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Oxford Instruments Cypher SPM User Manual

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

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Summary of Contents for Oxford Instruments Cypher SPM

  • Page 1 Cypher SPM User Guide Part No. XX-XXXX-XXX...
  • Page 2 B-2016, dated 05/10/2018. 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.

  • Page 3: Table Of Contents

    1 About this manual 1.1 Intended audience 1.2 Confidential information 1.3 Related Documentation 2 Health and safety 2.1 Warning symbols on the Cypher SPM 2.2 General safety precautions 2.3 Instrument weight 2.4 Motor safety 2.4.1 Avoiding unsafe situations 2.4.2 How to stop the motors 2.5 Light source safety...
  • Page 4 Cypher SPM User Guide 5.2 System power down Part II: Standard Scanner 6 Standard Scanner Overview 7 Standard scanner cantilever holders 7.1 Visual identification of SS cantilever holders 7.2 Electronic identification of cantilever holders 7.3 Cantilever holder changing stations 7.4 ORCA cantilever holder kit parts list 7.5 The ORCA Amplifier...
  • Page 5 Cypher SPM User Guide 10.4 Ambient sample stage 10.4.1 Ambient sample stage parts list 10.4.2 Ambient sample stage specifications 10.5 Heater sample stage 10.5.1 Heater sample stage parts list 10.5.2 Heater sample stage specifications 10.6 Cooler heater sample stage 10.6.1 Cooler heater sample stage parts list 10.6.2 Cooler heater sample stage specifications...
  • Page 6 Cypher SPM User Guide 14.3 Replacing the scanner 15 Light tubes 15.1 Types of light tube and how to identify them 15.2 Exchanging a light tube 15.3 Spot On calibration 15.3.1 Readjusting the Spot On calibration 15.4 Reconnecting the light tube cable 15.4.1 Plugging the light tube cable back in...
  • Page 7 Cypher SPM User Guide 25.3 4.4.3 Image Refinement 25.4 4.5 Stopping Imaging 25.5 26 Contact mode imaging in air 27 Preparing for conductive AFM imaging on the standard scanner 27.1 Zeroing the ORCA sample bias signal 27.2 Preparing the sample 27.2.1 Install the sample on the scanner and connect the bias lead...
  • Page 8 Part I: Getting Started System safety and overview...

  • Page 9: About 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.

  • Page 10: Health And Safety

    User Guide Health 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.

  • Page 11: Motor Safety

    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.

  • Page 12: Light Source Safety

    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-...

  • Page 13: The Laser Optical Path

    Cypher SPM User Guide 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.

  • Page 14: Laser Safety Interlocks

    Never 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.
  • Page 15 Cypher SPM User Guide Interlock Description Light source In case your laboratory safety specifications require extra measures such as remote jack (1) 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.

  • Page 16: Power Supply Safety And Thermal Management

    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.

  • Page 17: Overheating

    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.

  • Page 18: Contact, Shipping And Support Information

    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.

  • Page 19: What 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.

  • Page 20: Enclosure

    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...

  • Page 21: Scanner

    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. Page 21 of 243 4 What is a Cypher SPM system?

  • Page 22: Cypher Accessory Kit Parts List

    3A Tweezer, Extra Fine Sharp, Standard Grade. 290.139 Hex Driver, 1/16” Small Handle. 312.003 Renishaw Encoder Readhead Spacer (0.8 mm). 803. OLY. Olympus Cantilevers, Model AC 55 TS. AC 55 TS 4 What is a Cypher SPM system? Page 22 of 243...

  • Page 23: Recommended Usb Ports

    USB ports recommended in the following sections, depending on the computer that you are using. 4.3.1 Dell T3400 and T3500 Plug the Cypher, ARC, mouse and keyboard into the bottom USB ports as shown in the following image. Page 23 of 243 4 What is a Cypher SPM system?

  • Page 24: Dell T3600

    USB 2.0 and 3.0 devices like USB drives and printers and LCD monitor hubs may now safely be plugged into the remaining non-circled ports, including the four USB ports on the front of the com- puter. 4 What is a Cypher SPM system? Page 24 of 243...

  • Page 25: Dell T3610

    Plug the Cypher and ARC into the bottom-right USB ports as shown in the following image. Plug the mouse and keyboard into the top USB ports as shown below. Page 25 of 243 4 What is a Cypher SPM system?

  • Page 26: Computers That Do Not Have Two Usb 2.0 Host Controllers

    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. 4 What is a Cypher SPM system? Page 26 of 243...
  • Page 27 Upper left hand window (Ctrl + 5). It has five tabs with controls and data displays for: Image AFM imaging, see 4. Thermal Cantilever thermal spectroscopy. Force Cantilever force versus distance curves. Tune Cantilever vibrational tuning, see 4.3.2. Fmap Maps of force versus distance curves. Page 27 of 243 4 What is a Cypher SPM system?
  • Page 28 1. Q Oops! I accidentally closed one of the control panel windows. How do I get it back? 2. A You can reactivate the panels via AFM Controls in the top menu bar. A few other things of note are: Menu Bar 4 What is a Cypher SPM system? Page 28 of 243...
  • Page 29 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. Page 29 of 243 4 What is a Cypher SPM system?

  • Page 30: Starting And Stopping The System

    1. Power up. Boot up the computer. Turn on the Cypher SPM by depressing the power switch on the front of the ARC2 controller. If everything is working correctly, two different green LEDs are illuminated. The first LED is located above the power switch on the ARC2 and the second LED (labeled “power”) is located at the front of the Cypher enclos-...
  • Page 31 Cypher SPM User Guide 3. Turn off the laser key on the controller. 4. Power off the controller. Page 31 of 243 5 Starting and stopping the system...

  • Page 32: Part Ii: Standard Scanner

    Part II: Standard Scan- This part of the user guide is the principal reference for operating the Cypher SPM instru- ment with a standard scanner.

  • Page 33: Standard Scanner Overview

    Cypher SPM User Guide Standard Scanner Overview The standard scanner is included with the Cypher S AFM, but can also be purchased separately. This part of the user guide describes the use of the Standard Scanner and its many accessories.
  • Page 34 Cypher SPM User Guide Standard Scanner Names of the basic components. The 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.

  • Page 35: Standard Scanner Cantilever Holders

    Cypher SPM User Guide Standard Scanner Cantilever Holders Depending on your specific imaging application, the appropriate cantilever holder must be used. This section serves as a guide to the available standard scanner options and to help you identify the types of cantilever holders you may already own.
  • Page 36 Cypher SPM User Guide Part # Holder Description Front Photo Back Photo 901.730 Droplet For fluid imaging in a droplet. Fits in the Droplet Changing Station. For use in air or liquid. 901.740 iDrive For Electromagnetically Driven imaging in air and droplets.
  • Page 37 Cypher SPM User Guide Part # Holder Description Front Photo Back Photo 901.708 Dual Gain ORCA Conductive AFM with a two simultaneous current ranges. Fits in the Air Changing Station. For use in air or liquid. See also ORCA cantilever holder kit parts list on page 55...

  • Page 38: Electronic Identification Of Cantilever Holders

    Cypher SPM User Guide Part # Holder Description Front Photo Back Photo 901.750 AM-FM Viscoelastic Map- ping Fits in the Air Changing Sta- tion. For use in air or liquid. xxx.xxx Contact Resonance Vis- coelastic Mapping Fits in the Air Changing Sta- tion.

  • Page 39: Orca Cantilever Holder Kit Parts List

    Cypher SPM User Guide 7.4 ORCA cantilever holder kit parts list The following items are included in the ORCA cantilever holder kit. These accessories are included in both the single and dual gain versions of the holder. Item Part #...

  • Page 40: The Orca Amplifier

    Cypher SPM User Guide Item Part # Item Description Picture 448.081 Cypher ORCA 1M Resistor Assembly. A 1M Ohm Test Resistor (Dual Gain ORCA Only). See 9.5. 7.5 The ORCA Amplifier There are a variety of ORCA cantilever holders each based on either a single or dual amplification design.

