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Asylum Research cypher User Manual

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

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Summary of Contents for Asylum Research cypher

  • Page 1 Cypher SPM User Guide USER GUIDE 2 Cypher User Guide Including beta (complete, reviewed) chapters. Including draft (nearly complete, not reviewed) chapters. Version 13, Revision: A-1714 Dated 10/25/2013 Asylum Research an Oxford Instruments company...

  • Page 2: Table Of Contents

    Contents Contents Contents ......I System Overview and Powering Up ........System Overview .
  • Page 3 Contents Contents ..........17 Optics .
  • Page 4 There are many ways to get help with your Asylum Research instrument, and it is always Getting Help free: • Join the support site and download software, current manuals, and ask questions in our user forum.

  • Page 5: I System Overview And Powering Up

    Part I System Overview and Powering Up After the Cypher SPM has been installed in your lab and you (or someone in your Who is this part for? facility) have completed the initial training, this part of the user guide will review the main parts of the instrument and software.
  • Page 6 ....... . Basic Cypher SPM Hardware ......... .

  • Page 7: System Overview

    Figure 1.1.: Ideally the Cypher SPM is set up as shown, with the controller and computer on one table and the microscope on its own table. The air temperature controller (ATC) is not shown here. Please see Chapter 19 on page 203 for more information.
  • Page 8 The air temperature controller (ATC) is a Cypher option that can be used to maintain the temperature inside the enclosure. To learn more about the enclosure and its options, please refer to Part IV on page 181.
  • Page 9 The backpack, however, moves these electronics closer to the micro- scope; Cypher is able to achieve very low noise levels in part because of the proximity between some of its electronics and the actual microscope. Keeping these low noise electronics external to the enclosure balances noise performance with the management of the heat generated by electronics.
  • Page 10 (Scanning Tunneling Microscopy), optical fibers (NSOM) or tiny hollow glass tubes (SICM). Since Cypher is capable of both AFM and STM, it is classified as an SPM. You may see Cypher referred to in the context of an AFM when its AFM-like functions are being described.
  • Page 11 The scale in the photos is in cm and mm. 1.3. The Igor Pro Software Environment The Asylum Research software is primarily written within the programming environment of the com- mercially available software package Igor Pro, which is developed by WaveMetrics. Igor Pro itself has nothing to do with scanning probe microscopes.
  • Page 13 Along the top of the screen. There are many more controls which can be invoked by items in Menu Bar the menu bar. Menu items to the left are typically standard Igor Pro items, with some Asylum Research functionality. Items to the right of “help” are exclusively SPM related. In particular, the...
  • Page 15 . You will hear motors moving during the homing process, which will take ‘Yes’ about 20 seconds. 6. If you are new to the Cypher AFM system, please take the tutorial which is appropriate for your scanner: • For the standard scanner see: Chapter 4 on page •...

  • Page 16: Standard Scanner

    Part II Standard Scanner After the Cypher S SPM has been installed in your lab and you (or someone in Who is this part for? your facility) have completed the initial training, this part of the user guide will be the principal reference for operating the instrument.
  • Page 17 Part Contents Standard Scanner Overview ........Tutorial: AC Mode in Air, Std.
  • Page 18 PART CONTENTS PART CONTENTS Scanning Tunneling Microscopy ....... . 103 .

  • Page 19: Standard Scanner Overview

    Figure 3.1.: The Standard Scanner Figure Figure 3.1 on page 15 shows the standard scanner partially withdrawn from the rest of the AFM. The standard scanner is included with the “Cypher S” AFM, but can also be purchased separately. The BETA Page 15...
  • Page 20 Standard scanner is designed primarily for imaging in ambient conditions, either in air or in a liquid droplet. The optical access to the sample and cantilever is superior to other cypher scanner models. Many Standard Scanner cantilever holders allow for a variety of imaging modes. See...

  • Page 21: Tutorial: Ac Mode In Air, Std. Scanner

    ....... . . Shutting the System Down This tutorial provides a quick path to learning the basic operation of the Cypher SPM equipped with the Standard Scanner. If you own the Environmental Scanner, please follow the tutorial in...

  • Page 22: Required Materials

    AC160TS, with a spring constant of ~42N/m and a resonance frequency of ~300kHz, is a workhorse for AC mode imaging in air. Every Cypher ships with a package of AC160s, but if these can- tilevers are unavailable, any cantilever with a similar spring constant and resonance frequency should work fine.
  • Page 23 Ch. 4. Tutorial: AC Mode in Air, Std. Scanner Sec. 4.2. Loading Lever and Sample Open enclosure: • Lift the door latch and open the enclosure door. Unlock scanner: • Lift the lever to the right of the scanner. Pull the scanner out: •...
  • Page 24 Ch. 4. Tutorial: AC Mode in Air, Std. Scanner Sec. 4.2. Loading Lever and Sample 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 40μm. Release the cantilever holder: •...
  • Page 25 Ch. 4. Tutorial: AC Mode in Air, Std. Scanner Sec. 4.2. Loading Lever and Sample Select AC mode cantilever holder: • Identify the cantilever holder. This demo requires the standard “AC Air” holder, Asylum Part# 901.705. To learn more about cantilever holders Note for the standard scanner, please refer to Chapter 5 on page...
  • Page 26 Ch. 4. Tutorial: AC Mode in Air, Std. Scanner Sec. 4.2. Loading Lever and Sample Tighten the clamp: • Once the cantilever holder is fully inserted, use the ball head wrench to gently tighten the clamp. Remove the old cantilever: •...
  • Page 27 Step 5 on page 19) clean with a soft cloth. Any dust or grit will prevent the sample disk from being properly seated. • Place the Asylum Research calibration grating onto the scanner stage. It will attach magnetically. support.asylumresearch.com Page 23...
  • Page 28 Ch. 4. Tutorial: AC Mode in Air, Std. Scanner Sec. 4.2. Loading Lever and Sample Insert cantilever holder into scanner: • Remove the cantilever holder from the changing station. • Insert the cantilever holder into the scanner. Pay attention that the metal dovetail engages properly.
  • Page 29 SERIOUS damage to farther away. It will only cause the your cantilever holder and scanner. automated engage to take a little longer. 23. This concludes the manual interaction with Cypher. We next turn our attention to the computer. support.asylumresearch.com Page 25...
  • Page 31 6. Familiarize yourself with the Approach tab on the Engage Panel as described next in Step 7 on page 27. Failure to understand the Approach controls may lead to serious damage to the Cypher. support.asylumresearch.com Page 27...
  • Page 34 ‘Spot option. On’ 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...
  • Page 38 Ch. 4. Tutorial: AC Mode in Air, Std. Scanner Sec. 4.3. Engaging the Surface First view of new cantilever. Cantilever found and roughly centered on screen. Step 8 on page Cantilever in focus. See Step 9 on page Optimize Resolution. See Step 10 on page Figure 4.1.: Finding the cantilever and optimizing the video.
  • Page 39 Ch. 4. Tutorial: AC Mode in Air, Std. Scanner Sec. 4.3. Engaging the Surface Cantilever Zoom. See Step 10 on page Laser Spot ON. See Step 11 on page Spot On by right clicking. See Step 11 on Laser spot on the lever. See Step 12 on page page Figure 4.2.: Various methods for aligning the laser spot onto the cantilever.
  • Page 40 Ch. 4. Tutorial: AC Mode in Air, Std. Scanner Sec. 4.3. Engaging the Surface Offset. The focus offset is centered and the optical im- age is confocal with the focused laser 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.

  • Page 44: Imaging

    29) you must be sure to set the focus adjustment back to zero, as in Step 3 on page 26. Cypher includes a sensor to see that this has occurred and the software will warn you to zero the focus offset when necessary.
  • Page 46 Ch. 4. Tutorial: AC Mode in Air, Std. Scanner Sec. 4.4. Imaging 4.4.2. Start Imaging and Parameter Tuning • Click the button on the ‘Do Scan’ ‘Main’ tab of the , and imaging ‘Master Panel’ will begin after a moment. Scan initiation first moves the tip to the starting point of the image, then lowers the tip onto the surface, and then begins...
  • Page 47 Ch. 4. Tutorial: AC Mode in Air, Std. Scanner Sec. 4.4. Imaging In the previous image the tip is not following the surface. As the blue trace shows (left to right), the tip seems to climb up out of the pits of the calibration grating quite nicely (the left edge of each pit is quite sharp) but then it descends back into the next pit along a relatively gentle slope.
  • Page 49 4.4.3. Image Refinement To learn more about using the Asylum Research SPM software to refine your imaging parameters, please refer to Applications Guide, Chapter: AC Mode Imaging in Air and also MFP-3D User Guide, Chapter: Tutorial: AC Mode Imaging in Air. Also consider watching this introductory video:...
  • Page 52 Ch. 4. Tutorial: AC Mode in Air, Std. Scanner Sec. 4.6. Shutting the System Down 2. The tip will disengage automatically when imaging stops, but for added safety, motor the tip away from the sample. You may want to remove the sample at this point. 3.

