Asylum Research cypher User manual

Cypher SPM User Guide
USER GUIDE 2
Cypher User Guide
Including beta (complete, reviewed) chapters. Including draft (nearly complete, not
reviewed) chapters.
Version 13, Revision: A-1714
Dated 10/25/2013
Asylum Research
an Oxford Instruments company

Contents Contents
Contents
I System Overview and Powering Up .............................. 1
1 System Overview ....................................... 3
2 System Power Up ....................................... 10
II Standard Scanner ......................................... 12
3 Standard Scanner Overview .................................. 15
4 Tutorial: AC Mode in Air, Std. Scanner ............................ 17
5 Cantilever Holder Guide .................................... 49
6 Fluid Imaging in a Droplet ................................... 53
7 iDrive Imaging ......................................... 75
8 Conductive AFM (ORCA) ................................... 92
9 Scanning Tunneling Microscopy ............................... 103
III Environmental Scanner ...................................... 113
10 Environmental Scanner Overview ............................... 115
11 Tutorial: AC Mode in Air, ES .................................. 130
12 Cantilever Holder Guide .................................... 141
13 Cell Body and Sample Stage Guide .............................. 147
14 Gas Handling and Leak Testing ................................ 173
15 Conductive AFM ........................................ 178
IV Chassis and Enclosure ...................................... 181
16 Tutorial: Scanner Exchange .................................. 183
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Contents Contents
17 Optics .............................................. 188
18 Laser Sources ......................................... 190
19 Air Temperature Controller .................................. 203
V Safety, Specifications, Set-up, and Shipping ......................... 227
20 Safety Precautions ....................................... 229
21 Shipping or Moving ...................................... 236
22 Troubleshooting and Maintenance .............................. 263
VI Bibliography, Glossary, and Index ............................... 265
Index ................................................ 268
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Contents Contents
Introduction
CHAPTER REV. 1702, DATED 10/21/2013, 22:07. USER GUIDE REV. 1714, DATED 10/25/2013, 20:36.
AR Software Version It is assumed that AR Software version 13 or later is installed on your system. To
download the latest software, please register at our support site: http://support.asylumresearch.
com.
Getting Help There are many ways to get help with your Asylum Research instrument, and it is always
free:
• Join the support site and download software, current manuals, and ask questions in our user forum.
http://support.asylumresearch.com. Note that all Asylum scientists are forum members
and frequent contributors.
• E-mail us at [email protected].
• Call your local office or distributor.
• Call us at [phone]. During US west coast business hours you will get a human being to
speak with. After hours you still have a good chance of catching one of our scientists. Within the
US you can call our toll free number if you wish (1-888-472-2795).
• If necessary we can initiate a remote session and have one of our scientists operate your AFM over
the internet.
Updates to the Manual Bundled with the software updates.
Send Feedback Send e-mail to [email protected] (<– clickable link) and mention which ver-
sion of the user guide you are using and what chapter and section your commenting on.
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Part I
System Overview and Powering Up
Who is this part for? After the Cypher SPM has been installed in your lab and you (or someone in your
facility) have completed the initial training, this part of the user guide will review the main parts of the
instrument and software. Instrument power up is also covered.
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Part Contents
1 System Overview ........................................ 3
1.1 Basic Cypher SPM Hardware ................................ 3
1.2 Parts List .......................................... 6
1.3 The Igor Pro Software Environment ............................. 7
2 System Power Up ........................................ 10

Ch. 1. System Overview
1. System Overview
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Chapter Contents
1.1 Basic Cypher SPM Hardware ................................ 3
1.2 Parts List .......................................... 6
1.3 The Igor Pro Software Environment ............................. 7
1.1. Basic Cypher SPM Hardware
Before starting the tutorial, the user should be familiar with the names and functionality of each of the
components of the Cypher. Don’t worry if you don’t understand everything in this section; the main goal
is just to get familiar with the basic purpose of each component of Cypher. Figure 1.1 on page 3 shows
a typical set-up for the Cypher SPM. The top-level components are the computer, the ARC2 controller,
and the microscope itself.
Figure 1.1.: Ideally the Cypher SPM is set up as shown, with the controller and computer on one table
and the microscope on its own table. The air temperature controller (ATC) is not shown here. Please see
Chapter 19 on page 203 for more information.
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Ch. 1. System Overview Sec. 1.1. Basic Cypher SPM Hardware
Computer The computer is the primary interface for controlling the microscope; its main communi-
cation is via a USB1.1 connection to the ARC2 AND via USB 2.0 directly from the computer to the
Cypher. See Figure 22.1 on page 264 for recommended USB ports to use.
ARC2 The ARC2 (Asylum Research Controller 2) is what is colloquially referred to as “the controller”.
