Oxford Instruments Cypher SPM User manual

Cypher SPM
User Guide
Part No. XX-XXXX-XXX

Cypher SPM
User Guide
Revision History
Date Version Description of revision Name
May 2018 1.0 Content revised from Cypher User Guide v13
revision B-2016, dated 05/10/2018.
John Barnes
Disclaimers
Oxford Instruments assumes no liability for the use of this document if any unauthorised changes
to the content or format have been made.
Considerable care has been taken to ensure the accuracy of information contained but Oxford
Instruments NanoAnalysis cannot guarantee that it contains no errors, omissions or inaccuracies.
In addition the Oxford Instruments NanoAnalysis policy is one of continued product improvement.
Therefore, the company reserves the right to change the information contained herein without
notice.
This manual is provided without warranty of any kind, either implied or expressed, including, but
not limited to, the implied warranties of merchantability and fitness for a particular purpose.
Copyright
Information contained in this document is proprietary, and remains the intellectual property of
Oxford Instruments NanoAnalysis.
The document is distributed by Oxford Instruments NanoAnalysis on the understanding that any-
one entrusted with the document will use their best endeavours to prevent the disclosure of such
confidential information to any third parties without written consent from Oxford Instruments Nan-
oAnalysis.
No part of this document may be copied, transmitted or reproduced in any form, or by any other
means, without written consent from Oxford Instruments NanoAnalysis.
Page 2of 243
NanoAnalysis
Halifax Road
High Wycombe
HP12 3SE UK
Tel: [phone]
Fax: [phone]
Email: [e-mail]
www.oxford-instruments.com

Cypher SPM
User Guide
Contents
Part I: Getting Started
1 About this manual 9
1.1 Intended audience 9
1.2 Confidential information 9
1.3 Related Documentation 9
2 Health and safety 10
2.1 Warning symbols on the Cypher SPM 10
2.2 General safety precautions 10
2.3 Instrument weight 10
2.4 Motor safety 11
2.4.1 Avoiding unsafe situations 11
2.4.2 How to stop the motors 11
2.5 Light source safety 12
2.5.1 Non-visible laser diode or SLD light 12
2.5.2 The laser optical path 13
2.5.3 Laser safety interlocks 14
2.6 Power supply safety and thermal management 16
2.6.1 Power supply and earthing 16
2.6.2 Overheating 17
2.7 Disposal 17
2.8 Cleaning 17
3 Contact, Shipping and Support Information 18
4 What is a Cypher SPM system? 19
4.1 Microscope 19
4.1.1 Enclosure 20
4.1.2 Chassis 20
4.1.3 Backpack 20
4.1.4 Scanner 21
4.1.5 Camera 21
4.2 Cypher accessory kit parts list 22
4.3 Recommended USB ports 23
4.3.1 Dell T3400 and T3500 23
4.3.2 Dell T3600 24
4.3.3 Dell T3610 25
4.3.4 Dell T1650 25
4.3.5 Computers that do not have two USB 2.0 host controllers 26
4.4 AZtec AFM software environment 26
5 Starting and stopping the system 30
5.1 System power up 30
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5.2 System power down 30
Part II: Standard Scanner
6 Standard Scanner Overview 33
7 Standard scanner cantilever holders 35
7.1 Visual identification of SS cantilever holders 35
7.2 Electronic identification of cantilever holders 38
7.3 Cantilever holder changing stations 38
7.4 ORCA cantilever holder kit parts list 39
7.5 The ORCA Amplifier 40
7.5.1 Single gain 40
7.5.2 Dual gain 41
Part III: Environmental Scanner
8 Environmental Scanner Overview 43
8.1 Environmental scanner parts list 44
8.2 Reminders for imaging 49
8.3 Chemical compatibility 52
9 Environmental scanner cantilever holders 54
9.1 Visual identification of ES cantilever holders 54
9.1.1 ORCA cantilever holder kit parts list 55
9.2 Electronic identification of ES cantilever holders 57
9.3 Changing the cantilever clip 57
9.3.1 Removing the ES cantilever clip 57
9.3.2 Attaching the ES cantilever clip 58
9.4 Cleaning the ES cantilever holder 59
9.5 Storage 61
10 Cell Body and Sample Stage Guide 62
