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====== Atomic Force Microscopy ======

  *//See also: [[http://en.wikipedia.org/wiki/Atomic_force_microscopy|Wikipedia article on AFM]]//
  *//See also: [[AFM advanced techniques]].//
  *//See also: [[AFM upkeep]]//

New users on the AFM are expected to get AFM training and then pass the {{::afm_training_quiz5.doc|AFM quiz}}.
To find answers to some of the quiz questions, the "AFM Manualette" is a useful resource. 
  *T:drive/Minot Group/Group documents/Manuals and documentation/AFM/MFP-3D Manualette_v9.pdf

Note that OSU also has an AFM facility run by [[http://mime.oregonstate.edu/people/faculty/materials/gibbons.html|Brady Gibbons]] in Materials Engineering. 

===== Scheduling time =====
To book time on the AFM, please use the group calendar (contact Ethan for access to this google calendar). Basic rules about booking time:
  *People who have scheduled time get priority. 
  *Don't block off an entire 9am-5pm workday - leave at least an hour for someone to do a quick characterization.



===== AFM Log Book =====
Please record your usage of the microscope in the AFM Log. Include: 
  *Name (write it in **before** you start imaging)
  *Date
  *What tip you used, what condition it is in, and what tip is currently in the AFM (when you're done)
  *What sample you imaged
  *General comments, e.g. raised back legs for larger sample. 
If the Log Book is full, the word document of the form can be found in the Minot Group/Shared folder on the T drive. 


===== Learning The AFM =====
For an overview, you should first, spend 5 minutes reading the [[http://en.wikipedia.org/wiki/Atomic_force_microscopy|Wikipedia article on AFM]].

A useful YouTube video ([[https://youtu.be/2Kv6KwADn7Q?t=177|I made a giant atomic force microscope]]) shows a giant AFM to explains how the tip-cantilever-surface interact with each other, and how the image is acquired.

Training involves
  - A session where you watch an experienced user (and ask questions)
  - Reading the "AFM Manualette".
  - A session where you "fly the AFM" with an experienced co-pilot talking you through each step.
  - Take a written test to check that you understand the important concepts: {{::afm_training_quiz5.doc|AFM quiz}}.
  - A session where you "fly the AFM" with an experienced co-pilot watching you. You can follow your own written notes, or use the "step-by-step walk through" that is provided below. This final supervised session should include changing a tip. (Use an old tip first for practice). 

The "AFM Manualette" is located in two places: 
  *T:drive/Minot Group/Group documents/Manuals and documentation/AFM/MFP-3D Manualette_v9.pdf
  *Box folder "Minot Group Documents"

With the AFM Manualette, there are some useful concept videos. I recommend watching The movies "Amplitude Feedback" and "Cantilever SEM". There is also a comprehensive manual (Ver_04_08). I recommend reading chapter 5. 

You must understand basic questions like 
  *how does the sample move in the x-y plane?
  *how is the tip deflection measured?
  *how is the tip base position measured?
  *why is the cantilever oscillating, what makes it oscillate?
  *what does the feedback circuit do?

We use ac-mode imaging. So, it’s important to understand the basic idea of shaking a cantilever at its base to excite the first vibrational mode (the system achieves 100-nanometer-amplitude motion at the free-end of the cantilever, by shaking the base of the cantilever by a fraction of a nanometer)
[[https://www.youtube.com/watch?v=AA6gWHu7GRs&ab_channel=SLURocketry]]