It houses power supplies and the necessary electronics for controlling the scan motion and acquiring
image data from the microscope.
Microscope The microscope itself, where the actual imaging takes place, is the heart of the AFM
system. Although the computer, controller, and microscope all comprise the Cypher, the microscope
itself will often be referred to as the Cypher.
The microscope is comprised of five basic components (see Figure 1.2 on page 4): enclosure, chassis,
camera, scanner, and backpack. The enclosure, chassis, and backpack are common to all versions of the
Cypher. In contrast, the scanner and camera are designed to be modular and easily interchanged by the
user.
Objective
Scanner
View System
Enclosure
Chassis
(a) Front View. In this image the enclosure door is
open and the scanner is partially pulled out.
Backpack
(b) Rear View
Figure 1.2.: Cypher parts basic nomenclature
Enclosure The primary function of the enclosure is to isolate the imaging portion of the microscope
from acoustic noise such as talking or music. Acoustic noise can cause the mechanical components
holding the sample to move, thereby showing up as noise in the microscope images. The secondary role
of the enclosure is to provide a local environment for the microscope itself, in which the temperature can
be controlled. Keeping the microscope at a constant temperature is important for maintaining long-term
control of the relative position between the cantilever and the sample. The air temperature controller
(ATC) is a Cypher option that can be used to maintain the temperature inside the enclosure. To learn
more about the enclosure and its options, please refer to Part IV on page 181.
Chassis The chassis is the central structural unit supporting the scanner, camera, and head. While
the scanner and camera are modular units designed to be interchanged by the user, the head is just a
sub-assembly of the chassis and is permanently attached to the chassis. The head is responsible for
the detection of the cantilever deflection and has integrated motors that allow the user to automatically
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Ch. 1. System Overview Sec. 1.1. Basic Cypher SPM Hardware
position the laser spot onto the cantilever. The objective lens attached to the head has two important
functions: it focuses the laser light onto the cantilever and works with the camera to create an optical
view of the sample. To learn more about the chassis and its options, please refer to Part IV on page 181.
Camera The camera (also called the “view module”) is a user changeable module that provides a top
down optical view of the cantilever and sample. It is comprised of a tube lens, Koehler illumination
with an LED source, and a digital camera. The camera module uses the objective lens in the head to
create the optical view. The standard camera module has a bright field reflected light topology and has
a 690µm by 920µm field of view with sub-micron resolution. Depending on the application, the view
module can be swapped by the user in about 10 minutes, but requires Allen wrenches to complete.
Scanner The primary function of the scanner is to move the sample relative to the cantilever during
imaging and other measurements such as force curves. There are various scanner modules which excel
at various tasks. The Cypher scanners are “sample scanners”, which means that relative to the room
that the microscope is sitting in, the cantilever is stationary and the sample moves. The scanner is a
modular unit that can be interchanged by the user depending on the application, although at present
there is only a single scanner available. Thus far the scanner modules are based on a flexure design that
uses piezoelectric stacks to move the sample up to 30µm in XY and 5µm in Z. The secondary function
of the scanner is to provide motorized course positioning of the cantilever relative to the sample in
the Z-axis. The cantilever holder is a component of the scanner that physically holds the cantilever
during imaging. There are different cantilever holders for air and liquid operations, and there are also
application specific holders for techniques like scanning tunneling microscopy (STM), see Chapter 9
on page 103. Each scanner type has its own family of cantilever holders and other accessories. The
available scanner modules are:
• The Standard scanner, described in Part II on page 12.
• The Environmental scanner, described Part III on page 113.
Backpack The backpack is located on the backside of the enclosure and houses a very powerful set of
digital and analog electronics that extend the functionality of the ARC2. Like the ARC2, the backpack
has ADCs, DACs, BNC connections, and a CrossPoint switch. .
QWhy is there both a backpack and a controller? Isn’t the backpack redundant since there is
already a controller?
AIn a typical AFM design, most of the electronics housed in the Cypher backpack would be
located in the controller. The backpack, however, moves these electronics closer to the micro-
scope; Cypher is able to achieve very low noise levels in part because of the proximity between
some of its electronics and the actual microscope. Keeping these low noise electronics external
to the enclosure balances noise performance with the management of the heat generated by
electronics.
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Ch. 1. System Overview Sec. 1.2. Parts List
QAFM or SPM? What is the difference?
AAFM stands for Atomic Force Microscope. It scans a cantilever over a sample to generate an
image. SPM stands for Scanning Probe Microscope. It is the more general, all encompassing
term, which also includes techniques that image using non-cantilever probes such as sharp
metal needles (Scanning Tunneling Microscopy), optical fibers (NSOM) or tiny hollow glass
tubes (SICM). Since Cypher is capable of both AFM and STM, it is classified as an SPM. You
may see Cypher referred to in the context of an AFM when its AFM-like functions are being
described.