10.1 Gas cell 62
10.1.1 Gas cell parts list 63
10.1.2 Gas cell specifications 64
10.1.3 Gas cell cable installation 65
10.1.4 Applying sample bias or ground 67
10.2 Fluid Cell Body 68
10.2.1 Fluid cell parts list 68
10.2.2 Fluid cell specifications 69
10.3 Humidity cell 70
10.3.1 Humidity cell parts list 70
10.3.2 Humidity cell installation 71
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10.4 Ambient sample stage 74
10.4.1 Ambient sample stage parts list 74
10.4.2 Ambient sample stage specifications 74
10.5 Heater sample stage 75
10.5.1 Heater sample stage parts list 75
10.5.2 Heater sample stage specifications 75
10.6 Cooler heater sample stage 76
10.6.1 Cooler heater sample stage parts list 76
10.6.2 Cooler heater sample stage specifications 76
10.7 Reminders for cell exchange and handling 77
10.8 Disassembling the sample stage from the cell body 79
10.8.1 Separating the sample stage and chamber 80
10.8.2 Attach cell body and sample stage 82
10.9 Exchanging the sample stage and cell body 84
10.9.1 Required materials 85
10.9.2 Prepare the scanner 86
10.9.3 Remove the sample stage and chamber 86
10.9.4 Mounting the new stage and cell combination 88
10.9.5 Replacing the scanner 90
10.10 Storing sample stages and cell bodies 91
10.10.1 Storing sample stage and cell body combinations 91
11 Gas handling and leak testing 93
11.1 Removing the scanner faceplate 93
11.2 Manifold cell-side connection 94
11.3 Manifold lab-side connection 95
11.4 Gas perfusion imaging 96
11.5 Attaching threaded fittings to tubing 96
12 Glovebox Protocols 97
12.1 Establishing the maximum inert gas flow rate 97
12.2 Preparing the cell and gas lines 98
12.3 Seal the cell 100
12.4 Mount the sealed cell onto the AFM 102
Part IV: Instrument Components
13 Optical system 107
13.1 Microscope objective 107
13.2 View system 108
14 Scanner Exchange 109
14.1 Removing the scanner 109
14.2 Scanner storage 111
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14.3 Replacing the scanner 111
15 Light tubes 114
15.1 Types of light tube and how to identify them 114
15.2 Exchanging a light tube 116
15.3 Spot On calibration 118
15.3.1 Readjusting the Spot On calibration 119
15.4 Reconnecting the light tube cable 121
15.4.1 Plugging the light tube cable back in 121
15.4.2 Replacing the enclosure cover 121
16 blueDrive photothermal excitation 124
16.1 The principle of photothermal excitation 124
16.2 How much light power do you need? 125
16.3 39.2 Hardware components 126
16.4 Installing blueDrive 127
16.4.1 Changing filter cubes 127
16.4.2 Replacing the laser diode module 130
16.4.3 Focusing the blue laser spot 131
16.5 Choosing the correct cantilever 132
16.6 39.4.2 Choosing the correct filter cube 132
16.7 blueDrive software interface 134
16.7.1 Turning on blueDrive 134
16.7.2 39.5.3 Positioning the blue spot 135
16.7.3 39.5.4 Acquiring a cantilever tune 137
16.7.4 Operating on the thermal resonance 137
Part V: Tutorials and Workflows
17 Tutorials introduction 140
18 Removing the cantilever holder on a standard scanner 141
19 Changing the cantilever on a standard scanner 144
20 Inserting the cantilever holder on a standard scanner 148
21 Removing the cantilever holder on an environmental scanner 151
22 Changing the cantilever on an environmental scanner 154
23 Inserting the cantilever holder on an environmental scanner 157
24 Engaging the cantilever on the sample 160
24.1 Bringing the cantilever close to the sample 160
24.2 Tuning the cantilever for AC imaging 175
24.3 Landing the tip 177
25 AC mode imaging 180
25.1 4.4.1 Set-Up and Initial Parameter Selection 180
25.2 4.4.2 Start Imaging and Parameter Tuning 181
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25.3 4.4.3 Image Refinement 188
25.4 4.5 Stopping Imaging 188
25.5 188
26 Contact mode imaging in air 189
27 Preparing for conductive AFM imaging on the standard scanner 190
27.1 Zeroing the ORCA sample bias signal 190