===== Step-by-step walk through for AC mode imaging =====

  - Sign into the black notebook (on the table next to the AFM)
  - Open version 16 of the AFM software (not version 14). It is critical that you use the correct version (switching between older/newer versions can corrupt the x-y stage calibration, which causes violent shaking of the x-y stage when the user starts scanning). A copy of a V16 AFM control Igor experiment is in the local Public documents folder.
  - Click the first option, "Template"
  - Once software loads, set AC mode in master panel
  - Place the sample to be imaged on the tray. Make sure that the stage x-y control thumbscrews are centered.
  - Make sure the vibration isolation stage is on and isolation is enabled.
  - Raise the legs on the MFP-3D tripod by ~5 turns to ensure the tip does not smash into the sample.
  - Set the MFP-3D over sample
  - Align Laser:
    * Turn on the camera - Click the lower left icon with a picture of a camera on it
    * Turn on the camera light - Switch on the box which sits on top of the AFM
    * Align camera on cantilever - Two knobs sticking up at the very rear of the  MFP-3D
    * Turn on the laser - Key switch on the AFM computer
    * Focus camera on the tip - Use the the focus ring toward the rear of the MFP-3D
    * Move laser toward the tip of the cantilever - Use the thumbscrews on the back & right side of the MFP-3D to maximize the 'Sum' signal
    * Adjust the photodetector (PD) - Use the thumbscrews on the left of the MFP-3D
      * Set the 'Deflection' in the S&D meter to zero (tapping mode) or a sliver negative (contact mode)
  - X Set AC Mode - In main tab of the master panel select 'AC Mode' in the 'Imaging Mode' pull down menu
  - Tune the AFM
    *  Open 'Tune' tab in the master panel
    *  Set 'Target %' to -5.0 % (this setting favors repulsive mode imaging, often recommended for beginners)
    * Click the 'Auto Tune' button and wait for tuning to finish. Software will set drive frequency.
  - Engage the tip
    *  Set the I gain to 10
    * Make the 'Set Point Voltage' about 95% of the target amplitude (1 V by default)
    * Click 'engage' in the S&D meter and 
    * Lower the tip (tripod thumbwheel — left = up, right = down) while watching the amplitude. The amplitude will drop as you near the surface. The computer will beep when feedback kicks in to stop the amplitude from dropping below the setpoint. Continue lowering until the Z voltage is in the middle of its range. 
    * If the Z-voltage goes down instead of up, re-tune. If that doesn't fix it, you might have junk stuck to the tip.
    * Lower the 'Set Point Voltage' by about 10%. 
    * Lower the tip until the 'Z voltage' approximately in the middle of its range.
    * Lower the 'Set Point Voltage' by about 10%. Watch for "hard stop" on the Z-voltage.
    * Disengage the tip by clicking 'withdraw' in the S&D meter
  - Close AFM Hood
  - Set image details in the main tab
  - Scan the sample, clicking 'frame up' or 'frame down' will start a scan


**When done imaging**
  - Click 'Stop!!!' button to stop the current scan and withdraw the tip
  - Open AFM Hood
  - Manually retract tip from sample - Give the front thumbwheel a few clockwise twists
  - Turn off laser - Key on the AFM computer
  - Turn off camera light - Switch on the box sitting on top of the AFM
  - Place MFP-3D onto its shelf holder
  - Remove sample
  - Close software and log out
  - Leave controller and PC running unless expecting a power outage
===== Imaging rules of thumb =====
It is easiest to get a good image on a small scan area (~ 1 micron). Starting from the default settings you can fine tune the image and then start increasing the scan size. Good settings will minimize ringing and reduce shadows while keeping the scan rate reasonably fast.

**Beginner settings** 
  *Scan size 1 micron
  *Scan rate < 15 micron / s
  *Integral gain 10
  *Free amplitude 1 V (~ 100 nm)
  *Set point amplitude 0.65 V

**Rule of thumb: "One high quality slow scan is worth ~5 low quality fast scans."**

It is tempting to be impatient and try to 'tune' the imaging parameters to get the data you want from a 2 - 5 minute scan. This strategy often backfires though, if you need to return to old AFM images and find they are junk aside from the information you 'tuned' the parameters for. Also, 'tuning' these parameters in the first place probably takes ~10 minutes so you're not really saving time anyway. The best fix for many imaging problems is simply to lower the 'rate'. The price you pay is scan time. However, I've found that you actually save time (and headache) by taking a single high quality slow scan rather than a bunch of quick ones with little parameter adjustments in between. I find that adjusting the rate so that the scan speed is <10 micron/sec works well in nearly all cases.

**Using nanotubes as a diagnostic tool**

When imaging nanotubes they should not be blurry in xy. Rather, they should be sharp lines about 20-40 nm thick and a few nm tall. If tubes are blurry in the xy, verify you are using enough scan lines (try 256 or 512). If they are still blurry reduce the 'rate' and/or the 'set point'. If the tubes are still blurry, do a [[AFM advanced techniques|force curve]] to verify that the tip is intact. If the tubes are still blurry after following these steps then you've likely got a thin layer of crud on your nanotubes.

