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--- afm [2025/04/11 14:24] – ethanminot
+++ afm [2025/10/24 12:32] (current) – [Atomic Force Microscopy] ethanminot
@@ Line 4: / Line 4: @@
   *//See also: [[AFM advanced techniques]].//
   *//See also: [[AFM upkeep]]//
+  *//See also: [[AFM Image Anaylsis]]//
-New users of the AFM are expected to get AFM training and then pass the {{::afm_training_quiz6.doc|AFM quiz}}.
+New users of the AFM are expected to get AFM training and then pass the {{::afm_training_quiz6.doc|AFM quiz}}. More guidance about learning the AFM is given below.
-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:
+The AFM calendar is managed by [[https://relms.oregonstate.edu/facilities|RELMS]]. On the RELMS website, our lab is listed as "Quantum Materials Lab". RELMS is a university-wide system administered by a team of three OSU employees. If you have not registered with RELMS before, the RELMS team will help you sign up and associate your billing indexes with your account. You must be trained on the AFM before you can book time on the RELMS 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.
+  *For OSU internal users, please limit your bookings to 3 hours per day. On the day of your booking, you can extend your time if no one else has booked time.
+  *Only make a booking if you are 90% sure you will use the booking. When you make a booking, everyone else adjusts their schedule to work around your booking. Be respectful of the effort other users are making for you.
+Every time you use the AFM, follow these steps:
+  - Write your name and date in the physical logbook
+  - Open your RELMS booking on the computer (or your cell phone) and "begin" your reservation.
+  - Use the AFM
+  - Open your RELMS booking on the computer (or your cell phone) and "end" the reservation. RELMS will then bill your index for the actual time you used the AFM.
+  - Complete your logbook entry in the physical logbook.
+If you forget to begin and/or end the RELMS booking, you will get an email from RELMS asking you to enter the actual time that you used the AFM. Please follow the instructions in the email.
@@ Line 35: / Line 45: @@
   *[[https://www.youtube.com/watch?v=K9FgPWK3Co4|Using an oscillating cantilever]]. Animation of ac mode imaging (= non-contact mode). Attractive force and repulsive force imaging. Feedback control.
   *[[https://youtu.be/2Kv6KwADn7Q?t=177|I made a giant atomic force microscope]]) explains how the tip-cantilever-surface interact with each other, and how the image is acquired.
+  *[[https://youtu.be/AA6gWHu7GRs?t=157|Resonant modes of cantilever]]. We use ac-mode imaging. So, it’s important to understand the basic idea of shaking the base of a cantilever to excite the first vibrational mode. The AFM cantilever oscillates with an amplitude of about 100 nanometers.
 Training is similar to learning how to drive a car:
@@ Line 42: / Line 53: @@
   - When you have your "learner's permit", do a session driving the AFM with the help from an experienced co-pilot who talks you through each step.
   - A session where you drive the AFM while you explain each step and an experienced co-pilot watches you.
-  - A final driving test (typically Ethan will want to watch you drive).
+  - A final driving test (typically Ethan will want to watch you drive). The final test will include changing out an AFM tip (which is analogous to parallel parking during a DMV driving test!).
-  -  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
@@ Line 59: / Line 62: @@
   *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 =====
+//If a tip change is needed - see the //
-  - Sign into the black notebook (on the table next to the AFM)
+  - Sign into the log book (black ring binder) on the table next to the AFM. If Jesse from Inpria used the AFM last, you'll need to mount the standard AFM tip back in the machine: [[AFM tip change information]]
-  - 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.
+  - Start your RELMS reservation on the [[https://relms.oregonstate.edu/facilities|RELMS website]].
+  - Turn on the laser - Key switch on the AFM computer
+  - Open version 19 of the realtime AFM software (latest stable version as of July 2025).
   - 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.
+  - Place the sample to be imaged on the x-y stage. Adjust the x-y micrometers which control the coarse position of the x-y stage. The x-y stage should be centered so you have ability to move the sample in every direction.
   - 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.
+  - Lengthen the front leg on the MFP-3D tripod by ~5 turns to ensure the tip does not smash into the sample. There is an arrow that says "up", which refers to **raising up the AFM tip** by lengthening the leg.