  • Page 53: Cantilever Holder Guide

    Ch. 5. Cantilever Holder Guide 5. Cantilever Holder Guide . 1710, 10/23/2013, 21:54. . 1714, 10/25/2013, 20:36. HAPTER DATED UIDE DATED Chapter Contents ....... . Identifying Cantilever Holders .
  • Page 54 Ch. 5. Cantilever Holder Guide Sec. 5.1. Identifying Cantilever Holders Part # Holder Description Front Photo Back Photo For most contact and AC mode Imaging. It’s use is described well in this tutorial: 901.705 Section 4.2 on page 18. Fits in the Air Changing Station.

  • Page 55: Cantilever Holder Changing Stations

    Air Changing Station. For use in air or liquid. 5.1.2. Electronic Identification of Cantilever Holders 1. Attach the cantilever holder to the Cypher Scanner. (See Step 17 on page 23). 2. From the main menu bar in the software select...
  • Page 56 Ch. 5. Cantilever Holder Guide Sec. 5.2. Cantilever Holder Changing Stations Part # Item Description Picture Air Cantilever Holder Changing Station. Used with Cypher 901.716 cantilever holders that look like the Standard Droplet Cantilever Holder. BETA Page 52...

  • Page 57: Fluid Imaging In A Droplet

    6.6.4.1 Finishing up This chapter explains the use of the droplet cantilever holder designed for use with the Cypher Scanner. In this design, the sample is such that the scanning area is submerged in small volume of water (typically around 100uL) which encapsulates both the scanning area and the cantilever. The water environment is maintained by the meniscus bridge formed between the sample substrate and the underside of the glass window of the droplet holder.

  • Page 58: Nomenclature

    Ch. 6. Fluid Imaging in a Droplet Sec. 6.1. Nomenclature The cantilever holder can be used for contact mode and AC mode imaging in fluid. It has a built-in piezoelectric actuator for driving cantilevers at resonance. Please refer to Chapter 7 on page 75 specifics on iDrive imaging only.
  • Page 59 Ch. 6. Fluid Imaging in a Droplet Sec. 6.2. Parts List Part # Item Description Picture 114.181 Ring, Gasket Base 114.246 Shield, Low Profile Evaporation. Socket Head Cap Screw, 0-80 X 222.070 7/64” 222.072 Screw, M2 X 4, Stainless. Washer, 0.157” x 0.096” x 222.094 0.010”...

  • Page 60: Preparing For Imaging

    0.050”: Wiha Allen Driver 263 290.111 1,3 – 0.05” X 40. 290.136 Short arm hex key, 0.028”. 290.144 T5 2.5MM Torx Driver. Cypher Droplet Holder 901.738 Assembly, V2. Small Diameter Droplet Holder 901.739 Cup Assembly. 6.3. Preparing for Imaging Before you start: •...
  • Page 61 • You are familiar with the basic names of the hardware components and software controls (Chap- ter 1 on page • You have powered up the Cypher and launched the software: (Chapter 2 on page 10.) • You are comfortable with AC Mode Imaging in Air, as instructed by the tutorial:...
  • Page 62 Ch. 6. Fluid Imaging in a Droplet Sec. 6.3. Preparing for Imaging 6.3.2. Mounting the Cantilever This cantilever holder requires the 901.716 droplet changing station (See Figure 6.2a on page 58). Using the wrong changing station will not work and may damage your cantilever Warning holder.
  • Page 63 Ch. 6. Fluid Imaging in a Droplet Sec. 6.3. Preparing for Imaging Install the evaporation shield base • Place the base into the recess around the sample stage The top of the base has a lip where the Note: evaporation shield fits. Install the evaporation shield •...
  • Page 64 Ch. 6. Fluid Imaging in a Droplet Sec. 6.3. Preparing for Imaging Wet the cantilever: • Add a small drop of liquid to the window of the droplet holder to submerge the cantilever. • This prevents bubbles and unwanted bending of very soft levers. Mount the cantilever holder: •...
  • Page 65 Ch. 6. Fluid Imaging in a Droplet Sec. 6.3. Preparing for Imaging 6.3.6. Engaging 6.3.6.1. Pre-engage adjustments Coarse Engage: • Pull the scanner forward. • Using the control wheel on the instrument base, slowly lower the holder toward the sample. •...
  • Page 66 Ch. 6. Fluid Imaging in a Droplet Sec. 6.3. Preparing for Imaging 6.3.6.2. Focus on the cantilever Adjust objective focus ring: • Move the focus offset ring on the objective to the 2mm position. This is necessary in order to compensate for the change in focal depth of the objective focusing through the glass window and liquid.
  • Page 67 Ch. 6. Fluid Imaging in a Droplet Sec. 6.3. Preparing for Imaging Adjust the aperture diaphragm: • Adjust the Aperture Diaphragm lever ( labeled A) on the View Module to reduce the illumination by about 90%. • In the software, increase the illumination brightness to compensate for the reduction of light.
  • Page 68 Ch. 6. Fluid Imaging in a Droplet Sec. 6.3. Preparing for Imaging Lower the objective: • Lower the objective while watching for the surface to come into focus. • As you lower the objective, you will first see the edge of the field diaphragm come into focus.

  • Page 69: Imaging With The Droplet Holder

    Ch. 6. Fluid Imaging in a Droplet Sec. 6.4. Imaging with the Droplet Holder Going too far: • If you cannot confirm you are focused on the surface, slowly continue to lower the objective until you see lots of coarse looking features.
  • Page 70 Ch. 6. Fluid Imaging in a Droplet Sec. 6.4. Imaging with the Droplet Holder Once an amplitude peak is selected and the engage routine initiated it is not uncommon for the system to false engage as the driving forces on the cantilever change. It is therefore common to re-tune the system as the tip gets closer to the surface.
  • Page 71 6.4.2.1. Engaging in fluid in AC mode As the tip is being lowered to the surface during the engage routine, the Cypher is doing a series of triggered force curves looking for the free amplitude to equal the setpoint voltage. Once the free am- plitude is seen as equal to the setpoint voltage, the system stops the approach and is considered to have found the surface.
  • Page 72 Ch. 6. Fluid Imaging in a Droplet Sec. 6.4. Imaging with the Droplet Holder has false engaged and you should check the tuning of the lever and adjust as necessary. If you see the Z control voltage move to a value and stop then you most likely have correctly engaged. Begin scanning. One useful thing is to monitor the deflection signal.

  • Page 73: Removal And Storage

    Ch. 6. Fluid Imaging in a Droplet Sec. 6.5. Removal and Storage 6.5. Removal and Storage 6.5.1. Removing the Dish Please seeSection 6.3.1 on page 57for details. 1. Unscrew the sample dish from the scanner. 2. Thread the standard scanner magnetic insert into the scanner sample stage. 3.
  • Page 74 • Use only 0-80 x 1/16” Cup Point Socket Set Screws for the piezo preload screw. Due to wear and tear of use, the droplet holder accessory kit comes with replacement screws. Please contact Asylum Research for additional hardware if proper replacements cannot be obtained locally. Required tools and fasteners: •...
  • Page 75 Ch. 6. Fluid Imaging in a Droplet Sec. 6.6. Cleaning and Repair Loosen the piezo preload screw 0.028” hex driver or Allen wrench Tools • Loosen the piezo preload setscrew ¼ turn. Remove the spring clip T5 x 40 Torx driver Tools •...
  • Page 76 1. Fit the o-ring into the groove in the window mounting plate. Spare o-rings are supplied in the accessory kit for the droplet holder and more can be obtained from Asylum Research if necessary. 2. Place the window in the holder aligned so that the ramp in the glass points toward the hole for mounting the cantilever spring clip.
  • Page 77 Ch. 6. Fluid Imaging in a Droplet Sec. 6.6. Cleaning and Repair There is a small recessed area in the metal ring where the piezo actuator fits. Be careful not to hit Note: the piezo or twist the window into position. Secure the window assembly 0.050”...
  • Page 78 Ch. 6. Fluid Imaging in a Droplet Sec. 6.6. Cleaning and Repair 1. Install the Droplet holder into the scanner. 2. Lock the clamp on the scanner to secure the droplet holder. Activate the tune sweep • In the AR SPM Software, select the tune of the master panel...

  • Page 79: Idrive Imaging

    7.3.1.4 Adjusting Piezo Preload This section explains the use of the iDrive version of the Cypher Droplet Cantilever Holder. In addition to the standard Droplet Cantilever Holder’s functionality, the iDrive version has the ability to drive a small AC current through special iDrive compatible cantilevers. It also contains a small magnet, the field from which causes a torque on the current flowing through an iDrive cantilever causing it mechanically...

