited rights
Feb 2018 Revision A
C-ii
Entering commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-52
Using mouse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-52
Using keyboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-53
Chapter 4 Alignments
Common Rules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
Buttons and Control Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
Alignments List. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
Automatic Alignments. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3
Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4
5 - Emitter Startup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-5
Stage Alignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-6
154 - Water Bottle Venting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-7
Plasma Cleaning / External Plasma Cleaning . . . . . . . . . . . . . . . . . . . . . . . . . . 4-8
Pump Buffer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-9
Vacuum Actions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-10
254 – GIS Alignment (option) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-11
E-Column: Immersion Lens Mode Alignments . . . . . . . . . . . . . . . . . . . . . . . . . .4-12
E-Column: Lov Vac Alignments. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-13
Magnification Correction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-14
E-Column: Aperture Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-15
E-Column: Preventive Maintenance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-16
E-Column: Supervisor Alignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-17
Chapter 5 Operating Procedures
Specimen Preparation and Handling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Needed Items. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Natural Specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Coated Specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Mounting Specimen on Holder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Specimen Baking Unit. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-3
Microscope Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6
Operation Pre-Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6
Inserting / Exchanging Specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Selecting Vacuum Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Imaging Onscreen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8
Optimizing Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
Principles of SEM Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
Magnification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
Scan Speed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-10
Contrast & Brightness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-10
Focusing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
Correcting Astigmatism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
Direct Adjustments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-12
Digital Imaging Enhancement / Imaging Mixing / Coloring . . . . . . . . . . . . . . . . . . . . . . 5-13
Accelerating Voltage and Beam Currents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-15
Column Use cases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-16
Standard Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-17
Retractable Detectors Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
Infrared CCD Camera . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
Everhart Thornley Detector (ETD) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-18
Low Vacuum Detector (LVD) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-18
Trinity Detectors T1 / T2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-19
T1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-19
T2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-19
T3 (option) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-19
Beam Deceleration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-20

Table of contents
C-iii
CONFIDENTIAL – limited rights User Manual
Revision A Feb 2018
Detection Principles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-20
Beam Deceleration module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-21
Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-22
Stage Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-23
Eucentric Position . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-23
Software control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-25
Stage Related Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-29
Capturing and Handling Single Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-36
Image Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-36
Saving / Opening / Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-37
Recording Movies (Saving Multiple Images) . . . . . . . . . . . . . . . . . . . . . . . . . . 5-38
Movie Settings Dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-38
Movie Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-40
Movie Creator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-41
Patterns / Measurements / Annotations. . . . . . . . . . . . . . . . . . . . . . . . . . . .5-44
Chapter 6 Maintenance
Cleaning procedures overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
List of applied cleaners . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
Cleaning column parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
Materials and technique . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
Cleaning stage mechanics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
Cleaning stage parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
Refilling water bottle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Chapter 7 System Options
Manual User Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
Joystick . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
Uninterruptible Power Supply (UPS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-3
Optional Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-4
Optional detectors connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-4
Trinity Detector T3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-4
Directional Gaseous Analytical Detector (GAD). . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-5
Directional Backscattered Detector (DBS) – 
Angular Backscattered Detector (ABS) 
Concentric Backscattered Detector (CBS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-7
Retractable Annular Scanning Transmission Electron Microscopy Detector 
(STEM 3 / STEM 3+) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-8
Nav-Cam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-11
Capturing Navigation Image Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-11
External Current Measurement (Keithley Picoamper Meter) . . . . . . . . . . . . . . . . . . . 7-12
Energy Dispersive X-ray (EDX) Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-13
High Vacuum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-13
Low Vacuum EDX Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-13
STEM EDX Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-13
Patterning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-14
Patterning Control module. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-15
Patterns Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-18
Gas Injection module (option) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-20
Application Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-21
Remote Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-22
Connection to Microscope PC. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-22
Quick Loader. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-24
Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-24
Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-27
Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-28
UMB Stub Holder Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-29

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C-iv
CryoCleanerEC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-30
Parts and Accessories. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-30
CryoCleaner Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-31
Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-32
Spare Vessel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-32
Plasma Cleaner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-33
Sample Cleaning Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-34
Chamber Cleaning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-34