1.2. Parts List
The contents of the accessory kit which accompanies Cypher. Asylum Inventory Number 900.110.1.
These parts accompany the AFM irrespective of the type of scanners you purchased.
Itm Part # Item Description Qty Picture
1 080.122
15mm AFM Specimen Disc.
Also available from Ted Pella,
part number 16218.
50
2 290.101 2A Tweezer, SA Tapered Round
Blunt, Standard Grade. 1
3 290.102 7Tweezer, SA Curves Sharp,
Standard Grade. 2
4 290.103 3A Tweezer, Extra Fine Sharp,
Standard Grade. 1
5 290.139 Hex Driver, 1/16” Small Handle. 2
6 312.003 Renishaw Encoder Readhead
Spacer (0.8mm). 1
7803. OLY.
AC 55 TS
Olympus Cantilevers, Model AC
55 TS. 5
The scale in the photos is in cm and mm.
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Ch. 1. System Overview Sec. 1.3. The Igor Pro Software Environment
Itm Part # Item Description Qty Picture
8
803. OLY.
BL- AC 40
TS
Olympus Biolevers (Mini):
Model BL - AC40TS. 10
9
804. NW.
ARROW -
UHF AUD
Nanoworld Cantilevers, Model:
ARROW UHFAuD 5
10 900.237 AR calibration Grating - Steel
Puck Mounted. 1
11
1-72 x
3/16”
SHCS SS
1-72 x 3/16” screw, spares.
Fastens the cantilever holder
onto the standard scanner
(Step 6 on page 20) and also fits
the cantilever holder changing
stations.
5
The scale in the photos is in cm and mm.
1.3. The Igor Pro Software Environment
The Asylum Research software is primarily written within the programming environment of the com-
mercially available software package Igor Pro, which is developed by WaveMetrics. Igor Pro itself has
nothing to do with scanning probe microscopes. Rather it is a stand alone program that has extensive
scientific graphing, data analysis, image processing and macro programming capabilities.
Tip
The “Volume I - Getting Started” manual found on the WaveMetrics website
(www.wavemetrics.com) takes two to three hours to complete and is an excellent
way to learn about the basic graphing and analysis functionality of Igor Pro.
Although it is not necessary to complete the Igor Pro portion of the “Getting
Started” manual at this time, it is a highly recommended part of all new user
training.
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Ch. 1. System Overview Sec. 1.3. The Igor Pro Software Environment
Engage Panel (Ctrl + 8) This panel controls the entire process of the cantilever approach to the sample.
Its three tabs control:
Approach Motorized approach of cantilever and microscope objective toward the sample.
Detector Centering of reflected light beam (laser or SLD) onto the optical detector.
Prefs Preferences for the engage process such as approach speed and approach step size.
Real Time Image Display This is an example of an image window, in this case displaying the individual
lines of the sample topography as the cantilever moves left to right over the sample. There is usually
one such window per active tab in the ‘Master Channel Panel’ (Lower left hand window). The amplitude
and phase data windows are to the right of this clipped screen shot. While this panel is primarily a data
display, right clicking with the mouse can activate various commands such as ‘Zoom’ and ‘Translate’.
The white area at the bottom of this window shows a real time oscilloscope view of the most recent line
of image data.
Scope Graph This oscilloscope view shows a graph of the most current scan line. Both trace and retrace
can be selected on the ‘Master Channel Panel’.
QOops! I accidentally closed one of the control panel windows. How do I get it back?
AYou can reactivate the panels via AFM Controls in the top menu bar.
A few other things of note are:
Menu Bar Along the top of the screen. There are many more controls which can be invoked by items in
the menu bar. Menu items to the left are typically standard Igor Pro items, with some Asylum Research
functionality. Items to the right of “help” are exclusively SPM related. In particular, the AFM Controls
menu item is a complete list of all real time controls and the AFM Analysis menu item is a complete list
of all offline controls.
Status Bar Along the bottom of the screen. Icon controls relate to the status of connected instrument
components. The low level software version is also displayed.
We won’t dwell on the purpose of all these controls but will proceed with the general process of imaging
a sample. This will necessarily cover the most pertinent software controls.
Tip
Note that nearly each individual item in the software control panels has a small
question mark button next to it. Click the button to read the relevant parts of the
software help file.
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Ch. 2. System Power Up
5. • Once the software has finished initializing, you will get a prompt asking if you would
like to home the engage motors.
• If necessary, slide the scanner all the way into the chassis. Close the microscope
enclosure door. For safety reasons the motors cannot home unless the door remains
closed during the process.
• Click ‘Yes’. You will hear motors moving during the homing process, which will take
about 20 seconds.