  • Page 41: Dual Gain

    Cypher SPM User Guide The sample is biased from a voltage source within the Cypher electronics. The feedback resistor R1 sets the amplifier's sensitivity. The output signal representing tip/sample current flow can be mon- itored by enabling the 'Current' channel in the master channel control panel.

  • Page 42: Part Iii: Environmental Scanner

    Part III: Environmental Scan- This part of the user guide is the principal reference for operating the Cypher SPM instru- ment with an environmental scanner.

  • Page 43: Environmental Scanner Overview

    Cypher SPM User Guide Environmental Scanner Overview The Environmental Scanner is included with the Cypher model ES AFM. This part of the user guide describes the use of the Environmental Scanner and its many accessories. Once the scanner is exchanged for another, a different part of the user guide must be consulted.

  • Page 44: Environmental Scanner Parts List

    Cypher SPM User Guide Environmental Scanner Names of the basic components. 8.1 Environmental scanner parts list The following table describes all the tools and other items included with your Environmental Scan- ner. Please refer to the part number when seeking support or ordering replacements. The scale in the photos is in cm and mm.
  • Page 45 Cypher SPM User Guide Item Part # Item Description Picture 290.163 5/64” (2 mm) Hex Driver. Used to remove the cell body from the scan- ner. 080.165 1 cc HSW Norm-Ject Syringe. Typically used to perfuse fluid. 080.010 5 cc syringe, HSW. Typically used for fluid or gas perfusion.
  • Page 46 Cypher SPM User Guide Item Part # Item Description Picture 232.015 Fittings, 1/16”. Used to connect 1/16” tubing to the cell chamber wall. Use with tool 290.164. 114.800 Extender Tool Fitting Wrench. Use to tighten Fittings 230.015. Do not use on the cell body fit- tings.
  • Page 47 Cypher SPM User Guide Item Part # Item Description Picture 114.576 Stage locking screw with integrated ball end . Spare screws used to lock down the sample stage. Be careful, these are very expens- ive screws. 2-56 x 0.125 2-56 x 1/8” long screws. Spare screws...
  • Page 48 Cypher SPM User Guide Item Part # Item Description Picture 222.077 1/16” dowel pin. Used to restore slightly compressed fitting parts. 290.168 1.8 mm slotted screwdriver. Used to fasten the sample stage membrane to the cell body. 232.017 1/8” NPT x 6 mm tubing connector.

  • Page 49: Reminders For Imaging

    Cypher SPM User Guide Item Part # Item Description Picture 230.038 O-ring, 0.75"ID X 1"OD Kalrez 6375, Dur- ometer 75A. Equivalent FKM part is 230.044. Standard AS568-020 size, can also be purchased from other vendors. Sits around cantilever holder peri- meter.
  • Page 50 Cypher SPM User Guide 1. Remember to fully raise the engage stage before loading the cantilever holder. Compared to the S, on the ES scanner it is more dif- ficult to see if there is enough clearance for safely loading the cantilever holder.
  • Page 51 Cypher SPM User Guide 3. Never touch the Heater sample stage with your tweezers. The Heater sample stage is extremely fragile. In order to achieve high temperatures while still maintaining low drift performance, the Heater Sample Stage is constructed with fragile ceramics.

  • Page 52: Chemical Compatibility

    Cypher SPM User Guide 5. Always power off the microscope before exchanging scanners. Before exchanging scanners, remember to first motor the objective to its upper limit of travel. Power off the controller before disconnecting the scanner. Exchange scanners and then power the controller back on after the new scanner has been recon- nected.
  • Page 53 Cypher SPM User Guide When you no longer require these O-rings, please store them back in the case. FFKM Costs between 10 and 100 times more than FKM, so do not misplace them. Page 53 of 243 8 Environmental Scanner Overview...

  • Page 54: Environmental Scanner Cantilever Holders

    Cypher SPM User Guide Environmental Scanner Cantilever Holders Depending on your specific imaging application the appropriate cantilever holder must be used. This section serves as a guide to the available environmental scanner options and to help you identify the types of cantilever holders you may already own.

  • Page 55: Orca Cantilever Holder Kit Parts List

    Cypher SPM User Guide Part # Holder Description Top Photo Bottom Photo 901.745 Perfusion For fluid imaging in a droplet with flow. 901.767 ORCA Conductive AFM with a single current range, 2 nA/V. See also ORCA cantilever holder kit parts list below The ORCA Amplifier on page 40.
  • Page 56 Cypher SPM User Guide Item Part # Item Description Picture ASTELEC-01 10 pack of conductive levers. Used for the measurements described in this section. 823.009 HOPG sample. Used as a conductive AFM test sample. 448.079 Sample bias wire assembly. Connects sample to voltage source on top of the scanner.

  • Page 57: Electronic Identification Of Es Cantilever Holders

    Cypher SPM User Guide 9.2 Electronic identification of ES cantilever holders 1. Attach the cantilever holder to the Cypher Scanner. 2. In the AZtec AFM software, select Programming > Cantilever Holder and Sample Panel. XXX 3. Click Check Holder and the type of cantilever holder is highlighted.

  • Page 58: Attaching The Es Cantilever Clip

    Cypher SPM User Guide 9.3.2 Attaching the ES cantilever clip 1. Cantilever holder. The Cantilever holder should be sitting ready without a clip, as shown. 2. Prepare the clip. Put the screw, clip, and O-ring together as shown. Screw only a few turns into the threaded hole in the glass of the cantilever holder.

  • Page 59: Cleaning The Es Cantilever Holder

    Cypher SPM User Guide 3. Check clip rotation. Rotate the clip so it does not overhang any of the glass cutout's edges. Press down on the clip so it settles down into the cutout area of the glass. 4. Tighten the screw.
  • Page 60 Cypher SPM User Guide 1. Locate parts. Locate the Cleaning Cup (114.820). Select the cantilever holder you want to clean. Optionally, remove the screw and clip (see 18.2.1). 2. Attach holder to cup. Make sure the screws are loose enough.

  • Page 61: Storage

    Cypher SPM User Guide 9.5 Storage After cleaning, store the cantilever holder in the membrane box in which it originally shipped. Page 61 of 243 9 Environmental scanner cantilever holders...

  • Page 62: Cell Body And Sample Stage Guide

    Cypher SPM User Guide Cell Body And Sample Stage Guide The sealed environment around the sample and cantilever is formed by three components: The cantilever holder forms the lid. The cell body forms the sides. The sample stage forms the bottom.

  • Page 63: Gas Cell Parts List

    Cypher SPM User Guide Electrical Connector Magnetic Contacts 10.1.1 Gas cell parts list Part # Item Description Picture The scale in the photos is in cm and mm. 901.746 Gas Cell Body. 114.916 Boot Clamp Ring, 8 Bolt Pattern. Con-...

  • Page 64: Gas Cell Specifications

    Cypher SPM User Guide Part # Item Description Picture 1-72 x 0.25 1-72 x 1/4” long screw. Used to lock SHCS SS down the cantilever holder. 448.137 Gas Cell Cable. Cable to connect to magnet contacts. 10.1.2 Gas cell specifications Exposed materials Cell wall:...

  • Page 65: Gas Cell Cable Installation

    Cypher SPM User Guide 10.1.3 Gas cell cable installation 1. Raise the engage stage fully. Rotate the Engage Control Knob on the Cypher clock- wise and hold until the cantilever holder is far from the sample or is at its upper limit of travel.
  • Page 66 Cypher SPM User Guide 5. Grip the cable with tweezers. Using sharp straight tipped tweezers, grip the con- nector as shown. 6. Insert the connector. Carefully insert the connector as shown. 7. Insert the smaller connector. Insert the smaller connector as shown on the left.

  • Page 67: Applying Sample Bias Or Ground

    Cypher SPM User Guide 10.1.4 Applying sample bias or ground 1. Sample mounting. Mount your sample onto the Electrical Sample Puck Assembly (448.140) using silver paint or some other conductive adhesive. 2. Never load non-flat samples into the ES scanner.