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System overview
User manuals
Apreo User safety manual
The safety manual provides information for personal safety and maintenance procedures while
operating this system.
This manual is required reading for the end user.
User operation manual
The User Manual is delivered as an electronic PDF file only. However, it is possible to print parts of the manual if
this is desired.
We recommend reading the appropriate User Manual section before operating any microscope function. Most
importantly, you should locate the topics necessary to operate the microscope in the proper way to safely achieve
the best results.
The manual is divided into the following chapters:
1. System overview (this chapter) 
gives an overview of the user manual and system capabilities.
2. System control 
describes the system hardware (interface elements, vacuum system, system states, equipment).
3. Software control 
describes the interface that sets and controls system operation; gives the function of each tool, menu item and
control page.
4. Alignments 
explains how to align the equipment to achieve the optimal performance.
5. Operating procedures 
gives procedures for how to use the system’s features.
6. Maintenance 
gives allowed step by step cleaning and maintenance procedures.
7. System options 
explains relevant options that can be integrated into or added as accessories to the system.
One can take advantage of the search and navigation possibilities within the PDF file. In addition, the following
conventions are applied:
•A reference to the specific software element is highlighted in italics. For instance: 
“Clear the Stage menu / Beam Shift Reset item.”
•Some software functions use shortcuts, which are given beside the heading in brackets. 
For instance: Save (Ctrl + S). They are also given in the Help menu / Keyboard Shortcuts.

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System capabilities
The Apreo is a Scanning Electron Microscope (SEM) that produces enlarged images of a variety of specimens,
achieving magnification over 100 000× and provides high resolution imaging in a digital format. The instrument
provides optimum throughput, resolution and automation.
This important and widely used analytical tool provides exceptional field of view, requires minimal specimen
preparation, and has the ability to combine the technique with X-ray microanalysis.
The instrument provide an expanded range of capabilities:
•High-resolution electron beam images
•High resolution elemental microanalysis of defect cross sections
•Imaging of sample surfaces with the electron beam during navigation without erosion
System performance
The main instrument components used for imaging of the samples are:
•Electron source 
The beam of electrons (particles) is emitted within a small spatial volume with a small angular spread and
selectable energy.
•Lens system 
The beam enters the lens system consisting of several electromagnetic or electrostatic lenses and exits to hit
the specimen surface.
•Scan unit 
The scan generator signal, fed to the deflection systems, moves the beam in a raster pattern over the specimen
area. This signal, modulated by the detection system signal, produces the onscreen image of the specimen’s
surface.
•Detection unit 
Particles (electrons) striking the specimen react with atoms of the sample’s surface in various manners to
produce electrons and photons (X-rays).
The detector system picks up the particles or photons and converts them into a digital signal that is then sent to
the control PC and shown on the monitor.

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FIGURE 1-1: Column schematic overview
Computer control
The xT microscope Server and Microscope Control (User Interface) software integrate SEM functionality within a
Windows 7 operating environment.
This software consists of programs defining specific instrument settings for particular applications, ensuring
reproducibility of complex procedures (for instance imaging, management of image capture, storage, and data
output devices etc.). They also control instrument hardware (the column, detector(s), stage, EDX, vacuum
functions etc.).
Vacuum system
The entire particle path from a source to a specimen must be under vacuum so that the particles do not collide with
air molecules.
Various levels of vacuum are necessary, so a Turbo Molecular Pump (TMP) backed by a scroll pre-vacuum pump
(PVP) obtains the necessary specimen chamber pressure.
High Vacuum (HiVac) mode
This is the conventional operating mode associated with all scanning electron microscopes.
Low Vacuum (LoVac) mode
In the gaseous mode the electron column is under lower pressure than the specimen chamber. This mode can use
water vapors from a built-in water reservoir, or an auxiliary gas that is supplied by a user and connected to the gas
inlet provided for this purpose. Observation of outgassing or highly charging materials can be made using this
mode without the need to metal coat the sample, which would be necessary for the conventional HiVac mode.
Stage
The Apreo has a computer-controlled high-accuracy five-axis stage for small samples. It offers precision specimen
computer controlled manipulation and automation of all axes for overall spatial orientation on highly repetitive or
extremely irregular samples.
Specimen exchanges take place through a chamber door that exposes the specimen stage when opened or through
the Quick Loader (option). An exchange time takes a few minutes; with the Quick Loader, an exchange is much
faster. Software and interlocks protect the system against damage and users against an injury.
Electron
CONDENSER
LENS(ES)
SCAN GENERATOR M
FINAL LENS
DEFLECTION
SYSTEM
SCAN UNIT
SPECIMEN
DETECTION UNIT
DETECTOR
LENS SYSTEM
Source