  • Page 80: Nomenclature

    Ch. 7. iDrive Imaging Sec. 7.1. Nomenclature • You have mastered fluid imaging in a droplet: (Chapter 6 on page 53.) The iDrive cantilever is based on the Droplet Holder covered in Chapter 7 on page 75. Please Review: read this chapter for general use of the cantilever holder and the basics of using it for contact mode and AC imaging in liquid drops.
  • Page 81 Ch. 7. iDrive Imaging Sec. 7.1. Nomenclature Here are top and bottom views of the Figure: split clip assembly. Notice: • the exposed area of the clips which are the contacts for the pogo pins. • the step along the molded section is used for keying the clip into the droplet holder body.
  • Page 82 Ch. 7. iDrive Imaging Sec. 7.1. Nomenclature Here is a view of the surface of an iDrive Figure style cantilever. Note • The entire surface of the cantilever is coated with a layer of gold. • The insulating lines are etched in surface to create to contact pads.
  • Page 83 Ch. 7. iDrive Imaging Sec. 7.1. Nomenclature • mounting the sample and the sample dish, • using the evaporation shield, • installing the cantilever holder in the scanner, • contact mode or acoustic AC mode imaging specifics, • removal and storage. Only keep reading on here for the specifics of iDrive imaging and cleaning and assembly instructions.

  • Page 84: Cleaning And Repair

    Ch. 7. iDrive Imaging Sec. 7.2. Cleaning and Repair iDrive Tune Figure Here is an example of a magnetically driven iDrive cantilever Acoustic AC tune Figure Here is the same iDrive cantilever acoustically tuned using the piezo actuator. 7.1.4. Imaging Specifics Once the cantilever is tunes and you initiate the engage routine, you may notice the free amplitude slowly decreases as the tip gets closer.
  • Page 85 Ch. 7. iDrive Imaging Sec. 7.2. Cleaning and Repair 7.2.1. Disassembly Figure 7.2.: Droplet Cantilever Holder Assembly exploded view With the exception of the cantilever spring clip and the addition of a magnet to the window assembly, the iDrive Droplet holder is mechanically identical to the standard Droplet Holder. Please refer to the cleaning and repair section for the standard Droplet Holder.Section 6.6 on page 69 To summarize the steps to disassembling and cleaning the holder:...
  • Page 86 Ch. 7. iDrive Imaging Sec. 7.2. Cleaning and Repair You may ask why the acoustic AC mode piezo is necessary when the iDrive system is available as an AC drive for the cantilever. Practically speaking, it’s useful to switch back and forth between acoustically driving the cantilever and Attention using iDrive.

  • Page 87: Older Models

    Note cannot support it. If you have not yet received a replacement droplet holder, and are experiencing a failure please contact Asylum Research. 7.3.1. Cleaning and Repair In daily use, the iDrive cantilever holder can be cleaned by rinsing the exposed surfaces of the glass window and cantilever clips with clean de-ionized water.
  • Page 88 Ch. 7. iDrive Imaging Sec. 7.3. Older Models using low-pressure compressed air or by blotting with a soft tissue. For stringent cleaning, the iDrive cantilever holder must be disassembled. Only the parts exposed to the sample liquid should be cleaned. The cantilever holder body and associated electronics should be kept dry.
  • Page 89 • Use only 0-80 x 1/16” Cup Point Socket Set Screws for the piezo preload screw. Due to wear and tear of use, the droplet holder accessory kit comes with replacement screws. Please contact Asylum Research or your local Asylum distributor for additional hardware if proper replace- ments cannot be obtained locally.
  • Page 90 Ch. 7. iDrive Imaging Sec. 7.3. Older Models Remove the window assembly 0.050” hex driver or Allen wrench Tools • Remove the three screws holding the glass insert into the holder body. • Remove the window assembly. • Separate the silicone evaporation skirt if installed.
  • Page 91 Ch. 7. iDrive Imaging Sec. 7.3. Older Models 7.3.1.3. Reassembly Optional: Install the evaporation skirt • Stretch the evaporation skirt around the edge of the window. The edge of the window has a small groove where the skirt fits. • Align the cutout in the skirt with the cantilever pocket.
  • Page 92 Ch. 7. iDrive Imaging Sec. 7.3. Older Models Secure the window assembly 0.050” hex driver or Allen wrench. Tools • Secure the window to the holder using three 0-80 x 7/64” Socket Head Cap Screws. Do not over tighten the screws. A small Note amount of torque is all that’s required.
  • Page 93 Ch. 7. iDrive Imaging Sec. 7.3. Older Models Settle the parts together. • Adjust the clips so that they seat over the raised portions of the lower insulator. As you shift the position of the clips they will locate around the raised areas on the lower insulator.
  • Page 94 Install the cantilever holder 0.050” hex driver or Allen wrench Tools • Take the assembled cantilever holder, without cantilever installed, to the Cypher SPM. • Insert the cantilever holder into the scanner. • Finger tighten the screw which clamps it down.
  • Page 95 Ch. 7. iDrive Imaging Sec. 7.3. Older Models Activate the tune sweep • In the AR SPM Software, select the tune of the master panel • Under , set the parameters Manual Tune as shown to the right. Note the phase offset is not important and sweep time of 1s is fine too.

  • Page 96: Conductive Afm (Orca)

    Ch. 8. Conductive AFM (ORCA) 8. Conductive AFM (ORCA) . 1659, 10/07/2013, 22:54. . 1714, 10/25/2013, 20:36. HAPTER DATED UIDE DATED Chapter Contents ......... . Parts list .
  • Page 97 Ch. 8. Conductive AFM (ORCA) Sec. 8.1. Parts list Part # Item Description Picture ORCA Holder 2nA/V 901.730 Dual Gain ORCA 1uA/1nA/V 901.708 For other available versions see 8.2. 10 pack of conductive levers. ASTELEC- Used for the measurements described in this section. HOPG sample.

  • Page 98: The Orca Amplifier

    There are a variety of ORCA cantilever holders each based on either a single or dual amplification design. The design type and amplification gain are labeled on the top of the holder. Like all the Cypher cantilever holders, a built-in circuit in the holder allows the software to automatically sense the type of holder and configure the system accordingly.
  • Page 99 Ch. 8. Conductive AFM (ORCA) Sec. 8.2. The ORCA Amplifier Figure 8.1.: Single Gain ORCA 8.2.2. Dual Gain A conceptual diagram of the dual gain ORCA amplifier shows the initial current to voltage converter stage feeding the input of a second gain stage to create an additional output signal. In the case of this design the more sensitive signal comes from the second stage and is monitored as ’Current’...

  • Page 100: Preparing For Imaging

    8.3.1. Zeroing the ORCA Current and Sample Bias signals The signal path through the Cypher can pass through many stages of signal conditioning. Each particular circuit in the signal path can introduce a voltage offset which when added together can skew the zero point of your measurement.
  • Page 101 Ch. 8. Conductive AFM (ORCA) Sec. 8.3. Preparing for Imaging Press the ’Zero’ button to zero the current • The Software will add the appropriate offset from the Current data to make the Current 0A. • Verify that the current is zeroed. This is only a software offset.
  • Page 102 Ch. 8. Conductive AFM (ORCA) Sec. 8.3. Preparing for Imaging 8.3.2. Preparing the Sample Sample preparation varies but basically the goal is to provide an electrical path between the sample bias and the surface of your sample. In addition to the electrical connection, care should be taken to mount the sample mechanically to a sample puck as you would with any sample.

  • Page 103: Imaging With The Orca

    Conducting AFM (ORCA) requires a conductive path between the tip and the cantilever spring clip. The ORCA kit includes a sample pack of 10 Electrilevers. Additional levers can be pur- chased from Asylum Research. If you are not familiar with basic AFM operating practices, please review The basic operating tutorials section at the beginning of this guide.
  • Page 104 Ch. 8. Conductive AFM (ORCA) Sec. 8.5. Testing the ORCA Amplifier Install the test resistor under the clip on the ORCA holder • Hold the ORCA holder upside down in you hand and use a fingernail to press on the button on the top side of the holder to open the cantilever clip.
  • Page 105 Ch. 8. Conductive AFM (ORCA) Sec. 8.5. Testing the ORCA Amplifier Do an I/V plot and confirm the correct current flow • Go to AFM Controls-> Do IV panel and open the I/V voltage controls. • Press the Do I/V button to perform an I/V curve.
  • Page 106 Ch. 8. Conductive AFM (ORCA) Sec. 8.5. Testing the ORCA Amplifier Test the first gain stage of the Dual Gain ORCA Amplifier • Install the 1M Ohm test resistor. • Do an IV plot. • Monitor both the Current and Current 2 data channels.

  • Page 107: Scanning Tunneling Microscopy

    The Current2 Signal 9.1. Introduction and Preparation This is a fairly basic set of instructions on STM imaging with Cypher. At some point we hope to do a more proper STM tutorial chapter which focus on imaging graphite with atomic resolution.