  • Page 68: Fluid Cell Body

    Cypher SPM User Guide 4. Sample GROUND connection. Insert the sample puck as shown. Use blunt tipped tweezers to connect the wire as shown to the MIDDLE connection. This grounds the sample. Tip: Lower the cell body to get more sample access by rotating the Engage Control Knob coun- terclockwise until it reaches its lower limit of travel.

  • Page 69: Fluid Cell Specifications

    Cypher SPM User Guide Item Part # Item Description Picture Fluid Cell Body. 114.916 Boot Clamp Ring, 8 Bolt Pattern. Con- nects to the bottom of the cell to form the seal between the cell body and the sample stage membrane.

  • Page 70: Humidity Cell

    Cypher SPM User Guide 10.3 Humidity cell Part # Holder Description Front Photo Back Photo XXX.XXX Humidity Cell The Humidity Cell assembly consists of the cell body and an interconnect board called an Applic- ations Board. The humidity sensor is located behind the center hole in the side of the cell’s interior. The two elec- trodes located on either side of the sensor opening provide electrical connections to analog ground and sample bias.

  • Page 71: Humidity Cell Installation

    Cypher SPM User Guide Item Part # Item Description Picture Humidity Cell Body. 114.916 Boot Clamp Ring, 8 Bolt Pattern. Con- nects to the bottom of the cell to form the seal between the cell body and the sample stage membrane. See 3..
  • Page 72 Cypher SPM User Guide 3. Install the applications board. Place the applications board over the connections on the top right side of the Environmental scanner. 4. Seat the board. Gently push the board onto the connectors. 5. Fit the cell body into the scanner and secure it to the engage stage ring with 3, 2-56 x 1/8”...
  • Page 73 Cypher SPM User Guide 8. Rescan the smart start bus. Rescan the smart start bus to allow the software to detect the addition of the applications board and the cell body. Verify that the devices are now present in the device list.

  • Page 74: Ambient Sample Stage

    Cypher SPM User Guide 10.4 Ambient sample stage Part # Holder Description Front Photo Back Photo 901.761 For imaging at ambient temperatures. Safe for gas and fluid operation. The ambient sample stage is the first choice for imaging at room temperature.

  • Page 75: Heater Sample Stage

    Cypher SPM User Guide The whole stage can be immersed or sonicated in ethyl or isopropyl alcohol or water. Liquid use Safe for use with samples in liquid droplets. 10.5 Heater sample stage Part # Holder Description Front Photo Back Photo 901.747...

  • Page 76: Cooler Heater Sample Stage

    Cypher SPM User Guide Temperature range Ambient to 250 ºC as measured by a sensor embedded several 0.5 mm below the surface on which the sample sits. Cleaning Only wipe the sample stage with a swab dampened with alcohol. Liquid use Not for use with any kind of liquid.

  • Page 77: Reminders For Cell Exchange And Handling

    Cypher SPM User Guide Electrical Stage surface is not grounded (floating) and sufficiently isolated to be safe for use with high voltage applications. Temperature range 0 ºC to 120 ºC as measured by a sensor embedded several several mm below the surface on which the sample sits.
  • Page 78 Cypher SPM User Guide 2. Be careful not to poke the sample stage diaphragms. Be careful never to poke the sample stage dia- phragms with tweezers or screwdrivers as this may cause a hole in the diaphragm. Some versions of the sample stages have per- manently attached diaphragms.

  • Page 79: Disassembling The Sample Stage From The Cell Body

    Cypher SPM User Guide 5. Remember to cut off extra tubing before connecting gas lines to the cell body. If you are using a Cypher ES that shipped before 2014 it is likely that you need to cut off the extra length of tubing that extends past the end of the ferrule on the gas lines.

  • Page 80: Separating The Sample Stage And Chamber

    Cypher SPM User Guide The disassembly example describes replacing an ambient stage with a heater stage on a gas cell body. 10.8.1 Separating the sample stage and chamber 1. Locate the 1.7 mm slotted screwdriver and a pair of curved tweezers.
  • Page 81 Cypher SPM User Guide 4. Using a 1.7 mm flat tipped screwdriver, loosen all the screws. Be careful not to slip and possibly puncture the membrane with the screwdriver. 5. Remove the retaining ring and set it and the screws aside.

  • Page 82: Attach Cell Body And Sample Stage

    Cypher SPM User Guide 10.8.2 Attach cell body and sample stage 1. Prepare parts. Sample stage on the left. Cell body in the middle Membrane clamping ring and screws to the right. More screws (00-90 X 1/8”) can be found in the Envir-...
  • Page 83 Cypher SPM User Guide 5. Tighten the screws. Using a 1.7 mm flat tipped screwdriver, tighten all the screws. First tighten them in the pattern shown for the first four. When all 8 screws are snug, go around once more and tighten firmly while holding the tool only with fingertips to prevent over-tightening.

  • Page 84: Exchanging The Sample Stage And Cell Body

    Health and safety on page 10). You are familiar with the basic names of the hardware components and software controls (see What is a Cypher SPM system? on page 19). This example procedure uses an environmental scanner equipped with an ambient stage and fluid cell body combination and replaces that with a heater stage and gas cell body combination.

  • Page 85: Required Materials

    Cypher SPM User Guide The following image shows an ambient stage and fluid cell body combination on the left. and a heater stage and gas cell body combination on the right. 10.9.1 Required materials You need the following items: Tweezers, preferably with curved tip (for example, Asylum Part #290.102).

  • Page 86: Prepare The Scanner

    Cypher SPM User Guide 10.9.2 Prepare the scanner 1. Remove the cantilever holder and place it, cantilever tip facing upwards, to the side. See the four steps beginning with Loading the cantilever and sample on an environmental scan- ner on page 205 2.
  • Page 87 Cypher SPM User Guide 3. Pull the cell body partway out. Grasping the cell blocks, pull up on the cell body until the diaphragm is fully extended. 4. Loosen fittings of gas inlet and outlet lines. Grasp the cell body with your dominant hand.

  • Page 88: Mounting The New Stage And Cell Combination

    Cypher SPM User Guide 10.9.4 Mounting the new stage and cell combination 1. Check the membrane shape. Make sure the rubber membrane on the sample stage is properly formed as shown in the photo. See the three steps beginning with Preform the dia- phragm.
  • Page 89 Cypher SPM User Guide 5. As shown, guide the connector under the ring and leave it sitting loose on the top of the scan- ner. 6. Attach gas lines. Using only your fingers to tighten the screws, attach the gas lines to the cell body as shown.

  • Page 90: Replacing The Scanner

    Cypher SPM User Guide 9. Secure the cell body. Locate three 2-56 X 1/8” screws and the 1/16” hex driver tool. Fasten the screws as shown, using only your fin- gertips to hold the tool. This will prevent over tight- ening.

  • Page 91: Storing Sample Stages And Cell Bodies

    Cypher SPM User Guide 10.10 Storing sample stages and cell bodies Once a sample stage has been removed from a cell body, it should be stored in the membrane con- tainer in which it shipped. Various stages and cell bodies are shown below, stored in their con- tainers.
  • Page 92 Cypher SPM User Guide 3. Place the cap as shown, with the cutout placed where the cable exits the heater stage. 4. Close the box. Close the box and latch it. Inspect the other side to see that the diaphragm is not overly deformed.

  • Page 93: Gas Handling And Leak Testing

    Cypher SPM User Guide Gas Handling And Leak Testing The following image shows the front of the scanner with the cover removed. The two gas lines attached to the sample cell body are routed via tubing guides to the lower left of the scanner.

  • Page 94: Manifold Cell-Side Connection

    Cypher SPM User Guide 11.2 Manifold cell-side connection The following procedure describes how to remove the tubing connected on the cell-side of the valve manifold. 1. Remove the fitting using the tool. Place the tool on the fitting. The slot in the tool slides over the tubing.

  • Page 95: Manifold Lab-Side Connection

    Cypher SPM User Guide 3. Remove fittings while holding manifold. Pull the manifold forward a little. Pay attention not to apply tension to the tubing or the wires. Remove the fitting using fingers or the tool shown in previous steps.