**Ringing** 
On a perfectly flat surface, the amplitude should stabilize at the set point. If the amplitude cannot stabilize (often called "ringing"), the integral gain may need to be reduced.

**Shadows**
Tall objects cast shadows because it takes time for the AFM tip to relocate the surface after it steps off a cliff. The rate at which the tip finds the surface is proportional to

Gain x (Measured Amplitude - Set Point Amplitude)

Therefore, shadows are minimized by high gain and high amplitude difference (at the cost of more ringing and higher hammering force respectively). Shadows can also be minimized by slow scan velocity (at the cost of small scan area or lots of time). 

**Attractive vs repulsive**
When finding nanotube diameters, or looking at soft biological samples, it is useful to work in attractive mode imaging. The cantilever should be tuned above resonance (+5 %) and the amplitude should be small (for example 0.2 V). For more info see the Asylum phase imaging poster{{physics_of_phase_imaging_poster.pdf|phase imaging poster}}.

If the PhaseTrace switches from values below 90 to values above 90 then you're switching between repulsive and attractive mode respectively (see graph below). This wears out the tip and leads to weird artifacts in your height image. Black dots show up in the phase picture. To leave this unstable imaging condition, either de-/increase the Set Point (at the cost of more force/more shadows) or increase/reduce the Drive Amplitude. When changing Drive Amplitude, it is best to stop imaging and watch the measured amplitude and then choose an appropriate Set Point. In the following graph you can see the phase jumping from attractive to repulsive mode.

{{attractive_vs_repulsive.png|}}
{{ac-feedback.png|}} (pictures from //Asylum Research// poster)

**Understanding the AC feedback**
In the right picture above, you see a sketch of the AFM.
  *Set Point - photodetector measures an amplitude. By adjusting the z-voltage (press tip harder on sample) the feedback tries to reach this amplitude.
  *Integral Gain - reflects the strength of the feedback.
    *low number -> will not track the surface faithfully
    *high number -> will oscillate
      * best setting: right below oscillation
  *Proportin Gain - don't know. help says: "doesn't really matter". so "0" is a good choice.
  *Drive Amplitude - this is the amplitude the DAC puts on the piezo that drives the cantilever.
  *Drive Frequency - this number will be set by auto-tuning.

===== Replacing AFM Tips =====
**When to change an AFM tip**

AFM tips are like shaving razors. You use them until they are blunt (or until they get tenticals stuck to the tip which then stick to the surface).  There are tricks to prolonging the life of an AFM tip, and ways to know if it should be thrown out. 
  - Watch the phase image. If the phase is jumping from <90 to >90 degrees, you will quickly ware out the tip. Change imaging parameter to favor either repulse or attractive imaging. 
  - If the tip is blunt, sharp objects will look fat in your images. For example, a 1 nm tall nanotube which usually look 20 nm wide will start looking 100 nm wide. 
  - If something is stuck to your AFM tip, it will show up in a Force curve.

**To replace a tip**
  - Invert the AFM head onto the stabilization table. Remove the tip holder by pressing the black rubber button and secure it in the temporary mount by the laser.
  - Gently unscrew the clamp holding the tip down with a Phillips screwdriver. You don't want to completely unscrew it, just loosen it enough to remove the tip. 
  - Grab the old tip by its sides with a pair of tweezers and pull it away from the clamp. It should slide out freely.
  - Remove a new cantilever from the box with a pair of plastic tweezers using a twisting motion - be careful not to touch the end with the tip! Grab the new cantilever with your tweezers so the end you want to insert into the tip holder is pointing away from you and the tip is pointing upwards.
  - Slide the tip between the tip holder and the clamp (probably just as the old one was placed). The cantilever should be placed so it isn't inserted too far or too short. Too far, and the tip will not be well situated in the holder and zeroing the deflection will be impossible (see the figure below).
  - Once the tip is inserted properly, tighten the clamp and replace the holder in the AFM head. Make sure to rotate the AFM head in the opposite direction you used to invert the head, to avoid twisting the head cable.
  - Test the tip insertion two ways: i) Make sure the laser spot can be placed on the tip and the deflection can be zeroed without placing the wheels at their maximum range. ii) Auto tune the AFM, and make sure the amplitude and phase plots are free of any irregularities.