  • Page 108: Preparing An Stm Sample

    Ch. 9. Scanning Tunneling Microscopy Sec. 9.3. Preparing an STM sample Figure 9.1.: Cypher STM tip holder. Note the probe tip sticking from the small tube. 9.3. Preparing an STM sample 1. Place your sample on a steel AFM disc. It’s assumed the sample is conducting and has a relatively flat bottom.

  • Page 109: Load The Tip

    Ch. 9. Scanning Tunneling Microscopy Sec. 9.4. Load the tip Alternately, simply bonding a small length of wire directly to the sample puck with solder or silver epoxy works well. In many cases fixing the sample and bias voltage connections are sample specific. The sample socket on the terminal block is sized to accept the diameter of a standard 1/4watt resistor lead or similar diameter wire for making your own bias leads.

  • Page 113: Set Iv Parameters

    Ch. 9. Scanning Tunneling Microscopy Sec. 9.9. Set IV Parameters 2. Dwell at the surface using the Z position sensor to hold the tip at a constant Z height above the surface 3. Ramp the bias voltage using the ramp functions in the Do IV panel. 9.9.
  • Page 114 Ch. 9. Scanning Tunneling Microscopy Sec. 9.9. Set IV Parameters Drive Graph • Adjust the Amplitude Freq Optional Arg (Phase Offset), Optional Arg 4 (Voltage Offset) parameters to make the desired ramping waveform. Drive Graph • This is the result of the Ramp during IV measurements.

  • Page 115: Stm Probes

    9.10. STM probes The Cypher STM kit came supplied with 20 mechanically formed (i.e. carefully clipped with super sharp wire cutters) probes. Additional probes can be purchased from Asylum Research. If you wish to make your own probes the material and dimensions for making the supplied probes are: support.asylumresearch.com...

  • Page 116: Troubleshooting

    Wire size: 0.01” diameter (0.25mm) , cut approximately .3” long. Longer probes are usable but may introduce image distortion from drift due to the length. Contact Asylum Research about further tools and technique required to make the proper cuts.

  • Page 117: Environmental Scanner

    Part III Environmental Scanner After the Cypher ES Environmental AFM has been installed in your lab and you Who is this part for? (or someone in your facility) have completed the initial training, this part of the user guide will be the principal reference for operating the instrument.
  • Page 118 10.3 Cypher ES Quick Reminder List ........

  • Page 119: Environmental Scanner Overview

    ........10.4 Chemical Compatibility The Environmental Scanner is included with the Cypher model ES AFM. Please review the parts lists below and the basic imaging tutorial in Chapter 11 on page 130.
  • Page 120 Ch. 10. Environmental Scanner Overview Sec. 10.1. Parts list Part # Item Description Picture #00 Phillips Screwdriver. Used 290.106 to replace the cantilever. See Step 12 on page 134. 5/64” (2mm) Hex Driver. Used 290.163 to remove the cell body from the scanner.
  • Page 121 Ch. 10. Environmental Scanner Overview Sec. 10.1. Parts list Part # Item Description Picture Fittings, 1/16”. Used to connect 1/16” tubing to the cell chamber 232.015 wall. See Step 4 on page 167. IDEX part number M660. Use with tool 290.164. Extender Tool Fitting Wrench.
  • Page 122 Ch. 10. Environmental Scanner Overview Sec. 10.1. Parts list Part # Item Description Picture Stage locking screw with integrated ball end . Spare screws used to lock down the 114.576 sample stage. Step 8 on page 170. Be careful, these are very expensive screws.
  • Page 123 Ch. 10. Environmental Scanner Overview Sec. 10.1. Parts list Part # Item Description Picture 1/16” dowel pin. Used to restore 222.077 slightly compressed fitting parts. 1.8mm slotted screwdriver. Used 290.168 to fasten the sample stage membrane to the cell body. 1/8”...
  • Page 124 Ch. 10. Environmental Scanner Overview Sec. 10.2. Terminology Part # Item Description Picture O-ring, 0.75"ID X 1"OD Viton, Durometer 75A. Equivalent FFKM part is 230.038. Standard 230.044 AS568-020 size, can also be purchased from other vendors. Sits around cantilever holder perimeter.

  • Page 125: Terminology

    10.3. Cypher ES Quick Reminder List In this section, we provide a list of pitfalls to avoid during use of the Cypher ES. The target audience of this section is fairly specific: it is written for those users who are experienced Cypher S users but have had only a basic training on the Cypher ES.
  • Page 126 Ch. 10. Environmental Scanner Overview Sec. 10.3. Cypher ES Quick Reminder List 10.3.1. Reminders for imaging Remember to fully raise the engage stage before loading the cantilever holder. • Compared to the S, on the ES scanner it is more difficult to see if there is enough clearance for safely loading the cantilever holder.
  • Page 127 Ch. 10. Environmental Scanner Overview Sec. 10.3. Cypher ES Quick Reminder List Never load “non-flat” samples into the ES scanner. • 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 feature on the sample puck.
  • Page 128 Ch. 10. Environmental Scanner Overview Sec. 10.3. Cypher ES Quick Reminder List Hold the cantilever holder only by its handles. • Hold the cantilever holder only by its two plastic handles (upper image). • In particular, avoid contacting the wires running to the tapping piezo (lower image).
  • Page 129 Ch. 10. Environmental Scanner Overview Sec. 10.3. Cypher ES Quick Reminder List Make sure the scanner is fully seated against the chassis before locking in place. • Unlike the S scanner, which has a hard stop on the back of the scanner, the ES scanner has a spring loaded stop that needs to be fully engaged.
  • Page 130 Ch. 10. Environmental Scanner Overview Sec. 10.3. Cypher ES Quick Reminder List 10.3.2. Reminders for cell exchange and handling The fitting wrench should never be used to attach gas lines to the cell body. • The fitting wrench (114.800) supplied in...
  • Page 131 Ch. 10. Environmental Scanner Overview Sec. 10.3. Cypher ES Quick Reminder List Be careful when reattaching the cantilever clip to not crack the glass. • Anytime the cantilever clip has been completely removed - for cleaning - care must be taken when reattaching the clip.
  • Page 132 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 133: Chemical Compatibility

    Ch. 10. Environmental Scanner Overview Sec. 10.4. Chemical Compatibility 10.4. Chemical Compatibility The ES scanner is equipped with FKM (Viton equivalent) O-rings in the factory. For cases where viton is chemically attacked, please switch to the included FFKM (Kalrez equivalent) O-ring. These rings can be found in a small box, shown in 10.2.

  • Page 134: Tutorial: Ac Mode In Air, Es

    All new users should complete and understand this “AC Mode Imaging in Air” tutorial before attempting any imaging. The Cypher is a research grade instrument and improper use of the instrument can cause damage to the instrument and/or injury to the user. This tutorial will take approximately 3 hours.

  • Page 135: Loading The Cantilever And Sample

    4. Tweezers, “platypus style” (Asylum Part# 290.165). 5. A 1/16” ball head wrench (for example, Asylum Part# 290.139). 6. A Cypher equipped with the Environmental Scanner and a large spot SLD or Laser Module (See Chapter 18 on page 190).
  • Page 136 Ch. 11. Tutorial: AC Mode in Air, ES Sec. 11.2. Loading the Cantilever and Sample Unlock scanner: • Lift the lever to the right of the scanner. Pull the scanner forward: • Pull the scanner forward gently and stop when it is about halfway out. As you pull the scanner out, at some point you will feel resistance and should pull no farther.
  • Page 137 Ch. 11. Tutorial: AC Mode in Air, ES Sec. 11.2. Loading the Cantilever and Sample 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 cantilever holder.
  • Page 138 Ch. 11. Tutorial: AC Mode in Air, ES Sec. 11.2. Loading the Cantilever and Sample Set aside the cantilever holder: • Set the cantilever holder on its handles with the cantilever facing up so that you do not crush the cantilever. Locate your cantilever holder: •...
  • Page 139 Ch. 11. Tutorial: AC Mode in Air, ES Sec. 11.2. Loading the Cantilever and Sample Loosen the cantilever clip: • Unscrew the clamping screws by one half turn. • Do not unthread the screw completely. If you accidentally do, please refer to the cantilever holder chapter.
  • Page 140 Ch. 11. Tutorial: AC Mode in Air, ES Sec. 11.2. Loading the Cantilever and Sample Load 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.
  • Page 141 Replace with new sample: • Use “Platypus” tweezers (Asylum Part # 290.165) to place new sample on sample stage. For this tutorial, use the Asylum Research calibration grating sample, part # 900.237. It will attach magnetically. DRAFT Page 137...
  • Page 142 Ch. 11. Tutorial: AC Mode in Air, ES Sec. 11.2. Loading the Cantilever and Sample Prepare scanner to load cantilever holder: • RAISE THE COARSE ENGAGE STAGE by turning the Engage Control Knob clockwise.Raise the stage until it reaches its upper limit of travel. Before loading the cantilever Warning: holder, raise the coarse engage stage.
  • Page 143 Ch. 11. Tutorial: AC Mode in Air, ES Sec. 11.2. Loading the Cantilever and Sample Rotate: • Rotate the cantilever holder clockwise until you feel a hard stop. The cantilever holder contacts slip into the mating connector. Notice the screws cause the hard stop as they slip into the matching metal cutouts.
  • Page 144 If you crash the cantilever about 1 millimeter. holder you may cause SERIOUS damage to your cantilever holder and scanner. 29. This concludes the manual interaction with Cypher. We next turn our attention to the computer. Please jump to Section 4.3 on page DRAFT...