  • Page 96: Gas Perfusion Imaging

    Cypher SPM User Guide 3. Tighten fitting. Tighten the fitting as shown. Do not over tighten. Holding the tool with fingertips only should prevent any damage to the fitting. 4. Guide the tubing. Press the tubing into the guides. Tip: The tubing is not perfectly round and it may fit better if it is twisted a bit.

  • Page 97: Glovebox Protocols

    Cypher SPM User Guide Glovebox Protocols Cypher AFMs offer superb imaging performance inside of inert gas glovebox systems. While this solution offers the ultimate protection of the sample and cantilever from ambient conditions, it is not always practical to sequester an AFM inside of a glovebox for long periods of time. A decent alternative strategy is to assemble the cell inside of a glovebox and then to carry this assembly to the AFM which is located elsewhere.

  • Page 98: Preparing The Cell And Gas Lines

    Cypher SPM User Guide 3. Start imaging under the conditions (speed, scan size, and so on) you eventually plan to use on the sample which was mounted and sealed inside the glovebox. 4. Observe image quality while you experiment with the inert gas flow and note the maximum flow before imaging noise becomes noticeable.
  • Page 99 Cypher SPM User Guide 6. At one end of each of piece of tubing, secure a threaded fitting and a ferrule. Attaching threaded fittings to tubing on page 96. 7. At the other end of each piece of tubing, perform steps 8–10 to attach a female luer fitting.

  • Page 100: Seal The Cell

    Cypher SPM User Guide 13. Attach a valve to one of the two tubing ends, as shown: 12.3 Seal the cell Read ahead through the instructions and collect all the required items to place inside the glovebox. 1. Inspect the cantilever holder.
  • Page 101 Cypher SPM User Guide 5. Extend the membrane. Pull down on the bottom of the sample stage to fully extend the rubber membrane, carefully, as shown. 6. Place the cantilever holder. Remove the two screws indicated and set them aside. You will need to take them out of the glovebox along with the cell later.

  • Page 102: Mount The Sealed Cell Onto The Afm

    Cypher SPM User Guide 9. Close the valve. Make sure the valve is in the off position, if it was not already. The cell is now fully sealed on all sides. 10. Take the assembled cell out of the glovebox.
  • Page 103 Cypher SPM User Guide 1. Place the cell onto the scanner. Seat the foot of the cell onto the receptacle located on top of the scanner. The trapped air inside the cell will prevent the tip from colliding with the sample.
  • Page 104 Cypher SPM User Guide 4. Secure sample chamber to scanner with two screws. Secure the sample chamber with screw number 1. Do not over-tighten. If your cantilever holder has a hole in the position marked (2), secure that screw also.
  • Page 105 Cypher SPM User Guide 8. Attach the gas line to the valve, and turn on the gas flow to purge the interior of the valve. Gas flow rate is chosen by the user. Gas will flow to atmosphere. 9. Remove the syringe from the tubing at one end.

  • Page 106: Part Iv: Instrument Components

    Part IV: Instrument Components This part of the user guide covers the description, installation and exchange of hardware components of the instrument: scanner, optics, laser module, and blueDrive.

  • Page 107: Optical System

    Cypher SPM User Guide Optical System The Cypher AFM has an excellent optical system. A high quality microscope objective sits at the heart of this system. It affords an excellent optical view of the sample but also guides laser beams for the cantilever detection system.

  • Page 108: View System

    Cypher SPM User Guide 13.2 View system The view system protrudes from the top of the AFM enclosure. It contains a software controlled white light source and camera. It also has three user controls. Two levers for adjusting image bright- ness and contrast, and a focus ring.

  • Page 109: Scanner Exchange

    Cypher SPM User Guide Scanner Exchange The Cypher AFM can be purchased with various scanner modules. This section describes how to safely swap from one scanner to another. 14.1 Removing the scanner The following procedure shows the removal of the environmental scanner. The steps are the same for any other model.
  • Page 110 Cypher SPM User Guide 3. Power off the ARC2. Turn the ARC2 off before proceeding. Press the button as shown and verify the green light is off. Note: The light behind the display on the scanner front remains on because it uses a different power supply.

  • Page 111: Scanner Storage

    Cypher SPM User Guide 6. Detach the scanner from the chassis. Turn the knob on the right side of the scanner coun- terclockwise to unscrew. The knob disengages and retracts back towards the chassis. Tip: If the knob does not disengage readily, make sure the scanner body is pulled out sufficiently from the chassis.
  • Page 112 Cypher SPM User Guide 5. Make sure the locking lever on the chassis is in the raised position. 6. Set the scanner on the rails. Grasp both sides of the scanner and remove. Place your fingers under the two dovetail rails as shown in the photo.
  • Page 113 Cypher SPM User Guide 10. Turn the AC2 back on. Press the button as shown. The light must remain green. 11. If you are prompted to re-home the motors during the start-up process, please do so. 12. When the process completes, click The popup list of attached hardware should include the scanner.

  • Page 114: Light Tubes

    Cypher SPM User Guide Light Tubes The following instructions describe exchanging the light tube assembly in the Cypher AFM. The light tube can be exchanged without disassembly through the front of the instrument when you have some experience of the process. For clarity the instructions describe exchanging the light tube by disassembling the enclosure followed by the process done through the front of the instrument.
  • Page 115 Cypher SPM User Guide Part # Item Description Picture 901.601 SLD assembly, standard spot size. 901.602 SLD assembly, small spot size. 901.603 Laser diode assembly, standard spot size. Page 115 of 243 15 Light tubes...

  • Page 116: Exchanging A Light Tube

    Cypher SPM User Guide Part # Item Description Picture 901.604 Laser diode assembly, small spot size. 15.2 Exchanging a light tube You can exchange the Light tube without removing the top of the enclosure. However, we recom- mended that you first familiarize yourself with the system by removing the top cover at least once so that you are certain of the location of the components involved.
  • Page 117 Cypher SPM User Guide 4. Remove the optics cover. Grip the cover at its lower edge and gently pull for- ward. It is attached magnetically and will detach of smoothly. Note: This exposes the head assembly and enables access to the light tube from the front.

  • Page 118: Spot On Calibration

    Cypher SPM User Guide 9. Pull out the light tube. Touch a metal part of the SPM instrument to ground yourself. Grip the light tube's red handle. Gently push straight back. The light tube should slide out very smoothly. If not, further loosen the knob.

  • Page 119: Readjusting The Spot On Calibration

    Cypher SPM User Guide due to subtle position shifts in the relationship of the optical components, the light may settle in a new location. Once the light tube is installed and any corrections are made to the calibration, the spot accuracy of the Spot On routine is very repeatable. If the Spot On software routine appears to...
  • Page 120 Click in the center of the cantilever and confirm that Spot On is properly calibrated. The light tube is now calibrated for use (and re-use) in your Cypher SPM. Each light tube has a small memory element which stores the calibration values. To view the light tube infoblock, click on the gear icon at the bottom of the screen, then select Laser Module >...

  • Page 121: Reconnecting The Light Tube Cable

    Be especially careful while removing and replacing the cover and in general any time the cover is missing. The Cypher SPM is heavy, but it can slide around. If it does slide around, the elec- trical connections can be dislodged or even damaged.
  • Page 122 Cypher SPM User Guide 1. Make sure the right door is still open. 2. Note alignment pins. Note the pins which help the top cover align and find its proper place. When the top cover is removed, the weight of the doors can bend the enclosure's vertical support out- ward.
  • Page 123 Cypher SPM User Guide 11. Replace View System bracket. Replace the bracket in front of the view system. Tighten the screws. Page 123 of 243 15 Light tubes...

  • Page 124: Bluedrive Photothermal Excitation

    Cypher SPM User Guide BlueDrive Photothermal Excitation blueDrive is an optional accessory mounted onto the Cypher Chassis which focuses a blue laser spot onto the cantilever. The blue laser provides an alternative drive mechanism to the standard piezoacoustic drive mechanism used to excite the cantilever (a.k.a piezo drive).