-  - Set the MFP-3D over sample
+  - Set the MFP-3D tripod 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 - Click the lower left icon that looks like a camera.
-    * Turn on the camera light - Switch on the box which sits on top of the AFM
+    * 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
+    * Align camera on cantilever using two knobs sticking up at the very rear of the MFP-3D tripod.
-    * Turn on the laser - Key switch on the AFM computer
+    * Not usually needed, but you might need to focus the camera on the AFM tip - Use the the focus ring toward the rear of the MFP-3D. The ring is difficult to turn (as of July 2025).
-    * 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 - the control wheels are labeled LDX and LDY (laser deflection x and y). They are located on the back & right side of the MFP-3D tripod. Use these controls to maximize the 'Sum' signal. If the laser is badly misaligned, it can be hard to locate. If you "loss" the laser spot, ask an experienced user for help.
-    * 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) position. The control wheel for the photodetector is located on the left side of the MFP-3D tripod and is labeled PD. Set the PD 'Deflection' meter to near zero.
-    * 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)
+    *  Set 'Target %' to -5.0 %. This setting is a first guess at the ideal drive frequency (setting it slightly less than the resonant frequency). You may have to test different drive frequencies later if you notice "phase jumping" during imaging.
-    * Click the 'Auto Tune' button and wait for tuning to finish. Software will set drive frequency.
+    * Click the 'Auto Tune' button and wait for tuning to finish. Software will set drive frequency and drive amplitude. The graph of amplitude and phase should look like the textbook curves for a driven damped harmonic oscillator.
+    * In the read-out window of the software, you will now see a 1-volt amplitude signal underneath the sum signal. Maximize this amplitude signal by moving the laser along the length of the AFM cantilever. When the amplitude is maximized, the sum signal will be slightly less than its max value.
+    * Click 'Auto Tune' one more time (or manually adjust the drive amplitude).
   - Engage the tip
-    *  Set the I gain to 10
+    * Set the I gain to 10
-    * Make the 'Set Point Voltage' about 95% of the target amplitude (1 V by default)
+    * Make the 'Set Point Voltage' about 95% of the measured free-air amplitude signal. (The measured free-air amplitude signal is probably 1 V right now, but you need to watch this, it might be drifting.)
-    * Click 'engage' in the S&D meter and
+    * Click 'engage' in the S&D meter panel.
-    * 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.
+    * Lower the tip down towards the sample by shortening the front leg of the MFP-3D tripod. Watch the measured amplitude as you do this. Also watch the camera image. As the surface comes into focus (before the amplitude starts to drop), consider moving to a clean place on your sample (use the x-y stage coarse positioning micrometers).
-    * 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.
+    * If you have a clean landing area for your tip, continue lowering the tip down towards the sample. The amplitude will drop as you near the surface. You will also notice changes in phase. Pay attention to these "tell-tales". The computer will beep when feedback kicks in to stop the amplitude from dropping below the setpoint. Continue lowering until the Z voltage is just past the middle of its range. (If the Z-voltage is not behaving as expected, click withdraw and check the amplitude and phase).
-    * Lower the 'Set Point Voltage' by about 10%.
+    * Lower the 'Set Point Voltage' click by click. The Z-voltage will increase.
-    * Lower the tip until the 'Z voltage' approximately in the middle of its range.
+    * When the Z-voltage is above its midpoint, use the thumb wheel to lower the tripod leg until the Z-voltage is below the midpoint.
-    * Lower the 'Set Point Voltage' by about 10%. Watch for "hard stop" on the Z-voltage.
+    * Lower the 'Set Point Voltage' again, reducing it click by click. The Z-voltage will increase. Watch for a hard stop. If the Z-voltage increases past its midpoint without a hard stop, repeat the cycle of turning the thumb wheel and lowering the set-point voltage.
-    * Disengage the tip by clicking 'withdraw' in the S&D meter
+    * After you achieve a hard stop, disengage the tip by clicking 'withdraw' in the S&D meter
-  - Close AFM Hood
+  - Close AFM Hood gentle (don't bump the machine).
-  - Set image details in the main tab
+  - Check the Amplitude and Phase of the cantilever vibration. Re-tune if needed.