  • Page 145: Cantilever Holder Guide

    Ch. 12. Cantilever Holder Guide 12. Cantilever Holder Guide . 1707, 10/23/2013, 13:57. . 1714, 10/25/2013, 20:36. HAPTER DATED UIDE DATED Chapter Contents ....... . 12.1 Identifying Cantilever Holders .
  • Page 146 Typically used for 901.771 High Voltage PFM Imaging. 12.1.2. Electronic Identification of Cantilever Holders 1. Attach the cantilever holder to the Cypher Scanner. 2. From the main menu bar in the software select Programming Cantilever Holder and Sample Panel ⊲...

  • Page 147: Disassembly

    Ch. 12. Cantilever Holder Guide Sec. 12.2. Disassembly 12.2. Disassembly Only the cantilever clip can be removed from the cantilever holder. All other parts should not be removed or serviced by the user. 12.2.1. Removing the Clip Remove the screw: •...
  • Page 148 Ch. 12. Cantilever Holder Guide Sec. 12.2. Disassembly 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. • DO NOT TIGHTEN YET! Check clip rotation: •...

  • Page 149: Cleaning

    Ch. 12. Cantilever Holder Guide Sec. 12.3. Cleaning 12.3. Cleaning Only the glass parts of the cantilever holder should come into contact with fluid during cleaning. To prevent fluid from touching the circuit components, please use the cleaning cup as shown below. Locate parts: •...

  • Page 150: Storage

    Ch. 12. Cantilever Holder Guide Sec. 12.4. Storage Clean: • Use a soft swab to clean the surface of the cantilever holder. • Rinse and repeat as desired. 5. Blow dry with compressed filtered air. 6. Remove the holder from the cup. 7.

  • Page 151: Cell Body And Sample Stage Guide

    Ch. 13. Cell Body and Sample Stage Guide 13. Cell Body and Sample Stage Guide . 1711, 10/23/2013, 22:16. . 1714, 10/25/2013, 20:36. HAPTER DATED UIDE DATED Chapter Contents ........13.1 Cell Body Guide .

  • Page 152: Cell Body Guide

    Ch. 13. Cell Body and Sample Stage Guide Sec. 13.1. Cell Body 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. •...
  • Page 153 Ch. 13. Cell Body and Sample Stage Guide Sec. 13.1. Cell Body Guide Part # Holder Description Front Photo Back Photo Fluid This cell is the same ast the Gas cell, but 901.760 it does not have electrical feedthroughs. 13.1.2. Gas Cell The Gas cell has three magnetic contacts which can be used to route electrical signals to the sample.
  • Page 154 Ch. 13. Cell Body and Sample Stage Guide Sec. 13.1. Cell Body Guide Part # Item Description Picture Boot Clamp Ring, 8 Bolt Pattern. Connects to the bottom of the cell to form the seal 114.884 between the cell body and the sample stage membrane.
  • Page 155 Ch. 13. Cell Body and Sample Stage Guide Sec. 13.1. Cell Body Guide 13.1.2.3. Gas Cell Cable Installation 1. Raise the engage stage fully (see Step 1 on page 131). 2. Unlock the scanner and pull it all the way forward. This will give enough access to plug in the cable.
  • Page 156 Ch. 13. Cell Body and Sample Stage Guide Sec. 13.1. Cell Body Guide Insert the smaller connector: • Insert the smaller connector as shown on the left. • The final cable position is shown on the right. 13.1.2.4. Applying Sample Bias or Ground Sample mounting: •...
  • Page 157 Ch. 13. Cell Body and Sample Stage Guide Sec. 13.1. Cell Body Guide WARNING: Never load “non-flat” samples into the ES scanner. • 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 feature on the sample puck.
  • Page 158 Ch. 13. Cell Body and Sample Stage Guide Sec. 13.1. Cell Body Guide 13.1.3. Fluid Cell Body 13.1.3.1. Parts list Part # Item Description Picture Fluid Cell Body. Boot Clamp Ring, 8 Bolt Pattern. Connects to the bottom of the cell to form the seal 114.884 between the cell body and the sample stage membrane.

  • Page 159: Sample Stage Guide

    Ch. 13. Cell Body and Sample Stage Guide Sec. 13.2. Sample Stage Guide 13.2. Sample Stage Guide 13.2.1. Identifying Sample Stages Please use this table to identify your cantilever holders and find the relevant sections which describe them. Part # Holder Description Front Photo Back Photo...
  • Page 160 Ch. 13. Cell Body and Sample Stage Guide Sec. 13.2. Sample Stage Guide Top Surface Bottom View Figure 13.3.: Ambient Stage FFKM. Membrane: Stainless Steel Stage surface: Embedded magnets. Sample Hold down: Stage surface is not grounded (floating) and sufficiently isolated to be safe for use with Electrical: high voltage applications.
  • Page 161 Ch. 13. Cell Body and Sample Stage Guide Sec. 13.2. Sample Stage Guide Figure 13.4.: Heater Stage Ceramic. Stage surface: Stainless steel, Epoxy. Other surfaces: Embedded magnets. Sample Hold down: Stage surface is not grounded (floating) and sufficiently isolated to be safe for use with Electrical: high voltage applications.

  • Page 162: Sample Stage / Cell Body Disassembly

    Ch. 13. Cell Body and Sample Stage Guide S ec. 13.3. Sample Stage / Cell Body Disassembly Top Surface Bottom View Figure 13.5.: Cooler Heater Stage 13.2.4.2. Specifications Exposed Materials: FFKM. Membrane: Stainless Steel Stage surface: Embedded magnets. Sample Hold down: Stage surface is not grounded (floating) and sufficiently isolated to be safe for use with Electrical: high voltage applications.
  • Page 163 Ch. 13. Cell Body and Sample Stage Guide S ec. 13.3. Sample Stage / Cell Body Disassembly Figure 13.6.: Ambient stage / fluid cell body combination on the left. Heater stage / gas cell body combi- nation on the right. 13.3.1.
  • Page 164 Ch. 13. Cell Body and Sample Stage Guide S ec. 13.3. Sample Stage / Cell Body Disassembly Extend the membrane: • Place the assembly as shown. • Pull on the sample stage bottom and extend the membrane as shown. Loosen all the screws: •...
  • Page 165 Ch. 13. Cell Body and Sample Stage Guide S ec. 13.3. Sample Stage / Cell Body Disassembly Remove the sample stage: • Lift off the sample stage. Finished: • Your parts should now be as shown to the right. • Store the sample stage as discussed in Section 13.5 on page 171.
  • Page 166 Ch. 13. Cell Body and Sample Stage Guide S ec. 13.3. Sample Stage / Cell Body Disassembly Place the ring: • As shown in the photos, place the ring. • The ring has three small holes that line up with the pins. •...
  • Page 167 Ch. 13. Cell Body and Sample Stage Guide S ec. 13.3. Sample Stage / Cell Body Disassembly Tighten the screws: • Using a 1.7mm 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 168: Tutorial: Sample Stage Swap

    Section 13.2 on page 155 for various options). The Cypher is a research grade instrument and improper use of the instrument can cause damage to the instrument and/or injury to the user. This tutorial will take approximately 3 hours .
  • Page 169 Ch. 13. Cell Body and Sample Stage Guide Sec. 13.4. Tutorial: Sample Stage Swap Figure 13.7.: Ambient stage / fluid cell body combination on the left. Heater stage / Gas cell body combi- nation on the right. 13.4.1. Required Materials This tutorial is designed to be performed, not merely read.
  • Page 170 Remove the scanner: • Turn off the ARC2 controller power and remove the scanner from the Cypher Chassis (see Section 16.1 on page 183 for further details) and place it on a well lighted clean work surface.
  • Page 171 Ch. 13. Cell Body and Sample Stage Guide Sec. 13.4. Tutorial: Sample Stage Swap Loosen the cell body screws: • Use the 5/64” Hex Driver to loosen the screws at the top of the cell body. • Discard the screws. •...
  • Page 172 Ch. 13. Cell Body and Sample Stage Guide Sec. 13.4. Tutorial: Sample Stage Swap Lift out the sample stage: • Lift the sample stage out of the cell body. • If you encounter resistance, you may need to further loosen the sample stage clamping screw (see Step 1 on page...
  • Page 173 Ch. 13. Cell Body and Sample Stage Guide Sec. 13.4. Tutorial: Sample Stage Swap Place O-rings if necessary: • If no O-ring (230.040) is present, place it in the bottom of the port, up against the glass. • If the O-ring is not properly centered, remove it (preferably with a sharp wooden stick) and replace it.