  • Page 125: How Much Light Power Do You Need

    Cypher SPM User Guide The benefits of such a direct drive mechanism are similar to those of magnetic actuation (iDrive), but with the advantage of being applicable to cantilevers of all shapes and sizes. Photothermal excitation allows quantitative imaging in all environments, and the benefits are especially note- worthy in liquids, where blueDrive enables stable imaging for hours.

  • Page 126: Hardware Components

    Cypher SPM User Guide 16.3 39.2 Hardware components Item Part # Item Description Picture 934.001 The main blueDrive optomech- anical unit comes premounted onto the Cypher head 900.266.01-05 Filter cubes (900.266.01-05), labelled by their gain factor: 0.01x, 0.03x, 0.10x, 0.30x, or 1.00x 934.005...

  • Page 127: Installing Bluedrive

    Cypher SPM User Guide 16.4 Installing blueDrive 1. Connect interlock switch to blueDrive board. blueDrive is mounted to the Cypher Chassis when tested in factory. During shipping, it remains moun- ted to the Chassis and wired to the Cypher head board that controls blueDrive.
  • Page 128 Cypher SPM User Guide If you need to exchange a filter cube, follow this procedure. 1. Remove the installed filter cube. Grip the filter cube mounted to the blueDrive unit. Pull on the filter cube directly away from the blueDrive unit, towards the front of the Cypher, as shown by the arrow.
  • Page 129 Cypher SPM User Guide mW) accordingly. 3. Ensure high accuracy blue spot positioning. In some cases, the locating pins may have some fric- tion that prevents proper indexing of the filter cube, for example, if some dust gets into the indexing holes.

  • Page 130: Replacing The Laser Diode Module

    Cypher SPM User Guide 16.4.2 Replacing the laser diode module 1. Remove cover plate. Remove the optics cover if it is in place. See Installing blueDrive on page 127. Remove the filter cube, as described in Changing fil- ter cubes on page 127.

  • Page 131: Focusing The Blue Laser Spot

    Cypher SPM User Guide 3. Insert the replacement laser diode. Push the laser diode module inwards with your fin- ger with moderate force, while rotating the hex key clockwise to tighten the new laser diode module, as shown in the photograph to the right.

  • Page 132: Choosing The Correct Cantilever

    Cypher SPM User Guide 3. Focus the blue laser spot. This is achieved with a 0.050” hex wrench that is inser- ted into the filter cube hole, as shown to the right. Open the door to rotate the wrench. The blue spot turns off.
  • Page 133 Cypher SPM User Guide Some cantilevers are photothermally sensitive and provide large amplitudes, such as 100 nm, even with the lowest filter cube (0.01x). Using a 1.00x filter cube on such a sensitive cantilever could cause overheating and permanent damage to the lever.

  • Page 134: Bluedrive Software Interface

    Cypher SPM User Guide The DC power of the blue light at the cantilever is fixed. Meanwhile, the drive amplitude, which is the AC power modulation of the blue light at the drive frequency, can be adjusted continuously on the Tune panel as with a conventional piezo drive. It is the AC power, not the DC power, which determines the oscillation amplitude of the cantilever.

  • Page 135: Positioning The Blue Spot

    Cypher SPM User Guide 16.7.2 39.5.3 Positioning the blue spot The blue spot may be positioned in several ways using the new controls that appear on the View Window once “blueDrive” is selected on the Tune Panel, as shown in previous section.
  • Page 136 Cypher SPM User Guide Right-clicking on a partiular location of the View Window and clicking “Blue SpotOn” auto- matically moves the blue spot to that location. 16 blueDrive photothermal excitation Page 136 of 243...

  • Page 137: Acquiring A Cantilever Tune

    Cypher SPM User Guide (left) The blue arrows on the top/right of the View Window can be used to move the blue spot position in all directions. If enabled, the blue box follows the location of the moving blue spot.
  • Page 138 Cypher SPM User Guide It is not actually necessary to acquire a cantilever tune before imaging. Taking a thermal and fitting it to set the drive frequency to the cantilever resonance may suffice. That being said, cantilever tunes are very useful in determining whether everything is functioning appropriately.

  • Page 139: Part V: Tutorials And Workflows

    Part V: Tutorials and Workflows This part of the user guide provides tutorials for typical tasks and workflow examples built from the individual tuorials.

  • Page 140: Tutorials Introduction

    Cypher SPM User Guide Tutorials Introduction The following sections provide task-oriented procedures that cover typical setup and data acquis- ition using the Cypher SPM. Page 140 of 243 17 Tutorials introduction...

  • Page 141: Removing The Cantilever Holder On A Standard Scanner

    Cypher SPM User Guide Removing The Cantilever Holder On A Standard Scanner Note: If you own the environmental scanner, please follow the tutorial in Removing the can- tilever holder on an environmental scanner on page 151. 1. Raise the cantilever holder.
  • Page 142 Cypher SPM User Guide 3. Unlock the scanner by lifting the lever to the right of the scanner. 4. Pull the scanner forward. Pull the scanner forward gently and stop when it is about halfway out. If you continue pulling the scanner, at some point you will feel resistance and should pull no further.
  • Page 143 Cypher SPM User Guide 6. Release the cantilever holder. Locate the tool in the chassis to the left of the scan- ner. Loosen the screw clamping the cantilever holder. One turn counterclockwise should be enough - do not completely remove the screw.

  • Page 144: Changing The Cantilever On A Standard Scanner

    You need the following items to perform the tutorial: Cantilever You will need the chosen cantilever for the experiment you are preparing. Every Cypher SPM ships with a package of AC160s. Changing sta- The correct changing station for your cantilever holder.
  • Page 145 Cypher SPM User Guide 1. Select the cantilever holder. Identify the correct cantilever holder for your exper- iment. This tutorial uses the standard AC Air holder, part# 901.705. Tip: To learn more about cantilever holders for the standard scanner, see...
  • Page 146 Cypher SPM User Guide 4. After the cantilever holder is fully inserted, use the ball head wrench to gently tighten the clamp. 5. Remove the old cantilever. Position the changing station as shown, on a flat hard surface. Take the tweezers in your dominant hand.
  • Page 147 Cypher SPM User Guide 7. Load the new cantilever. Place and center the cantilever in the holder (also see image in next step for alignment). A good technique is to release pressure on the chan- ging station while still gripping the cantilever chip with tweezers.

  • Page 148: Inserting The Cantilever Holder On A Standard Scanner

    Cypher SPM User Guide Inserting The Cantilever Holder On A Standard Scanner Note: If you own the environmental scanner, please follow the tutorial in Inserting the can- tilever holder on an environmental scanner on page 157. You need the following items to perform the tutorial: Cantilever The cantilever holder with required cantilever installed for your experiment.
  • Page 149 Cypher SPM User Guide 3. Insert the chosen cantilever holder into scanner. Remove the cantilever holder from the changing sta- tion. Insert the cantilever holder into the scanner, ensur- ing that the metal dovetail engages properly. If it will not go in, loosen the screw by half a turn, using the tool in the chassis to the left of the scan- ner.
  • Page 150 Cypher SPM User Guide 6. Check correction collar. Check that the green correction collar on the object- ive is set properly. For example, for the air cantilever holder, set the cor- rection collar to 0. 7. Close the enclosure door and latch it.

  • Page 151: Removing The Cantilever Holder On An Environmental Scanner

    Cypher SPM User Guide Removing The Cantilever Holder On An Environmental Scanner Note: If you own the standard scanner, please follow the tutorial in Removing the cantilever holder on a standard scanner on page 141. 1. Raise the cantilever holder. Rotate the Engage Control knob on the Cypher clock- wise and hold it until the cantilever holder is far from the sample or is at its upper limit of travel.
  • Page 152 Cypher SPM User Guide 3. Unlock the scanner by lifting the lever to the right of the scanner. 4. Pull the scanner forward. Pull the scanner forward gently and stop when it is about halfway out. If you continue pulling the scanner, at some point you will feel resistance and should pull no further.
  • Page 153 Cypher SPM User Guide 6. Release the cantilever holder. Locate the tool with yellow tip in the chassis to the left of the scanner. Use tool to loosen the two screws clamping the can- tilever holder. One turn counterclockwise should be enough - do not completely remove the screws.