-  - Scan the sample, clicking 'frame up' or 'frame down' will start a scan
+  - Set imaging parameters in the main tab. For example, you might start with a scan size of 2 microns. See the imaging rules of thumb listed below.
+  - Do your first test scan the sample. Clicking 'frame up' or 'frame down' will start a scan. You should do a test scan before you spend much time searching for a specific location on your sample.
+  - Observe the quality of the scan. See the section below called "Tuning the AFM to get a good image". Look for phase jumps. Look for parachuting. Look for the tip loosing contact with the surface. Remedies are described below.
+  - If you got a good image, you are ready for the rest of your session. If you need the microscope to search a large area, raise the tip by one "swipe" of the thumbwheel so you can safely make coarse motion in the x-y plane.
@@ Line 106: / Line 110: @@
   - 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
+  - Manually retract tip from sample - turn the front thumbwheel in the "up" direction. Watch the camera feed and the tip amplitude to ensure you aren't inadvertently crashing the tip into the sample.
-  - Turn off laser - Key on the AFM computer
+  - Turn off laser - Key on the AFM controller.
-  - Turn off camera light - Switch on the box sitting on top of the AFM
+  - Turn off camera light - Switch on the box sitting on top of the AFM enclosure.
-  - Place MFP-3D onto its shelf holder
+  - Place MFP-3D tripod onto its shelf holder
   - Remove sample
-  - Close software and log out
+  - Close the AFM Hood to keep dust out of the machine.
+  - Close software.
+  - Sign out of the Log Book.
+  - End the reservation in RELMS.
   - 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.
+===== Tuning the AFM to get a good image =====
+Check the **scan rate**. Is it less than 15 microns/second? Slower scans are more stable and reproducible. You might save time in the long run (and headache) by keeping scan rate less than 15 microns/second. Use an even slower scan rate if the features on the sample are very tall.
+When you withdraw from the surface, check the free-air amplitude is the same as you when you first tuned the tip. If **free-air amplitude has drifted**, you can manually change the drive amplitude.
+Sometimes the image is improved by withdrawing and re-running the autotune procedure (**resonant frequency might have changed**). The autotune procedure will make changes to both the drive amplitude and drive frequency.
+Sometimes the image is improved by lowering the set-point amplitude a few clicks. For example, this might fix **parachuting**. Minor changes to set-point amplitude can be made in real time, during imaging. The set-point should be low enough that the tip stays in contact with the surface. However, don't make the set-point too low. The ideal set-point amplitude is typically about two clicks lower than loosing contact with the surface.
+If you notice **phase jumping** (a jump from below 90 degree to above 90 degrees), you need to make adjustments to the drive frequency. Phase jumping will wear out the AFM tip (making it blunt). Phase jumping also introduces artifacts in the height data. Make test images with different values of drive frequency such that the free-air phase is 70 degrees, 80 degrees, 100 degree and 110 degrees. To make these test images, you'll need to maintain a constant free-air amplitude by simultaneously adjusting drive amplitude. By doing this, you are searching for imaging parameters for which the cantilever oscillations are most stable.
+It’s hard to predict a priori whether the best images will be acquired with phase below 90, or above 90. The best imaging regime for a given day depends on tip sharpness, cantilever stiffness, the sample’s mechanical/adhesive properties, the material and coating of the tip, and the humidity in the room. These factors modify the functional form of long-range van der Waals forces, the electrostatic forces, the way the tip indents the sample, and the capillary forces related to the water meniscus. A nonlinear tip–sample force with respect of tip-sample separation leads to bistabilities, and these bistabilities cause the phase jumps which mess up the AFM image.
+===== Other imaging rules of thumb =====
+It is easiest to get a good image on a small scan area (~ 2 micron). A small scan also facilitates verification of tip sharpness. 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 size 4 micron (look at a random small feature on a flat background to verify the sharpness of the tip)
-  *Scan rate < 15 micron / s
+  *Scan rate < 15 micron/s
   *Integral gain 10
-  *Free amplitude 1 V (~ 100 nm)
+  *Free amplitude 1 V (corresponds to a cantilever motion of ~ 100 nm)
-  *Set point amplitude 0.65 V
+  *Set-point amplitude 0.75 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**
@@ Line 168: / Line 187: @@
   - 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