  • Page 175: Storage

    Ch. 13. Cell Body and Sample Stage Guide Sec. 13.5. Storage Connect the heater cable: • As shown, insert the heater cable connector. • Push it flush. Final checks: • Your scanner should now look like the photo to the right. The sample stage top surface sits CHECK quite deep as shown, below the glass...
  • Page 176 Ch. 13. Cell Body and Sample Stage Guide Sec. 13.5. Storage Heater Stage Gas Cell Body Passive Stage Figure 13.8.: Various stages and cell bodies stored in their containers. 13.5.2. Storing disassembled cell bodies Once a sample stage has been removed from a cell body (See 13.3.1), the cell body should be stored in the membrane container in which it shipped.

  • Page 177: Gas Handling And Leak Testing

    Ch. 14. Gas Handling and Leak Testing 14. Gas Handling and Leak Testing . 1702, 10/21/2013, 22:07. . 1714, 10/25/2013, 20:36. HAPTER DATED UIDE DATED Chapter Contents ........14.1 Gas Handling Overview .
  • Page 178 Ch. 14. Gas Handling and Leak Testing Sec. 14.1. Gas Handling Overview Figure 14.1.: Gas Handling Overview DRAFT Page 174...

  • Page 179: Manifold Connections

    Ch. 14. Gas Handling and Leak Testing Sec. 14.2. Manifold Connections 14.2. Manifold Connections 14.2.1. Scanner Faceplate Removal Remove the scanner cover: • Grip the cover as shown. • Pull forward. The cover is attached magnetically. 14.2.2. Manifold Cell-side connection Process for removing the tubing connected on the cell-side of the valve manifold.
  • Page 180 Ch. 14. Gas Handling and Leak Testing Sec. 14.2. Manifold Connections Remove the manifold (optional): • ONLY IF there was not enough room to complete the last step, remove the two screws shown in the photo. Remove fittings while holding manifold: •...

  • Page 182: Conductive Afm

    Ch. 15. Conductive AFM 15. Conductive AFM . 1711, 10/23/2013, 22:16. . 1714, 10/25/2013, 20:36. HAPTER DATED UIDE DATED Chapter Contents ......... . . 15.1 parts list .
  • Page 183 Ch. 15. Conductive AFM Sec. 15.3. Tutorial: Conductive AFM 3. Prepare the cantilever holder and AFM. Follow the AC Mode Tutorial from Step 1 on page 131 THROUGH Step 17 on page 136 to prepare your AFM system and cantilever holder. Sample mounting: •...

  • Page 184: Testing The Orca Amplifier

    Ch. 15. Conductive AFM Sec. 15.4. Testing the ORCA Amplifier Insert sample into the AFM: • Remove the cantilever holder. • Insert the sample puck as shown. • Use blunt tipped tweezers to connect the wire as shown., to the front connection. This applies a sample bias.

  • Page 185: Chassis And Enclosure

    Part IV Chassis and Enclosure This part covers general topics relating to the “frame” of the instrument, such as Who is this part for? scanner exchange, laser module exchange, and air temperature control. BETA Page 181...
  • Page 186 Part Contents 16 Tutorial: Scanner Exchange ........183 .

  • Page 187: Tutorial: Scanner Exchange

    ........16.3 Replacing the Scanner The Cypher AFM can be purchased with various scanner modules. This tutorial describes how to safely swap from one scanner to another. 16.1. Removing the scanner The photos show the removal of the Environmental Scanner.
  • Page 188 Ch. 16. Tutorial: Scanner Exchange Sec. 16.1. Removing the scanner Open the enclosure: • Lift the door latch and open the enclosure door. Power OFF the ARC2: • Turn the ARC2 off before proceeding. • Press the button as shown and verify the green light is OFF.
  • Page 189 Ch. 16. Tutorial: Scanner Exchange Sec. 16.1. Removing the scanner Begin to pull the scanner out: • Pull the scanner out about halfway. 6. Now go and clear out a place to set the scanner down once you remove it. We recommend you first place the scanner right in front of the AFM system, and then grip the scanner again to move it elsewhere.

  • Page 190: Scanner Storage

    Ch. 16. Tutorial: Scanner Exchange Sec. 16.2. Scanner Storage 16.2. Scanner Storage The scanner should be stored under basic laboratory conditions, preferably in a locked cabinet or drawer where it will not collect dust, be accidentally knocked over, or be “borrowed”. At the very minimum, place it on a shelf and cover it with a soft cloth.
  • Page 191 Ch. 16. Tutorial: Scanner Exchange Sec. 16.3. Replacing the Scanner Secure the scanner connector: • Press the connector into its mating socket. • Turn the knob on the right side of the scanner clockwise until firmly tight. Push the scanner in: •...

  • Page 192: Optics

    View system 17.1. Overview 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 193: View System

    Ch. 17. Optics Sec. 17.3. View system Zero Figure 17.1.: Some examples of correction collar settings. 17.3. 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 brightness and contrast, and a focus ring.

  • Page 194: Laser Sources

    18.4.1.3 Installing the Enclosure Cover The following instructions describe exchanging light tube assembly in the Cypher AFM. The light tube can be exchanged without disassembly through the front of the instrument with a little familiarity of the process. For the reason of clarity the instructions describe exchanging the light tube by disassembling the enclosure followed by the process done through the front of the instrument.
  • Page 195 Ch. 18. Laser Sources Sec. 18.1. Types of Light Tubes Also known as SLDs. Best all around choice for force curve measure- Super Luminescent Diodes: ments. Slightly higher noise than the laser diode sources, but remarkably lower oscillating background for force curve work. 3µm by 9µm spot size.

  • Page 196: Tutorial: Light Tube Exchange

    Beware of pinch points (Figure 20.1 on page 230). 3. Turn the ARC2 controller power off. This will shut off most of the Cypher’s power. It is not necessary to disconnect the motor power supply when exchanging the light tube assembly. BETA...
  • Page 197 Ch. 18. Laser Sources Sec. 18.2. Tutorial: Light Tube Exchange Remove optics cover: • Grip the cover at its lower edge and gently pull forward. It is attached magnetically and will detach of smoothly. This will expose the head assembly and Note allow access to the light tube from the front.

  • Page 198: Spot On' Calibration

    Ch. 18. Laser Sources Sec. 18.3. ’Spot On’ calibration Pull the light tube out: • 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.
  • Page 199 Allow an hour for the light tube to come to thermal equilibrium with the system. You may find that the error in the “Spot On” positioning will reduce. If the Cypher is left powered off for an extended amount of time, i.e. overnight or for a day, you may find that the Spot On position may be off.
  • Page 200 Ch. 18. Laser Sources Sec. 18.3. ’Spot On’ calibration Prepare to reset: • Click on “show reset spot on menu item” in the options pull down selection. Reset the spot position: • Zoom in at least once. • Point the mouse cursor to the center of the laser spot.
  • Page 201 ’Spot On’ is properly calibrated. From now on this light module should be properly calibrated for use (and re-use) in your Cypher SPM, since each light tube has a small memory element which stores the calibration values. Figure 18.1.: To open the Light Tube (Laser Module) infoblock, click on the “gear” icon at the bottom of the screen, then mouse up to the Laser Module and over to the infoblock.

  • Page 202: Troubleshooting

    Please follow the detailed instructions below to get the job done. 18.4.1.1. Removing the Enclosure Top cover The enclosure top is the only thing keeping your Cypher SPM from sliding around inside its enclosure. Be especially careful while removing and replacing the cover and in general any time the cover is missing.
  • Page 203 Ch. 18. Laser Sources Sec. 18.4. Troubleshooting 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. Remove backside screws: • Remove all 4 screws from back edge of the enclosure top plate.
  • Page 204 Ch. 18. Laser Sources Sec. 18.4. Troubleshooting Unscrew right door top: • Unscrew left door top inside screws and set aside. SCREW INFO: 8-32 x ½ BHCS SS. There may only be 1 screw. Note Open right enclosure door: • Fully open the right enclosure door. Adjust view system sliders: •...
  • Page 205 18.4.1.2. Plugging the Light Tube Cable Back in 18.4.1.3. Installing the Enclosure Cover The enclosure top is the only thing keeping your Cypher SPM from sliding around inside its enclosure. Be especially careful while removing and replacing the cover and in general any time the cover is missing. The SPM is heavy, but it can slide Warning around.
  • Page 206 Ch. 18. Laser Sources Sec. 18.4. Troubleshooting Close right enclosure door: • Close the right enclosure door. • While pressing it firmly closed to compress the rubber seal, install the two screws at bottom of the door. These screws were removed in Step 6 on page 199.