27.2 Preparing the sample 191
27.2.1 Install the sample on the scanner and connect the bias lead 192
27.3 Mounting the cantilever 192
28 Preparing for conductive AFM on the environmental scanner 193
29 Current imaging with conductive AFM 195
30 Workflows 198
30.1 Loading the cantilever and sample on a standard scanner 198
30.2 Loading the cantilever and sample on an environmental scanner 205
30.3 AC mode imaging in air with the standard scanner 214
30.4 AC mode imaging in air with the environmental scanner 214
Part VI: Shipping and Maintenance
31 Shipping or moving 217
31.1 A note on unpacking 217
31.2 Moving: what does it mean? 217
31.3 Instrument weight 218
31.4 Complete system shutdown 218
31.5 Scanner removal and packaging 218
31.6 Removing the enclosure top cover 222
31.7 Backpack removal and packaging 225
31.8 Chassis removal and packaging 227
31.9 Packaging the enclosure 233
31.10 View module removal and packaging 237
31.11 Packaging the accessories 240
31.12 Packaging computers and monitors 242
31.13 Weights and Dimensions 242
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Part I: Getting Started
System safety and overview

Cypher SPM
User Guide
1
1About This Manual
This manual covers the installation of the Cypher SPM.
1.1 Intended audience
This manual is specifically aimed at trained personnel who install, service, or repair Cypher SPM
from Oxford Instruments. That is, only personnel who have attended appropriate Oxford Instru-
ments training courses are permitted to install, service, and repair these systems.
Note: Customers must not install, service, or repair the equipment described in this manual.
Doing so may invalidate warranties.
1.2 Confidential information
Information contained in this manual is proprietary, and remains the intellectual property of
Oxford Instruments NanoAnalysis. The manual is distributed by Oxford Instruments NanoAnalysis
on the understanding that anyone entrusted with the manual will use their best endeavors to pre-
vent the disclosure of such confidential information to any third parties without written consent
from Oxford Instruments NanoAnalysis. No part of this manual may be copied, transmitted or
reproduced in any form, or by any other means, without written consent from Oxford Instruments
NanoAnalysis.
1.3 Related Documentation
LISTOFDOCUMENTATIONHEREor else delete this section.
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2
2Health And Safety
This section gives important health and safety information which must be read, understood, and
observed by all persons who install, service and repair the Cypher SPM.
2.1 Warning symbols on the Cypher SPM
Symbol Meaning
Caution, risk of danger.
Potential hazard present. Consult product documentation for any actions that
may have to be taken to avoid injury.
Caution, risk of electric shock.
Hazardous voltages present that have the potential to cause shock, burns or
death. Disconnect power before servicing.
Caution, radiation hazard.
Potential exposure to ionizing radiation exists.
2.2 General safety precautions
To avoid fire hazard and risk of electric shock:
lDo not use the equipment if any cable is damaged.
lDo not operate with suspected damage or failure to the equipment.
lDo not use a supply voltage that is outside the specified range.
lDo not operate the equipment with the covers removed.
lDo not operate in damp or wet conditions.
lDo not immerse in liquids.
lDo not use or store in corrosive or explosive atmospheres.
lDo not operate outside the specified temperature range.
lProvide proper ventilation to prevent overheating.
2.3 Instrument weight
The Cypher instrument is made of many heavy metal parts. Be prepared to have two people on
hand whenever lifting of the empty enclosure is required.
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Note: Even the scanner module is quite heavy. Be prepared to support its weight as you pull it
from the support rails.