{{AFMCantelieverPosition.png|}}
===== Trouble shooting =====
AFM doesn't do what you want it to do (e.g. laser doesn't turn on or z-voltage behaves strange) it is always a good idea to
  * check the plug of the gray cable on the backside of the AFM. To do this you should turn off the AFM (switch next to the laser switch)
  * restart the computer

The computer takes a long time to log in.
  * Last time this happened we contacted COSINe helpdesk (ph 75574) and they fixed it. Something about a log file becoming too large. COSINe will want to know the computer name. To discover the computer name there are two easy steps. If no one is logged in just click the Domain drop down list and it will be listed as "This Computer". If someone is already logged in, simply click Start --> Run --> type "wnetinfo" --> Enter. This will display information about the computer including the computer name.

You keep getting streaky images(Streaky images can have multiple sources)
  * If you're imaging a sample with large particles try reducing your setpoint/increasing your drive amplitude and lowering your scan rate.
  * If you're imaging a clean/flat area but still see small random streaks that seem to alternate every other scan line make sure the Isolation table display says "Isolation Enabled." If you see "Isolation Disabled", press the capital E on the panel to enable isolation.

**If you see an amplitude and phase image that look reasonable, but the height and z-sensor have no texture (like imaging air would look) be sure that the computer doesn't need to update. In the past, a pending windows update has caused this issue.**

===== Sample preparation =====
**Static**
When working with insulating substrates, charge build up can be a problem. You will have trouble engaging with the sample if it is charged. Try waving the "static master" plunomium alpha particle source over the sample for 30 seconds. 

**Mica** 
Mica is a silicate mineral that has a tendancy to split nearly perfectly between layers leaving a very very smooth surface. This quality allows us to use Mica as a testing ground to find the distribution of small particles. 

**Mica Preparation** 
  *Obtain a small disk of Mica (9.9mm Diameter found in the drawer to the right of the south fume hood)
  *Attach the disk to the center of a microslide using silver paint, super glue, or epoxy (all found in the same drawer)
  *Allow to dry. (The silver paint takes about 24 hours to fully set up)
  *Now take a small piece of scotch tape and stick it to the surface of the mica.
  *Using the edge of a pair of tweezers push firmly down on mica surface and "smooth" out any bubbles. The goal of this step is to get the tape evenly stuck to the entire Mica surface.
  *Now slowly pull back the tape removing the top layer of the Mica and look to see if you removed a perfectly circular layer. If not repeat this step until you do. (In my trials at this it took 3-5 attempts)
  *If you do this correctly you will be left with a surface that only varies on the picometer scale.

**Flat gold surfaces**
Atomically flat gold is the standard substrate for STM (scanning tunneling microscopy). It is tricky to get atomically flat gold. One technique is flame annealing. There is info at this website: http://www.arrandee.com/Products/Gold_on_Glass/body_gold_on_glass.html

===== Image analysis =====
The MFP-3D software in Igor offers many convenient analysis features. Such as roughness calculations, cross sections, etc. The detailed information on the image processing can be found below.