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Image viewing and capture
Because the amplified detector signal is shown synchronously with the beam scanning, there is a relationship
between brightness of an image point on the monitor screen and the signal detected at the corresponding point on
the specimen.
Magnification is the ratio of the size of the viewing monitor screen to the size of the area scanned on the specimen.
Higher magnification is achieved by reducing the size of the area scanned on the specimen.
Gas injection system (GIS)
Multiple GIS (option) can be installed for material deposition in conjunction with electron beam pattern definition.
Electron beam-induced deposition offers the advantage of not sputtering of the deposited material.
Several GIS chemistries can be installed on the instrument, depending on system configuration. This self-contained
apparatus allows the material to be contained entirely within the vacuum system for simple, flexible, and safe
operation.
Analysis capability
Convergence of the SEM and X-ray detection system (e.g.
EDX – Energy Dispersive X-ray – option) at a short
working distance allows precision chemical analysis at
high resolution of surface and subsurface features.
Various vendor options are compatible with the
instrument (see Chapter 7).

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System control
This chapter describes the layout of the system, interface elements and equipment.
System layout
The basic system layout is based around the dedicated Microscope computer with the LCD monitor and
Microscope console. Optionally it is possible to have a second LCD monitor with the Microscope computer or the
Support computer, using the LCD monitor and the switch box with keyboard and mouse to switch between the two
computers.
FIGURE 2-1: Apreo standard layout scheme
Caution! 
If the equipment is used in a manner not specified by the manufacturer, the protection provided by the equipment may be
impaired.
Mains power must be connected to a grounded socket that is visible and easily accessible!
A user must not disconnect any parts of the equipment or connect any equipment not approved in this manual or in the
Apreo User safety manual!
All power and external equipment connectors should be covered by stoppers (part of delivery) when not used!
Other software and hardware
Call Customer Service for advice before installing software or hardware that is not required for system operation.
Other software, such as screen savers or hardware network cards, may corrupt the xT microscope Server /
Microscope Control software under some circumstances and may invalidate the warranty.
For more detailed information about Windows 7™, refer to the Microsoft® Windows™ User’s Guide shipped with
your system.

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Interface elements
Software
The software control contains graphics applications within the Windows 7™ operating environment:
•xT microscope Server: starts and stops basic microscope functions
•Microscope Control (UI – User Interface): controls all system functions including imaging, image
and movie gathering / manipulation / output, detection and analysis, scanning, magnification,
stage navigation, chamber and column pressure, etc.
•User Management: ensures users admission to both the operating system, Windows 7, and the
Microscope Control software
For information on all the features of these applications see Chapter 3.
Password policy
After the software installation there are two initial users / passwords common for the OS Windows and the
Microscope Control software (UI):
•User: supervisor / Password: supervisor
•User: user / Password: user
The first time logging into the Windows 7 operating system, a user is automatically forced to change his or her
password. After that the UI accepts it and enables logging in from that point on.
Each password (either for any new user or after the 90 day period expiration) has to meet the following conditions:
•at least 7 characters long
•the stem must be significantly different from a previous password and shouldn't contain a complete dictionary
word or user name
•must contain at least one character from each of these character groups:
– Uppercase letter 
– Lowercase letter 
– Number 
– Symbol (/, *, –,+ etc.)
Hardware
The system is computer-controlled. As such, it has a Microscope Computer that must be turned on (use the power
button on the PC) to operate the microscope by means of the software. The
support computer (option) can hold some
other software utilities. The
switch box switches the keyboard and the mouse to either of the two computers. The
control software facilities and data are shown graphically on the
LCD monitor and are superimposed around and on
the image. The other LCD monitor is used either as an extended desktop of the Microscope computer or as the
Support computer monitor. To control software utilities, one can use a
keyboard , a mouse , the joystick (option) or the
Manual User Interface (option).
Power button
The console / system power is activated by pressing the power button located on the microscope console front
panel. This switches the sub-systems on and allows the interface and communication with the Microscope
computer, from which most of the functions are activated via the software control.
The power button indicates several system states:
•green lit – the Full Operation state
•amber lit – the Standby system state
•not lit – the Complete shutdown system state
FIGURE 2-2: Control panel Power button