  • Page 207: Air Temperature Controller

    ......... . . 19.10 Alarms 19.1. Overview This chapter covers the installation and operation of the Cypher ATC (Air Temperature Controller). BETA Page 203...
  • Page 208 Figure 19.1.: Basic Diagram of ATC airflow. Cool lab air enters via a HEPA filter at the bottom of the Cypher ATC and then passes through fans and heater coils and travels via corrugated hose to the Cypher enclosure. Temperature signals travel from the Cypher back to the ATC (dotted line). Air exits the Cypher from the bottom rear.

  • Page 209: Parts List

    • It can take between 6 and 12 hours for all the metal and components of the cypher AFM to thermally stabilize. Therefore the best approach is to always leave the Cypher AFM turned on and the ATC regulating the instrument temperature.

  • Page 210: Hardware Setup

    Ch. 19. Air Temperature Controller Sec. 19.3. Hardware Setup Part # Item Description Picture 113.407 Hose Fitting. 279.066 Hose Clamp. 409.002 AC power Cable. ATC Control Cable. 449.025 Auxiliary Temperature Sensor. 448.088 290.118 5/64” Hex wrench. 19.3. Hardware Setup 19.3.1. Power requirements The ATC has a fixed power input for use with either 100/120VAC or 220/240VAC.
  • Page 211 The hose feeding the ATC air connects to a fitting on the lower half of the enclosure. If the ATC was purchased with the Cypher, the fitting will be attached. If the ATC was a separate purchase after the Cypher, the fitting will need to be attached using the following instructions.
  • Page 212 Connect the air hose to the ATC: • Place the ATC on the floor below the table under the Cypher. • Move the Cypher back to its normal location. • Route the air hose over the edge of the table and down to the ATC.
  • Page 213 • Connect the ATC Control cable to the ATC. 2. Connect the AC power cord to the ATC and plug it into wall power. Reconnect: Reconnect the Cypher cables: • The Motor Power • The Main controller cable • The USB cable •...

  • Page 214: Operation

    19.3.4. Power-up and Software Initialization 1. Turn the ATC power on. 2. Turn the ARC2 controller on. 3. Re-Start the AR SPM software and home the Cypher motors. Check connectivity: • In the status bar of the software, click on the “gear” icon and confirm that the ATC is indeed in the list of attached instruments.
  • Page 216 Ch. 19. Air Temperature Controller Sec. 19.4. Operation Choosing the temperature setpoint: • Make sure the feedback is set to off. • Make sure the mode is set to manual. • Set the to ~3 degrees C ‘Target Temp’ above the room temperature recorded in the previous step.
  • Page 217 flat surfaces, you may see periodic noise from the fans. Reducing the fan speed will eliminate this but be aware that you need to circulate air through the Cypher in order to maintain thermal stability. In most cases, reducing the speed to 39% for a few hours will not be a problem as long as the lab temperature is sufficiently below the Target Temperature.
  • Page 218 Exit Air hose is connected to the ATC. Used for diagnostic purposes. This sensor is located on the back of the Cypher Chassis about 1 inch above the Head Temperature rear air vent in the enclosure floor. This sensor is used by the ATC as the primary feedback source. Its location allows the sensor to be shielded from abrupt thermal changes when the door is opened.

  • Page 219: Enclosure Door Function

    When the enclosure door is open, the ATC cannot realistically attempt to control the temperature inside the Cypher enclosure. Therefore the ATC senses the opening of the door and temporarily freezes the feedback process but keeps the fans running and also keeps the air heater power at the same level when the door opened.
  • Page 220 Sec. 19.6. ATC Front Panel LEDs The ATC ATC temperature control OFF: power is on, the Cypher enclosure door is closed and the ATC Feedback is OFF. • This is a normal condition until the feedback is activated in the software.

  • Page 221: Data Logging

    Door just closed, but feedback still on hold: The ATC power is on, the door is CLOSED and the ATC Feedback is in Standby mode. • The is a typical condition when the Cypher door is opened and closed. • The Feedback loop will stay in standby...
  • Page 222 ATC unit under feedback set for 29 degrees C. The fan was set to 100% Notice: • The data between the green lines. The feedback loop has shut the heater power off. The Cypher was already warmed up so all that needed to happen was for the fan to cool the head sensor down.

  • Page 223: Using The Remote Temperature Sensor

    The Remote Temperature Sensor can be used to monitor the temperature of a particular location inside the Cypher enclosure and can even be used as a feedback source for the ATC. 1. Turn off the power to the ARC2 controller and the ATC box.
  • Page 224 • Log the sensor data in the data logger as an additional channel. Additional sensors can be purchased Note from Asylum Research. 3. Remove the top of your Cypher enclosure by following these instructions: Section 21.4.2 on page 242. Insert Sensor inside the Cypher enclosure: •...
  • Page 225 The sensor is on a 12” cable and can be moved or a replacement sensor can be purchased and substituted leaving the original one in place. Please contact Asylum Research for additional information. Open the ATC default parameter window: •...

  • Page 226: Error Messages

    A critical error requires that a service technician reset the system. In the event of a crit- ical error, please contact Asylum Research for assistance. A report log is generated by the system computer which can be sent to us to help diagnose the reason for the error. Please go to: my docu- ments\asylumresearch\devices\ATC.
  • Page 227 ATC to ramp up the heat to try to compensate for the heat loss. • The ATC air hose has fallen off or is disconnected. Same situation as above. The interior of the Cypher enclosure is cooling down while the ATC continues to heat up trying to compensate. 19.9.3. Noncritical Error messages Noncritical error messages indicate a problem with the setup and can be cleared after the fault is cor- rected.
  • Page 228 Ch. 19. Air Temperature Controller Sec. 19.9. Error messages This error is caused by the Feedback Sensor (Head Sensor) not being read. The possible causes can be: • The ATC power was shut off for more than a minute while the software was running. •...

  • Page 229: Alarms

    Ch. 19. Air Temperature Controller Sec. 19.10. Alarms 19.9.3.3. Error: 2 Phase Power The ATC requires single phase power. This error is typically caused by the wrong type of wall power • The earth ground connection may be faulty • There is current flowing in the neutral power line which may indicate a disconnected neutral line and the return path is though the earth ground connection.
  • Page 230 support.asylumresearch.com Page 226...

  • Page 231: Safety, Specifications, Set-Up, And Shipping

    Every new user should read the safety section at least one. If you need to move Who is this part for? your AFM or ship it to Asylum Research for any reason, please consult this manual. Beyond that, this portion of the manual will probably not see much day to day use.
  • Page 232 ....... 263 ....22.1 Using a USB drive causes Cypher to lose communication...

  • Page 233: Safety Precautions

    Cypher. 20.1. 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.
  • Page 234 In case of an emergency, the motors can be stopped in one of the following ways: • The 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.

  • Page 235: Light Source Safety

    50, dated 24 June 2007. 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. Nonetheless, it is still good to have an understanding of the laser in the instrument and the safety features.
  • Page 236 20.2.2.1. Laser Safety Interlocks The laser on the Cypher AFM is turned on an off by a control voltage which originates inside the ARC2 controller. On its way to the laser the voltage passes through various safety switches. This electrical path is explained in Figure 20.5 on page 234...
  • Page 237 Sec. 20.2. Light Source Safety Figure 20.4.: Light source module removed from the Cypher AFM. During the removal process 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 this image).

  • Page 238: Power Supply Safety And Thermal Management

    20.3. Power Supply Safety and Thermal Management 20.3.1. High Voltage The voltages inside the Cypher SPM are as dangerous as those present in a standard wall socket; there- fore, you should respect all of the components under the instrument covers as you would a wall socket.

  • Page 239: Instrument Weight

    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 240: Shipping Or Moving

    ....... . . 21.6.2 Crate Dimensions This chapter contains instructions on how to take a fully operational Cypher AFM, partially disassemble it, and move it to another location. 21.1. “Moving,” what does it mean? Grip the AFM by its base and slide it around on your workbench by a few inches.
  • Page 241 Research and request empty cartons with foam. 21.1.1. Shipping a Cypher component When shipping or moving all of the Cypher AFM, follow this chapter start to end. When only shipping one component (say scanner, or camera view system) then jump straight to the section which focuses on that component.