2.4 Motor safety
The Cypher SPM contains six motors which direct the laser beam and move the objective lens and
cantilever holder into position. All the motors are highly geared and can generate powerful torques
that could seriously pinch a finger. The most important moving parts to be aware of, from a safety
perspective, are the cantilever holder and the objective lens, along with its carriage. Always keep
your hands clear of the Cypher SPM when performing any software or manually controlled motor
moves.
2.4.1 Avoiding unsafe situations
The following image indicates the main potential pinch points: directly under the objective lens and
cantilever holder, at the edges of the scanner module, and both above and below the two cross-
roller bearing stages.
We recommend that you always leave the optics cover in place. Removing it exposes additional
pinch points.
Note: Operate motors only with the enclosure door closed.
2.4.2 How to stop the motors
In case of an emergency, the motors can be stopped in one of the following ways:
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lThe motor control knob at the lower front of the Cypher can be used at any time to override
computer commanded objective lens or cantilever holder motor moves. Turning the knob will
immediately stop any current motor moves and will transfer control of both the cantilever
holder and objective motion to the knob.
Note: Turning the knob always moves BOTH the cantilever holder and the objective lens
simultaneously. This means that if your finger is pinched between the cantilever holder and
the objective lens, the best way to release your finger is to use the software to motor the
objective lens upwards while leaving the cantilever holder stationary.
lPress and hold down the Esc key on the PC keyboard. This stops any automated motor moves.
lTurn off the ARC2 controller or unplug the power brick, which is connected to the Cypher SPM.
Note: We do not generally recommend these methods because then you cannot use the
knob or software to control the motors and manually move them to a safer position.
lIf the power is cut and you must move the objective, you can reach inside the enclosure and
feel for a wheel at the lower left hand side near the rear of the chassis. This wheel turns the
motor manually. Ten turns are required for every millimeter of objective motion. Turn clock-
wise to move the objective down and counter-clockwise to move the objective up.
2.5 Light source safety
Use of controls or adjustments or performance procedures other than those spe-
cified herein may result in hazardous invisible laser energy exposure.
Note: While it is safe to operate the system with the optical system cover removed, keep it in
place at all times to avoid the temptation of touching the inner workings around the laser
optical path.
2.5.1 Non-visible laser diode or SLD light
The Cypher SPM contains a laser diode (LD) or super luminescent diode (SLD) light source. SLDs are
like lasers, but have a shorter coherence length. As of the writing of this manual, all Cypher light
sources have an output of several mW around 850 nm, which is non-visible.
From a safety perspective LDs and SLDs can be regarded as identical and the terms will be used
interchangeably.
The Cypher laser is sufficiently well shielded that the Cypher SPM qualifies as IEC Class 1 laser
product that complies with 21 CFR 1040.10 and 1040.11, except for deviations pursuant to Laser
Notice No. 50, dated 24 June 2007. It complies with IEC/EN 60825-1, Ed.2:2007.
In layman’s terms this means the Cypher SPM is in the same class as a home DVD player, and in a
safer class than a laser pointer. When used as prescribed there is no danger of exposure. Non-
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etheless, it is still good to have an understanding of the laser in the instrument and the safety fea-
tures.
2.5.2 The laser optical path
Understanding the laser optical path is the best way to reduce the possibility of harmful exposure
to non-visible light, which may cause eye damage. The following image shows a simplified picture of
the laser optical path.
Removing the optics cover exposes the hot mirror and laser module. The non- visible laser light ori-
ginates in the laser module and comes out as a collimated beam. The collimated beam is reflected
off of the hot mirror and into the objective lens, which focuses it onto the cantilever. During nor-
mal operation the only place a person can be exposed to the light is where the light exits the object-
ive.
There are numerous interlocks to minimize the possibility of exposure. However, you should avoid
the following:
lWhile unlikely, it is possible to place a small mirror below the objective and reflect the light in
the direction of the user. Even then the beam spreads rapidly and is not powerful enough to
classify the instrument differently. Nevertheless, you should be aware of the fact that non-vis-
ible light is coming out of the objective.
lWhile it is not recommended, it is possible to unscrew the objective lens by overcoming the loc-
tite glue used to keep the lens in place. At this point a flat mirror placed under the beam exit can
reflect approximately 1 mW of collimated IR light into your eye. Never remove the objective
lens or you may void your warranty.