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External connectors panel
The External connectors panel is located on the back of
the microscope console.
It is used to connect 3rd party equipment to the
following connectors:
CONTROL SIGNALS / E-BEAM SCAN INPUT / VIDEO
OUT
These connectors are used for the connection of EDX,
WDX and lithography systems, provided by 3rd party
suppliers. Do not connect anything else to these
connectors!
SPECIMEN CURRENT
This connector is used together with the Keithley
picoamper meter (option) equipment.
Ground point
The point is intended for a defined ground connection
between a microscope and a 3rd party module. This
connection is not a safe ground!
ELPHY SCAN & BLANKING IN
Not used.
Mains switchboard
Power off
The system has protection against power failures in the sense that the different components of the system are not
likely to be damaged. However, a power failure is never good for the system. It might affect the ultrahigh vacuum
levels of the columns and the overall stability of the system.
Take sufficient measures to avoid power failures. If a power failure occurs while the instrument is completely
operational, the microscope enters a safe state and the following happens:
•Electron accelerating voltage is switched off.
•Electron emission is switched off.
•The specimen chamber automatically vents gently.
The vacuum in the instrument is no longer supported by running pumps. The column isolating valves close to
save the vacuum in the source area.
•The microscope computer and the support computer are switched off. The momentary adjustments of all
system parameters (accelerating voltage, magnification, stage positions, etc.) are lost if they were not saved.
Note 
If mains failures occur occasionally, using the Uninterruptible power supply (UPS – option) is recommended.

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Emergency off
To switch off the electrical power completely in case of emergency, follow this quick and safe procedure:
1. Push the red EMERGENCY OFF (EMO) button (option – see the Apreo User safety manual).
If the button is not installed proceed as follows:
2. Switch off the breaker switch labeled Main switch S1 at the cabinet back, which is placed at the very left side of
the row of three, or disconnect the power cord labeled Main input 230 VAC.
FIGURE 2-3: Mains switch board
If this is not easily accessible:
3. Turn off the mains wall switch (if present), and / or disconnect the mains plug from the mains socket.
WARNING! 
The microscope console water chiller (option – separate device in the microscope vicinity) is powered separately via its
individual power cord. Hazardous voltages may be present in this equipment even when the microscope power plug is
disconnected!

System control: System states
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System states
There are several system states:
•Complete shutdown – for service and emergency reasons
•Standby – for when the system will not be used for a longer period
•Overnight – for when the system will not be used overnight
•Full operation – when the system working
The Complete shutdown system state can be set only by a supervisor. 
See the detailed descriptions of all of the following processes and elements further in this manual.
System startup
In the Complete shutdown state the system is disconnected from all sources used for an operation. Connect the
following sources:
•electrical – power cord
•pneumatic – compressed air inlet
•cooling water – hose flanges
•operating gas – nitrogen inlet
The amber color Power button on the Microscope console panel
starts to shine.
To bring the system to the Full operation state, follow this procedure:
1. Push the amber Power button on the Microscope console panel
– it changes to green (a).
2. Switch on the Microscope computer. The operating system,
(b) Windows 7™, loads and shows the appropriate icons on the
monitor desktop.
3. Double-click the xT microscope Server icon to start the software
(all visible LED’s should be green – Initialized).
4. Click the Start button to start the server. Wait until all
elements are fully functional (green – Initialized).
5. Click the Start UI button to start the Microscope Control
software. The main window appears behind the UI Log On
dialog.
Note 
This step can take place automatically, if the Advanced / Autorun
UI check box has been ticked.
6. Enter your Username and Password (b).
7. Start the electron column IGP pumps using the 5 - Emitter
Startup alignment – Step 1 of 2. This procedure takes a few
minutes and the final IGP Upper pressure should be 
< 5.10-7 Pa to start the emitter.
8. Switch on the Emitter using the 5 - Emitter Startup alignment –
Step 2 of 2. This procedure can take about 2 or 40 minutes
(short or long procedure), depending on the emitter’s conditions. 
If this is not possible, call service!