  • Page 154: Changing The Cantilever On An Environmental Scanner

    You need the following items to perform the tutorial: Cantilever You will need the chosen cantilever for the experiment you are preparing. Every Cypher SPM ships with a package of AC160s. Tools Part# 290.102: Tweezers with curved tips. Part# 290.106: 300 Philips screwdriver..
  • Page 155 Cypher SPM User Guide 3. Loosen the cantilever clip. Unscrew the clamping screws by one half turn. Do not remove the screw completely. If you do, refer Attaching the ES cantilever clip on page 58. 4. If a cantilever is already in place, use tweezers to remove it from the cantilever holder.
  • Page 156 Cypher SPM User Guide 6. Load the new cantilever. Use tweezers to slide the new cantilever under the clip. You can push or pull the cantilever into place as you find comfortable. Nudge the cantilever chip from the side so that the tip is approximately centered in the cantilever holder window.

  • Page 157: Inserting The Cantilever Holder On An Environmental Scanner

    Cypher SPM User Guide Inserting The Cantilever Holder On An Environmental Scanner Note: If you own the standard scanner, please follow the tutorial in Inserting the cantilever holder on a standard scanner on page 148. You need the following items to perform the tutorial: Cantilever The cantilever holder with required cantilever installed for your experiment.
  • Page 158 Cypher SPM User Guide 3. Place the cantilever holder that you want to insert. Position the cantilever holder in the cell body as shown in the image to the right. The cantilever holder should sit level and be rota- tionally aligned so that the cantilever holder board is almost touching its mating connector.
  • Page 159 Cypher SPM User Guide 7. Slide scanner into chassis. Use firm pressure until you feel a hard stop. Before you feel a hard stop you will feel a spring-like res- istance. You are making thermal contact between the scan- ner and the chassis. This is necessary for best per- formance.

  • Page 160: Engaging The Cantilever On The Sample

    Cypher SPM User Guide Engaging The Cantilever On The Sample Prerequisite: The sample must be loaded and the cantilever positioned about 1 mm above the sample. Loading the cantilever and sample on a standard scanner on page 198. Loading the cantilever and sample on an environmental scanner on page 205.
  • Page 161 Cypher SPM User Guide Prepare the view module: Turn the focus offset ring until the white dot is centered on the alignment mark. There will be a gentle click when this occurs. Fully open the field and aperture diaphragms by pushing both levers toward the front as shown.
  • Page 162 Cypher SPM User Guide Locate cantilever in image: The goal of this step is just to get the cantilever into the field of view. Use the four arrows at the top left of the video window to look for the edge of the cantilever chip and/or the cantilever.
  • Page 163 Cypher SPM User Guide Observe spot on lever: Motors inside Cypher will now move to bring the laser spot where you clicked. The spot position does not need to be perfect here, only roughly centered on the cantilever to produce a decent reflected beam (measured by the Sum signal in the Sum and Deflection Panel).
  • Page 164 Cypher SPM User Guide Prepare to land the tip: Click the Move to Pre-Engage button. Motors automatically bring the tip to 50μm from the sur- face. WARNING: If you set a bad sample height and/or tip position you may ram your cantilever into the sample and break it.
  • Page 165 Cypher SPM User Guide Sub-Figure a: First view of new cantilever. 24 Engaging the cantilever on the sample Page 165 of 243...
  • Page 166 Cypher SPM User Guide Sub-Figure b: Cantilever found and roughly centered on screen. 8.. Page 166 of 243 24 Engaging the cantilever on the sample...
  • Page 167 Cypher SPM User Guide Sub-Figure c: Cantilever in focus. See 9.. 24 Engaging the cantilever on the sample Page 167 of 243...
  • Page 168 Cypher SPM User Guide Sub-Figure d: Optimize Resolution. See 10.. Figure 4.1: Finding the cantilever and optimizing the video. Page 168 of 243 24 Engaging the cantilever on the sample...
  • Page 169 Cypher SPM User Guide Sub-Figure a: Cantilever Zoom. See 10.. 24 Engaging the cantilever on the sample Page 169 of 243...
  • Page 170 Cypher SPM User Guide Sub-Figure b: Laser Spot ON. See 11.. Page 170 of 243 24 Engaging the cantilever on the sample...
  • Page 171 Cypher SPM User Guide Sub-Figure c: Spot On by right clicking. See 11.. 24 Engaging the cantilever on the sample Page 171 of 243...
  • Page 172 Cypher SPM User Guide Sub-Figure d: Laser spot on the lever. See 12.. Figure 4.2: Various methods for aligning the laser spot onto the cantilever. Page 172 of 243 24 Engaging the cantilever on the sample...
  • Page 173 Cypher SPM User Guide Sub-Figure a: Offset. 24 Engaging the cantilever on the sample Page 173 of 243...
  • Page 174 Cypher SPM User Guide Sub-Figure b: The focus offset is centered and the optical image is confocal with the focused laser Page 174 of 243 24 Engaging the cantilever on the sample...

  • Page 175: Tuning The Cantilever For Ac Imaging

    Cypher SPM User Guide spot. Figure 4.3: By turning the focus offset knob, it is possible to focus on optical image on the sample while the laser stays focused on the cantilever. 24.2 Tuning the cantilever for AC imaging Initiate cantilever tune: Select the tune tab in the master panel.
  • Page 176 Cypher SPM User Guide Sub-Figure a: Master Panel, Main Tab. Page 176 of 243 24 Engaging the cantilever on the sample...

  • Page 177: Landing The Tip

    Cypher SPM User Guide Sub-Figure b: Master Panel, Tune Tab. Figure 4.4: 24.3 Landing the tip The preceding sections have left the tip vibrating about 50 microns above the sample surface. It's time to land. Start final tip approach: Locate the Engage Panel.
  • Page 178 Cypher SPM User Guide Wait for tip to reach sample: For the next minute or so Cypher will systematically move the tip closer to the sample until the set point is reached. You can cancel the approach at any time by pressing AND HOLDING the Esc key on your com- puter keyboard.
  • Page 179 Cypher SPM User Guide Question Why does the sample look out of focus when the tip is on the surface? How do I fix this? Answer The laser and video image both pass through the same microscope objective. While performing AFM, the objective must remain focused on the back of the cantilever to keep the laser focused.

  • Page 180: Ac Mode Imaging

    Cypher SPM User Guide AC Mode Imaging Prerequisite: You must engage the cantilever on the sample surface. Engaging the cantilever on the sample on page 160. Basic AC mode imaging comprises four parts: 1. Setup and initial parameter selection. 2. Imaging and parameter tuning.

  • Page 181: Start Imaging And Parameter Tuning

    Cypher SPM User Guide Image channel selection: Go to the Master Channel panel Select the leftmost tab and confirm the default setting of Height under the Input pull-down menu. For the next two tabs do the same for Amplitude and Phase.
  • Page 182 Cypher SPM User Guide Determining Image Quality: Start the learning process on a sample with a known topography, like the Asylum Research Cal- ibration Grating being used in this tutorial. Look at the 'Scope Trace' below the image. This graph represents the most recent line of the image.
  • Page 183 Cypher SPM User Guide Hamster The next steps will go into the details of strategies for tuning parameters in the main panel. Use the arrow clickers (to right of variable fields) to adjust parameters, rather than typing the values in. Alternatively, you can fine-tune the parameters using the Hamster wheel on the front of the controller.
  • Page 184 Cypher SPM User Guide Adjusting Set-Point, i-gain, and scan speed: The goal is to get trace and retrace to fall on top of each other (as shown above). Increase the Integral Gain or i-gain parameter (second highlighted item in 1.) and see what hap- pens.
  • Page 185 Cypher SPM User Guide View Data in Real Time 3D: Open the Master ArGL Panel by selecting from the menu bar AFM Analysis ⇒3D Surface Plots. From the Surface pull-down select Real time From the Data Type pull-down to the right of it, select the desired channel in that image (usually Height or Zsenor).
  • Page 186 Cypher SPM User Guide Sub-Figure a: Before the Move. Page 186 of 243 25 AC mode imaging...
  • Page 187 Cypher SPM User Guide Sub-Figure b: After the Move Figure 4.5: Moving a Sample After a Scan 25 AC mode imaging Page 187 of 243...