  • Page 242: Nomenclature

    AFM within its normal laboratory setting. 21.4. Shipping a Complete Cypher AFM System Call or otherwise contact Asylum Research and talk to us before moving anything. Chances STOP!! are that with a few phone calls and the help of this chapter you can do the job yourself. Not calling us will likely result in instrument damage, costly repairs and downtime, and the voiding of your warranty.
  • Page 243 Ch. 21. Shipping or Moving Sec. 21.4. Shipping a Complete Cypher AFM System 21.4.1. Scanner: Removal and Packaging 991.001: Carton: 10”x10”x10” Materials 990.035: Foam: (Scanner) Asylum Par# 290.111: 0.050” Hex Driver. Tools 14 lbs / 6 kg Final Wt System Shut Down: (Section 21.3 on page...
  • Page 244 Ch. 21. Shipping or Moving Sec. 21.4. Shipping a Complete Cypher AFM System Once the scanner cable is released, slide the scanner all the way out. Anticipate the significant weight of the scanner as you slide it off the rails.- HANDLE CAREFULLY.
  • Page 245 Ch. 21. Shipping or Moving Sec. 21.4. Shipping a Complete Cypher AFM System Tape the bag shut. Kapton tape is preferred. Place the scanner carefully on the bottom foam. Be careful putting on the top foam; make sure it is the right side and lines up with scanner already in box.
  • Page 246 Sec. 21.4. Shipping a Complete Cypher AFM System 21.4.2. Enclosure: Remove Top Call or otherwise contact Asylum Research and talk to us before moving anything. Chances STOP!! are that with a few phone calls and the help of this chapter you can do the job yourself. Not calling us will likely result in instrument damage, costly repairs and downtime, and the voiding of your warranty.
  • Page 247 Ch. 21. Shipping or Moving Sec. 21.4. Shipping a Complete Cypher AFM System Remove all 4 screws from back edge of the enclosure top plate. They are visible above the backpack. (SCREW INFO: 8-32 x ¼ BHCS SS) Unscrew 2 screws in the right door on the bottom and set aside (note: there may only be 1 screw) - (SCREW INFO: 8-32 x ½...
  • Page 248 248. 21.4.3. Backpack: Removal and Packaging Call or otherwise contact Asylum Research and talk to us before moving anything. Chances STOP!! are that with a few phone calls and the help of this chapter you can do the job yourself. Not calling us will likely result in instrument damage, costly repairs and downtime, and the voiding of your warranty.
  • Page 249 Ch. 21. Shipping or Moving Sec. 21.4. Shipping a Complete Cypher AFM System Loosen the 2 side screws (only loosen from Enclosure – do not remove completely) using the 3/32 Hex Driver. Remove the piece of foam from inside the chassis nearest the backpack screws you just loosened.
  • Page 250 11. Put it in the backpack box and tape shut. 21.4.4. Chassis: Removal Call or otherwise contact Asylum Research and talk to us before moving anything. Chances STOP!! are that with a few phone calls and the help of this chapter you can do the job yourself. Not calling us will likely result in instrument damage, costly repairs and downtime, and the voiding of your warranty.
  • Page 251 Ch. 21. Shipping or Moving Sec. 21.4. Shipping a Complete Cypher AFM System 1. Undo the HDMI cable from the back of the chassis (The stiff blue ribbon cable). a) Slide the AFM chassis about 1-2 inches forward. Put your hand down between the chassis...
  • Page 252 Sec. 21.4. Shipping a Complete Cypher AFM System 21.4.5. Enclosure: Packaging Call or otherwise contact Asylum Research and talk to us before moving anything. Chances STOP!! are that with a few phone calls and the help of this chapter you can do the job yourself. Not calling us will likely result in instrument damage, costly repairs and downtime, and the voiding of your warranty.
  • Page 253 Ch. 21. Shipping or Moving Sec. 21.4. Shipping a Complete Cypher AFM System Screw in the 2 screws on right side door using the 3/32 Hex Driver (part#290.134). Note: There may only be 1 screw in which case do the front screw closest to you. (SCREW INFO: 8-32 x ½...
  • Page 254 Ch. 21. Shipping or Moving Sec. 21.4. Shipping a Complete Cypher AFM System Replace the bridge in the front top of the enclosure. Slide it in so the screw holes and foam line up. 9. Screw in 2 screws to secure the bridge.
  • Page 255 SHIPPING IN A CRATE OR ON A PALLET 21.4.6. View Module: Removal and Packaging Call or otherwise contact Asylum Research and talk to us before moving anything. Chances STOP!! are that with a few phone calls and the help of this chapter you can do the job yourself. Not calling us will likely result in instrument damage, costly repairs and downtime, and the voiding of your warranty.
  • Page 256 Ch. 21. Shipping or Moving Sec. 21.4. Shipping a Complete Cypher AFM System System Shut Down: (Section 21.3 on page 238) Minimum Preparation Scanner Removal: (Section 21.4.1 on page 239) Enclosure Top Removal: (Section 21.4.2 on page 242) Backpack Removal [partial]: (Section 21.4.3 on page 244...
  • Page 257 Ch. 21. Shipping or Moving Sec. 21.4. Shipping a Complete Cypher AFM System 4. Set down the view module, then set aside the 2 screws and the L-key tool. Use Kapton tape to secure lens tissue over the view module lens.
  • Page 258 15. Close the box and tape it shut. 21.4.7. Chassis: Packaging Call or otherwise contact Asylum Research and talk to us before moving anything. Chances STOP!! are that with a few phone calls and the help of this chapter you can do the job yourself. Not calling us will likely result in instrument damage, costly repairs and downtime, and the voiding of your warranty.
  • Page 259 Ch. 21. Shipping or Moving Sec. 21.4. Shipping a Complete Cypher AFM System 991.016: Cardboard Carton 16”x14”x17” 990.034: Foam (Chassis Foam) 113.495: Chassis Packing Guard a.k.a “the Mullet” 10-32 x ¼ or ½ BHCS SS Bolts (2EA) depending on which guard you have Materials 10-32 x1 ½...
  • Page 260 Ch. 21. Shipping or Moving Sec. 21.4. Shipping a Complete Cypher AFM System Slide the light cube out carefully. d) Turn the clamping screw to close – only ¼ turn back – DO NOT OVER TIGHTEN! (See Figure in Step 1a on page 255) 2.
  • Page 261 Ch. 21. Shipping or Moving Sec. 21.4. Shipping a Complete Cypher AFM System Kapton tape the ground cable (green & yellow cable on back side of chassis) straight down behind the board (Do not tape to the side, as it must be back to be safe from the shipping guard/mullet).
  • Page 262 Ch. 21. Shipping or Moving Sec. 21.4. Shipping a Complete Cypher AFM System If this is shipping for the first time, put 5 pieces of foam tape inside the pullet (2 on each side and one in the middle ) to pad it and make it slide easier –...
  • Page 263 Ch. 21. Shipping or Moving Sec. 21.4. Shipping a Complete Cypher AFM System 2 screws need to go in the bottom back using 1/8” Hex Wrench L-key (part#290.119). Include a nut on each screw. The nut sits between the mullet and the chassis.
  • Page 264 Ch. 21. Shipping or Moving Sec. 21.4. Shipping a Complete Cypher AFM System CANNER BOX SHOULD REMAIN UPRIGHT AT ALL TIMES IF POSSIBLE WHEN Warning SHIPPING ON CRATE OR PALLET 21.4.8. Accessories: Packaging 991.014: Cardboard Carton 12”x12”x10 Materials 990.040: Foam (Cypher Optics & Accessory)

  • Page 265: Ancillary Equipment

    Bag all the cantilever holders and accessories and place them in the Cypher Accessory Kit. 7. Close the Cypher Accessory Kit and place it in a foam slot in the accessory foam/box. If this is anew system, put the Olympus Sample Pack in a slot in the foam/box.

  • Page 266: Weights And Dimensions

    Sec. 21.6. Weights and Dimensions 21.5.2. Computer and monitors Pack computers and monitors in the original Dell Computer boxes. 21.6. Weights and Dimensions 21.6.1. Standard Cypher System Weights (packed in Carton) 51 lbs / 23 kg Chassis/Head 14 lbs / 6 kg...

  • Page 267: Troubleshooting And Maintenance

    22.1.2. Workaround This applies only to Dell T3400 and T3500 computers. • Plug Cypher, ARC, mouse and keyboard into the bottom USB ports. • USB 2.0 devices like USB drives and printers and LCD monitor hubs may now safely be plugged into the remaining non-circled ports, including the two USB ports on the front of the computer.

  • Page 269: Bibliography, Glossary, And Index

    Part VI Bibliography, Glossary, and Index support.asylumresearch.com Page 265...
  • Page 270 Part Contents Index ..........268...
  • Page 271 PART CONTENTS PART CONTENTS Bibliography Cited Scientific References Cited Asylum Research Documents Applications Guide, Chapter: AC Mode Imaging in Air. Applications Guide, Chapter: Conductive AFM. Applications Guide, Chapter: PFM Using DART. Applications Guide, Chapter: Single Frequency PFM. Applications Guide, Chapter: Thermals.

  • Page 272: Index

    Index Index Index About the index: • Page numbers are preceded by the user guide part. The two are separated by a dash. • Bold printed page numbers are references to the definition of terms. • Other page numbers indicate the use of a term. Approach Force panel,...
  • Page 273 Index Index view module, support.asylumresearch.com Page 269...
  • Page 274 Index Index support.asylumresearch.com Page 270...

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