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lNever change or remove the laser module without first turning off the laser power key on the
ARC2 controller.
lNever look directly into a plugged-in laser module.
2.5.3 Laser safety interlocks
The laser on the Cypher SPM is turned on and off by a control voltage which originates inside the
ARC2 controller.
On its way to the laser the voltage passes through various safety switches, as shown in the fol-
lowing image.
The relevant parts of the Cypher SPM in terms of laser safety are:
lLaser Voltage Source (A)
lLaser Module LED (B)
lCypher enclosure laser LED (C)
lOptical system cover (E)
lObjective lens (F).
The following table describes the safety interlocks.
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Interlock Description
Light source
remote jack (1)
In case your laboratory safety specifications require extra measures such as
a door or foot interlocks to operate laser equipment, you can attach such a
switch to a connector on the back of the ARC2 controller. If this switch is
open, the laser power will be interrupted. Since such requirements are rare,
the ARC2 controller ships with a shorted connector, keeping this switch per-
manently closed. Removing the connector will shut the laser off. Call Asylum
Research for an additional connector to which you can attach your own cus-
tomized interlock system.
Front panel laser
power key switch
(2)
The laser is generally turned on and off by means of the key on the front of
the ARC2 controller. The key is captive when the laser is on, but can be
removed in the ‘off’ position.
Scanner laser inter-
lock (3)
When the scanner module is removed there is significantly more space
under the objec- tive lens to insert objects which might reflect the laser light
in the direction of the user. To prevent this, the laser power circuit is broken
as soon as the scanner cable is disconnected, a necessary step for scanner
removal.
Laser module dual
magnetic switch
interlock (4,5)
The laser module (or collimated laser source) includes magnetically activated
switches that cut the laser power unless the module is inside its cradle. This
prevents the module from emitting collimated light when it is outside the
confines of the instrument. The presence of strong magnetic fields can over-
ride the interlock operation. For additional safety always turn the laser key
on the front of the ARC2 controller to the off position and/or turn off the
controller power.
Note: A red LED on the front of thelaser module indicates whether col-
limated light is being emitted. Never look into the module if this LED is
on. An additional precaution is to simply never look into the module’s
collimating lens.
Light source module
When you remove the light source module it is possible to tamper with safety overrides in such a
way that collimated light shines out of the module. As a safety precaution, never look directly into
the module while its power cable is attached (power cable not shown in the following image).
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2.6 Power supply safety and thermal management
Caution, risk of electric shock.
The Cypher SPM and ARC2 controller contain internal voltages up to 165 V DC,
0.5 A. Use caution when handling system pieces to avoid electrical injury. These
voltages may be lethal.
The voltages inside the Cypher SPM are as dangerous as those present in a standard wall socket;
therefore, you should respect all of the components under the instrument covers as you would a
wall socket. Never touch anything or insert anything conductive under the instrument covers.
The piezoelectric actuators in the scanner have a large capacitance and can hold charge for many
minutes after the scanner is disconnected from any power supply. For this reason, never touch the
scanner connector, unless it has been unplugged for at least 10 minutes.
Adhere to the fuse ratings appropriate to the main supply voltage listed on the back side of the
ARC2 controller. Not following the recommended ratings may cause the instrument to overheat or
sustain damage.
2.6.1 Power supply and earthing
The mains connection should be made to an accessible mains outlet, within reach of the operator.
It should be positioned near to the equipment and should be accessible so that power can be eas-
ily disconnected.
The Cypher SPM must be earthed. Do not remove, disconnect or disable the ground wires, or any
other protective earth because this could make the equipment dangerous.
Replace power cords if they are damaged. Contact your local agent or distributor to ensure the cor-
rect replacement part for your country is used.
Avoiding equipment damage when connecting cables
One of the most common causes of damage when connecting cables is an electrostatic discharge.