===AFM Image Processing===
  * Load the AFM image to analyze. There are three panels used for the analysis: Representation panel (Panel in the picture itself), Statistical Analysis panel (Click on A in the representation panel) and Modify panel (Click on M in the representation panel).
==Representation Panel:==
  * After loading the AFM image, by changing the color map, range and offset, the basic analyzed image can be obtained. 
  * In the Commands options, image can be transported using the export command.
  * Argyle Light Program can be used for height measurements. This program can be loaded from the Start menu.  To load the image in this program, drag the picture into the work space. By changing the color, the corresponding measurements on the bar at the right hand side represents the height measurements. 
==Analyze Panel:==
  * Roughness icon can be used to study the surface by modifying the box size and ratio.
  * Section icon can be used to measure the height of an object on the surface by drawing the line across. Cursors A and B below the height plot can be used to measure the diameter of an object.
  * Histogram icon can be used to plot Height versus Current data.
  * Clear icon can be used to erase all the changes and get back to the original data.
==Modify Panel:==
  * Flatten icon can be used to load raw data by clicking on ultra restore layer icon. Different orders can be used to flatten the image by clicking on the order, generally, 1st order flattening is good enough.
  * Mask icon is used to exclude undesired data manually. Exclude points button can be used to draw a box/circle around the undesired objects. Fill button can be used to cover the boxed/circled area. Cal mask button is used to mask the undesired area automatically by changing the threshold value and the range.
  * Plane fit icon can be used to change the order (ask Landon)
FFT icon can be used to fill mask and exclude the undesired data points. (ask Landon)
The processed image can be found in the representation panel, named as HtT* 0 which can be saved.


For more specialized image analysis try [[http://rsbweb.nih.gov/ij/docs/index.html|ImageJ]]. ImageJ is a free software from the National Institutes of Health (NIH). It is a useful tool for doing complex image analysis tasks, such as [[http://rsbweb.nih.gov/ij/docs/index.htmlhttp://rsbweb.nih.gov/ij/docs/examples/dna-contours/index.html|measuring the length of wiggly CNTs or DNA]], or [[http://rsbweb.nih.gov/ij/docs/index.htmlhttp://rsbweb.nih.gov/ij/docs/examples/dna-contours/index.htmlhttp://rsbweb.nih.gov/ij/docs/pdfs/examples.pdf|measuring particle sizes and outputting size distributions]].

[[http://gwyddion.net/|Gwyddion]] is another free software designed for analyzing scanning microscope probe images. It is intuitive and has many features to improve image quality. Carly has found it useful for looking at images of graphene.

===== Supplies =====
Silicon AFM tips can be bought in boxes of 10 or 50 units, or as an entire wafer (380 units). There is a big discount for buying a full wafer. 

A spring constant of 40 Newton/meter is very common because it can be used for very small tapping amplitudes without snapping to the surface. It is widely used and therefore reasonably cheap. However, it is not great for pushing into the surface because the tip breaks off easily.

A spring constant of 2-5 Newton/meter is very versatile. It can be used for tapping mode imaging, nanolithography, electric force imaging, contact mode imaging in liquids and force distance curves.


Recommended AFM tips: 

  *Budget Sensors BS-Tap300AL tapping tips (40 N/m), and Tap150AL (5 N/m) www.budgetsensors.com/. Gold coated tips (more expensive) are also available. These tips were originally recommended to us by Scott MacLaren at the Univerisity of Illinois AFM center. "very inexpensive but good". We have also been very impressed with the consistent good quality. Prices are:
    *$3900/380 = $10.26 each
    *$890/50 = $17.80 each
    *$210/10 = $21.00 each

  *Olympus AC 160 TS (40 Newtons/meter) & AC 240 TS (2 Newtons/meter),  www.asylumresearch.com. Recommended by Jason Li at Asylum Research. Prices are
    *$6000/375 = $16.00 each
    *$1850/70 = $26.43 each
    *$1000/35 = 28.57 each

===== Data export for visitors =====
The easiest way for visitors to take home their data is the IgorPro format (.ibw files). IgorPro is the platform on which the Asylum Research AFM has been built. A trial copy of IgorPro software is available from the [[http://www.wavemetrics.com/support/demos.htm|IgorPro website]]. The trial version of the software will get you a long way. The academic copy costs $400. The MFP3D software (written by Asylum Research to run on the Igor plaform) is open source. We can supply you with a copy. 

===== Contacting Asylum Research =====
Asylum Research has a very friendly and helpful support department. Using the long distance access number (ask Ethan for this number) you can reach AR support at 888-472-2795 or email them at support@asylumresearch.com. When emailing about a specific AFM image related using and you need to send them files, you need to upload the files to their FTP server using a Java interface at www.asylumresearch.com/upload. You should put all the files together in a zip file if your sending more than one file. If you're having a technical issue with the AFM software, the AR support guys can remotely control the MFP-3D software and try to figure out whats going on.  For the quickest results calling them is the best method.
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