6. If you are new to the Cypher AFM system, please take the tutorial which is appropriate for your
scanner:
• For the standard scanner see: Chapter 4 on page 17.
• For the Environmental Scanner see: ?? on page ??.
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Part II
Standard Scanner
Who is this part for? After the Cypher S SPM has been installed in your lab and you (or someone in
your facility) have completed the initial training, this part of the user guide will be the principal reference
for operating the instrument. Although written with the novice user in mind, experienced SPM users
should complete the basic imaging tutorial at least once before attempting to use this instrument.
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Part Contents
3 Standard Scanner Overview ................................... 15
4 Tutorial: AC Mode in Air, Std. Scanner ............................. 17
4.1 Required Materials ..................................... 18
4.2 Loading Lever and Sample ................................. 18
4.3 Engaging the Surface .................................... 26
4.4 Imaging ........................................... 40
4.5 Stopping Imaging ..................................... 47
4.6 Shutting the System Down ................................. 47
5 Cantilever Holder Guide ..................................... 49
5.1 Identifying Cantilever Holders ................................ 49
5.2 Cantilever Holder Changing Stations ............................ 51
6 Fluid Imaging in a Droplet .................................... 53
6.1 Nomenclature ........................................ 54
6.2 Parts List .......................................... 54
6.3 Preparing for Imaging .................................... 56
6.4 Imaging with the Droplet Holder .............................. 65
6.5 Removal and Storage .................................... 69
6.6 Cleaning and Repair .................................... 69
7 iDrive Imaging .......................................... 75
7.1 Nomenclature ........................................ 76
7.2 Cleaning and Repair .................................... 80
7.3 Older Models ........................................ 83
8 Conductive AFM (ORCA) .................................... 92
8.1 Parts list .......................................... 92
8.2 The ORCA Amplifier .................................... 94
8.3 Preparing for Imaging .................................... 96
8.4 Imaging with the ORCA ................................... 99
8.5 Testing the ORCA Amplifier ................................. 99

PART CONTENTS PART CONTENTS
9 Scanning Tunneling Microscopy ................................ 103
9.1 Introduction and Preparation ................................103
9.2 Required Equipment ....................................103
9.3 Preparing an STM sample .................................104
9.4 Load the tip .........................................105
9.5 Zero Various Offsets ....................................105
9.6 Set up to engage ......................................107
9.7 Set scan parameters ....................................108
9.8 STM IV Curves .......................................108
9.9 Set IV Parameters .....................................109
9.10 STM probes ........................................111
9.11 Troubleshooting .......................................112
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Ch. 3. Standard Scanner Overview
3. Standard Scanner Overview
CHAPTER REV. 1659, DATED 10/07/2013, 22:54. USER GUIDE REV. 1714, DATED 10/25/2013, 20:36.
The module dubbed “the scanner” contains the entire mechanics of the AFM except for the optical
means for detecting cantilever deflection. This includes:
• Actuators and sensors for closed loop XY scanning of the sample.
• An actuator and sensor for the sample Z motion.
• A cantilever holder and mechanical means for engaging the cantilever with the sample surface.
Since Cypher’s scanners are whole AFMs unto themselves, each comes with its own dedicated collection
accessories such as cantilever holders and sample stages. In other words, a cantilever holder for one
scanner usually does not fit onto a different scanner. Also, an expert user of one model of scanner will
not necessarily know anything about operating another model.
This part of the user guide describes in many chapters the use of the Standard Scanner and its many
accessories. Once the scanner is exchanged for another, as described in Chapter 16 on page 183, an
different part of the user guide will need to be consulted. Typically the first user of a new scanner will
need to be trained by Asylum Research personnel.
(a) Standard Scanner. (b) Names of the basic components.
Figure 3.1.: The Standard Scanner
Figure Figure 3.1 on page 15 shows the standard scanner partially withdrawn from the rest of the AFM.
The standard scanner is included with the “Cypher S” AFM, but can also be purchased separately. The
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Ch. 3. Standard Scanner Overview
Standard scanner is designed primarily for imaging in ambient conditions, either in air or in a liquid
droplet. The optical access to the sample and cantilever is superior to other cypher scanner models.
Many Standard Scanner cantilever holders allow for a variety of imaging modes. See Chapter 5 on
page 49 for more information.
The Scanner itself comes in regular and high voltage models. Figure 3.2 on page 16 shows the a
magnetic high voltage contact and specialized cantilever holder with high voltage connection to the tip.
This arrangement is typically use for PFM techniques. This topic is covered in depth in Applications
Guide, Chapter: PFM Using DART and Applications Guide, Chapter: Single Frequency PFM.
Figure 3.2.: Detailed view of the high voltage option.
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