  • Page 188: Image Refinement

    Cypher SPM User Guide 25.3 4.4.3 Image Refinement To learn more about using the Asylum Research SPM software to refine your imaging parameters, please refer to and also ??. Also consider watching this introductory video: AC Mode Imaging in (requires an internet connection).

  • Page 189: Contact Mode Imaging In Air

    Cypher SPM User Guide Contact Mode Imaging In Air 26 Contact mode imaging in air Page 189 of 243...

  • Page 190: Preparing For Conductive Afm Imaging On The Standard Scanner

    Cypher SPM User Guide Preparing For Conductive AFM Imaging On The Standard Scanner This section explains the use of the ORCA cantilever holder. In practical terms, the ORCA cantilever holder is simply a standard air cantilever holder with the addition of a current to voltage converting amplifier.

  • Page 191: Preparing The Sample

    Cypher SPM User Guide 1. Measure the Sample Bias voltage on the scanner's terminal block. Check the 'Use' check box next to the Sample Voltage parameter in the DoIV control panel. Note: In this example, the measured offset Bias voltage is -46 mV.

  • Page 192: Install The Sample On The Scanner And Connect The Bias Lead

    Cypher SPM User Guide 27.2.1 Install the sample on the scanner and connect the bias lead 1. Place the sample on the scanner stage and connect the bias lead. Position the sample so that the magnet is on the right hand side of the scanner to prevent inter- ference with the cantilever holder.

  • Page 193: Preparing For Conductive Afm On The Environmental Scanner

    Cypher SPM User Guide Preparing For Conductive AFM On The Environmental Scanner Conductive AFM works only with the gas cell body, but with any sample stage. Prerequisites: Assemble your sample stage and gas cell body, as described in Attach cell body and sample stage on page 82.
  • Page 194 Cypher SPM User Guide 3. Mount your sample. Use the low profile electrical sample puck assembly (448.140) using silver paint or some other conductive adhesive (upper image). Unlike the S scanner, the ES scanner cannot accept non-flat samples. A non-flat sample is any sample in which the region to be scanned is not the tallest fea- ture on the sample puck.

  • Page 195: Current Imaging With Conductive Afm

    Cypher SPM User Guide Current Imaging With Conductive AFM Mode Master The Mode Master panel appears when you first open up the AFM software. If it is not present, click the Mode Master button at the bottom in the taskbar: Select Orca Mode Load the Orca template from the Mode Master .
  • Page 196 Cypher SPM User Guide Open the Channels 2. Select Current as one of the channel Inputs under the Master Channel Panel (AFM Con- trols ⇒Master Channel Panel (Ctrl+7)). For the Dual-gain ORCA holder you will have two channels instead, Current 1 and Current 2.
  • Page 197 Cypher SPM User Guide Current Offset There are often small, persistent current offsets associated with the AFM electronics that must be subtracted. Zero the Current Offset by pressing the Zero button in the AR Do IV Panel. Applying Voltage Like the current, there are also often small, persistent voltage offsets between the AFM and the sample.

  • Page 198: Workflows

    This tutorial covers sample and cantilever loading as well as the coarse approach of the cantilever tip toward the sample. It is designed for a Cypher SPM equipped with the standard scanner and a standard spot SLD or laser module (see Types of light tube and how to identify them on page 114).
  • Page 199 Cypher SPM User Guide 1. Raise the cantilever holder. Rotate the Engage Control knob on the Cypher clock- wise and hold it until the cantilever holder is far from the sample or is at its upper limit of travel. If you turn the knob counterclockwise you will lower the cantilever holder, risking collision with the sample and damage to the scanner.
  • Page 200 Cypher SPM User Guide 5. Familiarize yourself with the sample area. While it may look solid, the scanner stage moves the sample in the X, Y, and Z directions imperceptibly up to 40 μm. 6. Release the cantilever holder. Loosen the screw clamping the cantilever holder.
  • Page 201 Cypher SPM User Guide 8. Select the AC mode cantilever holder. Identify the correct cantilever holder. This demo uses the standard AC Air holder, part# 901.705. Tip: To learn more about cantilever holders for the standard scanner, see Visual identification of SS can- tilever holders on page 35.
  • Page 202 Cypher SPM User Guide 11. After the cantilever holder is fully inserted, use the ball head wrench to gently tighten the clamp. 12. Remove the old cantilever. Position the changing station as shown, on a flat hard surface. Take the tweezers in your dominant hand.
  • Page 203 Cypher SPM User Guide 14. Load the new cantilever. Place and center the cantilever in the holder (also see image in next step for alignment). A good technique is to release pressure on the chan- ging station while still gripping the cantilever chip with tweezers.
  • Page 204 Cypher SPM User Guide 18. Tighten the cantilever holder. Use the ball headed wrench to gently tighten the screw that clamps the cantilever holder. Don't use your whole hand! Be gentle! 19. Secure scanner in place. Gently slide the scanner back into the chassis.

  • Page 205: Loading The Cantilever And Sample On An Environmental Scanner

    This tutorial covers sample and cantilever loading as well as the coarse approach of the cantilever tip toward the sample. It is designed for a Cypher SPM equipped with the environmental scanner and a standard spot SLD or laser module (see Types of light tube and how to identify them on page 114).
  • Page 206 Cypher SPM User Guide 1. Raise the cantilever holder. Rotate the Engage Control knob on the Cypher clock- wise and hold it until the cantilever holder is far from the sample or is at its upper limit of travel. If you turn the knob counterclockwise you will lower the cantilever holder, risking collision with the sample and damage to the scanner.
  • Page 207 Cypher SPM User Guide 4. Pull the scanner forward. Pull the scanner forward gently and stop when it is about halfway out. If you continue pulling the scanner, at some point you will feel resistance and should pull no further.
  • Page 208 Cypher SPM User Guide 7. Rotate the cantilever holder. Place your fingers on the two side cantilever holder handles. Rotate counterclockwise a few degrees. The cantilever holder circuit board comes out of its mating connector (1). Stop when the board has cleared the connector.
  • Page 209 Cypher SPM User Guide 11. Prepare the cantilever mounting workspace. Set out your cantilever holder, tweezers, and can- tilevers on a clean, well lighted surface. A low power binocular dissection stereoscope with light source can be useful for some of the following steps.
  • Page 210 Cypher SPM User Guide 15. Load the new cantilever. Use tweezers to slide the new cantilever under the clip. You can push or pull the cantilever into place as you find comfortable. Nudge the cantilever chip from the side so that the tip is approximately centered in the cantilever holder window.
  • Page 211 Cypher SPM User Guide 17. Rotate the Engage Control knob counterclockwise until it reaches its lower limit of travel. 18. Remove old sample. Use Platypus tweezers (part # 290.165) to remove the old sample from the sample stage. Wipe the sample stage clean with a cloth or use com- pressed air.
  • Page 212 Cypher SPM User Guide 21. Place the cantilever holder. Position the cantilever holder in the cell body as shown in the image to the right. The cantilever holder should sit level and be rota- tionally aligned so that the cantilever holder board is almost touching its mating connector.
  • Page 213 Cypher SPM User Guide 25. Slide scanner into chassis. Use firm pressure until you feel a hard stop. Before you feel a hard stop you will feel a spring-like res- istance. You are making thermal contact between the scan- ner and the chassis. This is necessary for best per- formance.