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9. Select the desired Vacuum module / Vacuum mode radio button
and click on the Vacuum module / Pump Button. Wait for the
Pumped status.
10. Click on the Column module / Beam On button to start the
beam. The source awaking progress bar indicates the actual
status. The button turns orange when finished.
See Chapter 5 to set the desired imaging conditions.
Note 
a) When switching the console on (starting from the Standby state),
the SEM aperture becomes heated. It may take several (5 – 10)
minutes before it is at the proper temperature. Do not make any
adjustments during this interval (aperture, source or lens alignment)!
The microscope could become misaligned when the aperture reaches
the operational temperature.
b) Once you have your microscope user account set up via the User
management software or by the account administrator (see Chapter
3), you can use your name and password to access both the
Windows 7 system and the Microscope Control software. Take note of
the Password policy (see above), which helps protect individual settings and results.
c) Usually, the system remains on with the vacuum system in operation, but typically the emitter and accelerating voltage
remain off. The system starts with the setting last in use when the Microscope Control software was closed. This allows
quick resumption of daily operation.
Overnight and Standby
In the Full operation state all microscope equipment and accessories are in use or are ready to use. When leaving
the system, we advise bringing it to the Overnight state by following this procedure:
1. Click on the Column module / Beam On button to switch off the beam.
2. If you need to remove a sample, select the Stage menu / Tilt 0° (Ctrl + E). Click on the Vacuum module / Vent
button. Wait for the Vented status, then remove your sample.
3. Click on the Vacuum module / Pump button to pump to the High Vacuum. (d)
Select (e) the File menu / Log Off “present user”; the Log On dialog appears
for entering another one. Switch off the monitor.
Now the system is in the Overnight state. To proceed to the Standby state,
follow this procedure:
4. Click on the xT microscope Server window / Standby button.
This stops the UI, the xT microscope Server application services and
switches off the console (the green power button on the microscope
front control panel changes to the amber button).
In the Standby state, electron emission remains on, and the chamber vacuum
is maintained by running vacuum pumps.

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To bring the system back to operation, follow this procedure:
Caution! 
When the Standby state was just entered, wait a minimum of 10 seconds before starting the microscope operation again
(by pressing the power button on the microscope front control panel)!
1. Push the amber Power button on the Microscope console panel
– it changes to green (a).
2. Double-click on the xT microscope Server icon to start the
software (all visible LED’s should be green – Initialized).
3. Click on the Start button to start the server. Wait until all
elements are fully functional (green – Initialized).
4. Click on the Start UI button to start the Microscope Control
software. The main window appears behind the UI Log On
dialog.
Note 
This step can take place automatically, if the Advanced / Autorun
UI check box has been ticked.
Now the system is in the Overnight state. To proceed to the Full
operation state, follow this procedure:
5. Enter your Username and a Password (b).
6. Click on the Column module / Beam On button to start the
beam. The source awaking progress bar indicates the actual
status and the button turns orange when finished.
Note
d) We strongly recommend always leaving the chamber evacuated
when it is not being used. When the sample chamber is left in the
LoVac mode, water vapor is likely to accumulate in it, PVP lifetime
decreases, and the water reservoir or gas cylinder empties prematurely.
e) Waiting for a new user leaves the status of the Microscope Control
software non-operational and only the xT microscope Server software
is running. Therefore changing users does not require Logging off /
Logging on at the Windows 7™ level.

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System shutdown
In case of emergency, bring the system to the Complete shutdown state by following this procedure:
1. Click on the Column module / Beam On button to stop the
accelerating voltage. A Column module / Source progress bar
indicates the actual status; the button turns gray when
finished.
2. Click on the Vacuum module / Vent button to vent the chamber.
3. Switch off the Emitter with the use of the 5 - Emitter Startup
alignment – Step 2 of 2. (f)
4. Click on the xT microscope Server software / Standby button.
This stops the UI, the xT microscope Server application
services, and the console (the green power button on the
microscope front control panel changes to amber). (g)
5. Shut down Windows 7™ and switch off the monitor.
6. If needed, disconnect the power cord and any other input /
output used. (h)
Note
f) Switching off the console when the Emitter is on is not optimal for
the emitter – it may deteriorate its filament lifetime.
g) The system can be left in this state if electrical power is supplied to
the instrument because the pumps are running and pumping the
column.
h)
The Complete shutdown procedure brings the system to the non-
powered state, in which the vacuum in the column area is no longer
supported by running pumps. All valves are closed, and the electron
column and specimen chamber areas are vented. Normally this is used
for system transportation or for service actions, such as repair to
essential systems (electrical and air supplies).