Therefore:
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lEnsure you ground yourself using a high resistance earth strap.
lEnsure the equipment is connected to ground before you connect its individual parts.
If cables are connected while power is being applied then the incoming voltage may exceed the
limit of some circuitry. Therefore, only connect cables to the equipment when the power is off.
2.6.2 Overheating
Keep the backside of the ARC2 clear. Cool air is drawn into the heat sinks on the back of the ARC2
controller and two fans exhaust warm air from the same place. Obstructing any part of the ARC2
back will cause power supplies and electronics to overheat.
Keep the top of the Cypher SPM backpack clear of items. The backpack is passively cooled and
requires all the heat fins on the side and top be in open air. Don’t place paper or notebooks on top
of the backpack.
2.7 Disposal
European Directive on Waste Electrical and Electronic Equipment (WEEE)
When disposing of the system or any of its components, users in the
European Union should contact Oxford Instruments or the system vendor.
Do not dispose of the equipment with normal domestic or business waste,
which is sent to landfill.
Disposal of Waste Electrical and Electronic Equipment in Other Regions
When disposing of the system or any of its components, users outside the
European Union should comply with the regulations in their country, state,
region or province to ensure that the system is disposed of legally and cor-
rectly.
2.8 Cleaning
Always switch off the Cypher SPM and disconnect the mains power supply cable
before attempting to carry out any cleaning.
For general cleaning, wipe the Cypher SPM with a damp cloth. Do not use detergent solution or
any other chemicals.
For microscope interface seals and “O” rings use isopropyl alcohol and lint-free cloth.
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3
3Contact, Shipping And Support Information
Tech support
Region Email Telephone
Global & EMAI [e-mail] [phone]
USA/South America [e-mail] [phone]
Japan [e-mail] [phone]
China [e-mail] [phone]
Declaration of Conformity
The Cypher SPM conforms to the appropriate EEC device directive for this type of instrument and
has been subject to the conformity assurance procedures laid down in the Council Directive.
The Declaration of Conformity is available on request from your local support office.
Support Policy, Shipping and Returns
Oxford Instruments guarantees the equipment against defects in materials and workmanship for a
period of one year from the date of installation, or 15 months from shipment, whichever is sooner.
Subject to the availability of components, Oxford Instruments NanoAnalysis shall use reasonable
endeavours to provide support for the Cypher SPM for a period of seven years after the date of
last production. Please contact your local support office to establish whether this product is still in
production. If your product is older than this please contact your local support office to see if we
can help further.
In the unlikely event that you need to return any Oxford Instruments Nano Analysis equipment for
repair or exchange, you MUST submit a completed RMA request form to the NA-HW-Returns
department. Your RMA request will then be processed and you will be advised of the RMA number.
Please clearly indicate the RMA number on the outside of the item being returned.
Do not return any item until you have received a RMA number.
lOxford Instruments NanoAnalysis, Halifax Road, High Wycombe, Bucks HP12 3SE, UK
lTel: [phone]
lEmail: [e-mail]
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4
4What Is A Cypher SPM System?
A typical Cypher SPM system consists of a computer, the ARC2 controller, and the microscope
itself.
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 computer is the primary interface for controlling the microscope; its main communication is
through a USB1.1 connection to the ARC2 and a USB 2.0 directly to the Cypher SPM. For further
information, see Recommended USB ports on page23.
The ARC2 (Asylum Research Controller 2) is 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.
4.1 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.
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For detailed information on connecting these various components, see Cable Connections on
page1.
The microscope is comprised of five basic components: enclosure, chassis, backpack, scanner, and
camera. The enclosure, chassis, and backpack are common to all versions of the Cypher. The scan-
ner and camera are designed to be modular and easily interchanged by the user.
(a) Front View. The enclosure door is open and
the scanner is partially pulled out.
(b) Rear View
4.1.1 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 hold-
ing 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 tem-
perature 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.
4.1.2 Chassis
The chassis is the central structural unit supporting the scanner, camera, and head. While the scan-
ner 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 auto-
matically 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.
4.1.3 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
4 What is a Cypher SPM system? Page 20 of 243