  • Page 214: Ac Mode Imaging In Air With The Standard Scanner

    All new users should complete and understand this tutorial before attempting any ima- ging. This tutorial provides a quick path to learning the basic operation of the Cypher SPM equipped with the standard scanner. It contains a set of steps that will teach a new user with a basic under- standing of AFM operation how to obtain an AC mode topography image in air.
  • Page 215 Cypher SPM User Guide This tutorial provides a quick path to learning the basic operation of the Cypher SPM equipped with the environmental scanner. It contains a set of steps that will teach a new user with a basic understanding of AFM operation how to obtain an AC mode topography image in air. The tutorial takes approximately 3 hours to complete.

  • Page 216: Part Vi: Shipping And Maintenance

    Part VI: Shipping and Maintenance This part of the user guide covers moving and shipping the instrument.

  • Page 217: Shipping Or Moving

    Cypher SPM User Guide Shipping Or Moving This chapter contains instructions on how to take a fully operational Cypher AFM, partially dis- assemble it, and move it to another location. When shipping or moving all of the Cypher AFM, follow this chapter from start to finish. When ship- ping only one component, jump straight to the section which focuses on that component.

  • Page 218: Instrument Weight

    Cypher SPM User Guide Use only the original cartons and foam for shipping this delicate equipment. If you do not have the cartons described in this chapter, contact Asylum Research and request empty cartons with foam. 31.3 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.
  • Page 219 Cypher SPM User Guide 1. Raise the coarse engage stage. Rotate the Engage Control Knob on the Cypher clock- wise and hold it until the cantilever is at its highest position. You will probably need to change a cell body after scan- ner removal, so it is best to raise the stage now to make those later actions possible.
  • Page 220 Cypher SPM User Guide 4. Unlock the scanner by lifting the lever to the right of the scanner. 5. Begin to pull the scanner out. Pull the scanner out about halfway. Unscrew the scanner connector cable on the right side of scanner.
  • Page 221 Cypher SPM User Guide 7. Remove scanner. Grasp both sides of the scanner and remove. Place your fingers under the two dovetail rails as shown in the photo. Use care because the scanner is heavy. Preferably place the scanner right in front of the AFM and then pick it up again to move it to its storage loc- ation.

  • Page 222: Removing The Enclosure Top Cover

    Be especially careful while removing and replacing the cover and in general any time the cover is missing. The Cypher SPM is heavy, but it can slide around. If it does slide around, the elec- trical connections can be dislodged or even damaged.
  • Page 223 Cypher SPM User Guide 3. Locate the 3/32 Hex Driver (part#290.134). 4. Lift the door latch and open the enclosure door. 5. Remove bracket. Take out two screws on the bracket in front of the view system. After removing both screws pull this piece out and set aside.
  • Page 224 Cypher SPM User Guide 7. Unscrew right door bottom. Unscrew 2 screws in the right door on the bottom and set aside. SCREW INFO: 8-32 x ½ BHCS SS Note: There may be only one screw. 8. Unscrew right door top.

  • Page 225: Backpack Removal And Packaging

    Cypher SPM User Guide 11. Adjust view system sliders. Adjust the view system slider controls to their half- way positions. This puts them safely out of way of the top cover. 12. Remove enclosure top. Lift upward while wiggling to remove the enclosure top.
  • Page 226 Cypher SPM User Guide 1. Loosen the 2 side screws. Use the 3/32" hex driver. Do not remove the screws completely. 2. Remove the piece of foam from inside the chassis nearest the backpack screws you just loosened. 3. Disconnect the ground cable.

  • Page 227: Chassis Removal And Packaging

    Cypher SPM User Guide 5. Separate the backpack from the chassis. Slowly pull the backpack toward yourself. Guide both the disconnected pass-through board and the ground cable through the hole. Remove the pass-through board from the backpack by pulling it out toward yourself. Set this board aside...
  • Page 228 Cypher SPM User Guide Materials Part# 991.016: Cardboard Carton 16" x 14" x 17" Part# 990.034: Foam (chassis) Part# 113.495: Chassis Packing Guard a.k.a “the Mullet” 10-32 x 1/4 or 1/2 BHCS SS Bolts (2EA) depending on which guard you...
  • Page 229 Cypher SPM User Guide 3. Remove the chassis from the enclosure. Use the handles on either side of the chassis, as indic- ated in the picture. The chassis is heavy. Use all your fingers to lift it. Set aside on a safe, hard surface.
  • Page 230 Cypher SPM User Guide 6. Tape down the clamping screw. 7. Tape both the phone cable & the laser module cable to the top bridge of the chassis in the cen- ter. 8. Put lens tissue and Kapton tape over the hot mirror and wrap tape around to cover the side port hole 9.
  • Page 231 Cypher SPM User Guide 10. Use lens tissue and Kapton tape to fill and cover the objective hole in the underside of the head. 11. Secure remaining scanner items. Tape down the scanner release lever. Tape down the scanner connector cable so it does not move in shipment.
  • Page 232 Cypher SPM User Guide 13. Slide on the guard carefully. 14. Secure side screws. 1-2 screws need to go in either side. Use a 1/8" hex wrench L-key (part#290.119). SCREW INFO: 10-32 x 1/4 or 1/2 BHCS SS, depending on which guard you have.

  • Page 233: Packaging The Enclosure

    Cypher SPM User Guide 16. Tighten the nuts. There is one nut on each side. Turn the nut back toward the screw head and tighten it with pliers (pliers not provided with sys- tem). SCREW INFO: 10-32 x1 1/2 or1 3/4 BHCS SS, depend- ing on which guard you have &...
  • Page 234 Cypher SPM User Guide 1. Secure all 3 cables inside the enclosure by taping them down to the center floor with Kapton Tape. 2. Replace enclosure top cover. The right door of the enclosure should still be open. With the door open, put the roof of the enclosure...
  • Page 235 Cypher SPM User Guide 4. Replace the right door top inside screws. There may be only one screw on each side. SCREW INFO: 8-32 x 1/2 BHCS SS. 5. Replace the left door top inside screws. There may be only one screw on each side.
  • Page 236 Cypher SPM User Guide 8. Tape the side lock down with Kapton tape. 9. Prepare the box and foam. The cutout in the foam aligns with the rear of the enclosure. 10. Place enclosure in the box. Carefully lift the enclosure and place in the bottom of the box.

  • Page 237: View Module Removal And Packaging

    Cypher SPM User Guide 12. Place the foam on top, one piece on each side. 13. Place the power cord for the airbase in the foam cut-out. 14. Place the 3/32 Hex Driver in the foam cut-out. 15. Close the box and tape it shut.
  • Page 238 Cypher SPM User Guide 1. Remove the phone cable. The cable is located on the bottom side of the View module. You must pinch one side of the connector to remove 2. Remove the FireWire cable. The cable is located on the bottom side of the View module.
  • Page 239 Cypher SPM User Guide 4. Use Kapton tape to secure lens tissue over the lens. 5. Put the module in a plastic bag and tape shut. 6. Secure the parts. Put the module in the view module foam, which has a square spot in the far corner.

  • Page 240: Packaging The Accessories

    Cypher SPM User Guide 8. Secure the objective parts. Place the objective in the round hole in the View module foam and push it all the way in; the lid should be flush with the top of the foam. Put the chassis/optics cover and airflow shield in the View module foam.
  • Page 241 Cypher SPM User Guide Final weight 5 lbs / 2 kg 1. Store the laser cube. Put the laser cube in an anti-static bag. Note: You must do this. After bagging, put into the plastic case (Part# 279.055). Open and close the case with yellow plastic clips C.

  • Page 242: Packaging Computers And Monitors

    Cypher SPM User Guide 3. Pack the cantilever holders and accessories. Place the cantilever holders and any small accessor- ies in the Cypher accessory kit. Close the Cypher accessory kit and place it in a foam slot in the accessory foam.
  • Page 243 Cypher SPM User Guide Item Weight (lbs / kg) Accessories box 5 / 2 Crate or pallet 46 / 21 Standard Total: 383 / 174 Options affecting shipping weight Item Weight (lbs / kg) TS-150 48 / 22 30" monitor...

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