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Vacuum system
Model difference
There are the High Vacuum and Low Vacuum variations of the
Apreo system. This manual describes the Low Vacuum model.
For the High Vacuum model, some controls are missing and
functionality is modified accordingly.
The system has the these vacuum sections:
•Electron source
•Electron column
•Specimen chamber
When in operation, the electron source and column section are
always under high vacuum. The specimen chamber is at the
pressure required for the given state (Pump / Vent) or mode
(HiVac / LoVac).
Note 
When the LoVac mode is chosen, the ChIV is closed. All valve and
pump operations are fully automatic.
FIGURE 2-4: Apreo high vacuum / Apreo low vacuum Vacuum system
AGV . . . . . . Auxiliary Gass Valve
BPV . . . . . . . By Pass Valve
BG . . . . . . . . Buffer Gauge
BV . . . . . . . . Buffer Valve
CIV . . . . . . . Column Isolation Valve
ChEV . . . . . . Chamber Evacuation Valve
ChIV . . . . . . Chamber Isolation Valve
EG . . . . . . . . Environment Gauge
HVG . . . . . . High Vacuum Gauge
IGP . . . . . . . .Ion Getter Pump
NAV . . . . . . .Nitrogen Admittance Valve
NVC . . . . . . .Needle Valve Control
PVP . . . . . . .Pre Vacuum Pump
SIV . . . . . . . .Servo Isolation Valve
TMP . . . . . . .Turbo Molecular Pump
TVV . . . . . . .Turbo Venting Valve
VV . . . . . . . .Venting Valve
WBV . . . . . .Water Bottle Valve

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Vacuum status
The vacuum status controls are in the Vacuum module. The Pump
button starts pumping the chamber for the operating pressure
and the Vent button starts venting the chamber for a sample
exchange.
At the bottom right side of the status bar the actual vacuum
status is represented by the colored icon, which may have three
possible colors with the following meanings:
•Green: PUMPED to a desired vacuum mode
•Orange: TRANSITION between vacuum modes 
(pumping / venting / purging)
•Gray: VENTED to atmospheric pressure
Pump button
When the Pump button is clicked and the status is Vented or when changing the vacuum mode, the system starts to
pump. The target pressure depends on the selected vacuum mode. The Pump button is highlighted and is not
accessible.
For High Vacuum, the system achieves the lowest pressure possible. For Low Vacuum, it achieves the pressure
specified in the Vacuum module / Chamber Pressure adjuster. The purge function can be defined in the Preferences…
dialogue / Low Vacuum tab (see Chapter 3).
When the Pump button is clicked and the status is Transition (venting), the venting procedure stops and the system
immediately starts to pump to the actually selected vacuum mode.
Vent button
When the Vent button is clicked and the status is Pumped, the
confirmation dialog appears. After confirmation, the system
switches off the detector voltages, high voltage supplies, vacuum
pumps and uses the appropriate valves to vent the system with
the use of the dry nitrogen brought to the Nitrogen Inlet. Nitrogen
is recommended to obtain a better vacuum for high resolution
imaging in HiVac mode.
The Sample Exchange window and progress bar are shown; the
Vent button is highlighted but not accessible. After a specified venting time, the venting valve closes and the
vacuum status should indicate Vented (see Preferences… dialogue / General tab / Venting valve opening time item).
The chamber door can be opened and the button is again enabled.
When the Vent button is clicked and the status is Transition (pumping), this dialog appears. After confirmation, the
pumping procedure stops and the venting procedure starts.
When the Vent button is clicked and the status is Vented, this dialog appears. After confirmation, the venting valves
re-open for the specified venting time and then the valves close.
Note 
If you vent the system in order to change a detector, wait until the icon with a gray specimen chamber appears in the Status
module. Otherwise there is a risk of a detector assessment malfunction, and as a result, the PLA will not be known by the
system.