phase image composite resinrequimte     The Manager of this instrument is:                 Francisco  Jorge Caldeira.
     Contact: This email address is being protected from spambots. You need JavaScript enabled to view it. or This email address is being protected from spambots. You need JavaScript enabled to view it. 

          AFM Lab DQ-FCT-UNL, Caparica.

I am a TT-AFM from AFM I was born (Jorge Caldeira assembled me) in Signal Hill CA USA, so he named me...Signal Hill !
I travel from Signal Hill CA USA to Monte de Caparica Portugal ... Later I visit my twin machine Long Beach in Porto for the 2013 AFM  course, and to pay its visit to Caparica in the 2011 AFM course.
So both TT-AFM's were the first machines assembled and we traveled each almost 10 000 km far...
See the place were I was made .... and Leonor's hair that I imaged and got her the AFM 2013 course prize...
Can I use AFM ?     Yes you can   ...

 signalhill Leonor hair details s


GPS: LAT=38.66219, LONG -9.20867  Location: Room 119 DQ FCT UNL PT
Current Projects:

PEDOT on Paper 

Cesar Laia

Jorge Caldeira




Pf1 bacteriophage cytochrome c

electrostatic complex macroscopic fibers


Heber Silva

Ruben Chaves

Jorge Caldeira

Peter Eaton





Tooth dentinal tubes

Acid atacked hipoclorite cleaned


João Oliveira

Jorge Caldeira




Polymeric nanoparticles, formed from polystyrene with pending hydrophilic glucose moieties


Krasimira Petrova

Requimte FCT UNL



Polymeric nanoparticles (PNPs) based on amphiphilic polymeric conjugates composed of cholic acid, sucrose and PEG. 

Carina Crucho

Teresa Barros

Requimte FCT UNL



Dental restoration resins and polishing systems


Rita Simões

Jorge Caldeira





Classic Maya chrysoprase maskette pendant ca. 800 AD 


Hugo Miguel Crespo

Faculdade de Letras Universidade de Lisboa


Ana Pereira






Core-shell polymeric nanoparticles, formed from polystyrene with pending bifunctional glucose

 Krasimira Petrova

Requimte FCT UNL



Nanoestructured (nanocal), synthesized from metallic Ca

CaO Þ Ca(OH)2 + CO2    Þ CaCO3

Giovanni Borsoi

LNEC Portugal

TU Delft Holland


Photochemical dendrimeric polymerization of tripodal coumarin

 João Avo

João Lima

Jorge Parola

Requimte FCT UNL



Pseudomonas aeruginosa with bacteriphage Pf1 | Patricia Montez  Héber Silva, Ruben Chaves Jorge Caldeira

Dechorosprillium sp Bacteria | Cristina Costa

Yeast | Madalena Oom

Magnetically Aligned Pf1 Virus + Protein assocaition | Ruben C., Héber S., Celina S., P. Eaton

Magnetic Nano Particles Fe3O4 "bare" 10x10 μm Image | Cecília Roque,  Sara Santana

 afm_scan_2011-01-24_03.22.11 10um 256 pixels right







 Vertically polsihed Tooth sample  20x20 μm Image  | J.Martins dos Santos, Ana Mano Azul,  Mario.Polido, João Oliveira e Jorge Caldeira



                               Instrument Information

signal hilll instrument with computer










This instrument is a modified TT-AFM from AFMWorkshop.

  • Instrument Configuration: Light lever (optical lever) - based sample-scanning AFM
  • Sample Sizes:ca. 13x13x5 mm
  • Imaging Modes: vibrating (tapping), non-vibrating (contact), phase imaging, lateral force microscopy (friction force microscopy)*
  • Imaging Environment: Air or Liquid* (experimental).
  • Z-translation: Vertical direct drive (1micron resolution)
  • XY Translation: manual micrometers
  • Video Optical Microscope: Zoom to 400X, 3 micron resolution (3M pixel camera)
  • Scan Range: 70x70x17 microns
  • Linearisation: All axes (x, y and z) with strain guages, can be turned off for enhanced signal to noise ratio.
  • Z noise level: less than 0.2 Angstrom
  • Vibration isolation: homemade passive solution


signal hill

Signal Hill Instrument closeup


  • Startup Procedure
  • Shutdown Procedure
  • Scanning in contact "non-vibrating" mode
  • Scanning in tapping "vibrating" mode
  • These protocols are currently in development, meanwhile, here is a link to the latest version of the protocols word document for use of "Long Beach": TTAFM_protocols.doc

Back to Requimte Page           Go to Porto Lab Page

1. Startup Procedure


  1. Turn on PC: Allow to boot to Windows. Turn on monitor
  2. Turn on EBox; all seven green lights should come on1
  3. Start Software (e.g. AFM Workshop 1.5.6.exe)
  4. Remove dust sheet from AFM
  5. Connect video camera to USB if necessary
  6. Turn on video camera light source
  7. Remove dust cap from video microscope
1. Insert Probe and align

 This procedure is for inserting a new probe into the TT-AFM AFM and aligning the laser on it.


  1. Remove the probe holder cassette from the instrument and place it, upside-down on probe insertion base, see figure 1.

  probe holder with probe


Figure 1: Probe holder cassette in Probe insertion base.


  1. Open box with probes, next to probe insertion base.
  2. Use probe tweezers to move probe to “landing pad” on probe insertion base.
  3. With one hand, push down on cassette until brass spring rises a little (it moves less than one millimetre). With your other hand, use rubber brush to move probe under spring, and then release. Check probe is seated all the way back in the slot.
  4. Lift probe cassette from probe insertion base, turn the right way up and slide into AFM instrument.


  1. If using a reflective sample, insert it now as it makes alignment easier.
  2. Start video microscope software, App300 .exe
  3. Push play button in app300.exe
  4. Locate probe in video microscope. This may be as simple as moving the focal plane of the microscope up and down using the wheel on the side.

10.  If laser is not on, turn it on in AFM Workshop software. Also check, that motor is responding.[1]

11.  Align laser on probe using the two laser translation thumbscrews located at the top and front of the AFM head; see figure 2.


figure 2 controls on head


Figure 2: AFM Head, indicating location of thumbscrews for translation of laser and photodetector



12.  For details on alignment of laser see page 89 of Eaton and West. Get the maximum signal. The laser may not look like a discreet spot, see figure 3.

laser on probe 

FIGURE 3: Laser alignment, often you get diffraction pattern instead of a visible spot

13.  You may not be able to get the top-bottom(T-B) and left-right(L-R) signals to zero, without reducing the Top+Bottom, the important thing, is that they should change when you move the photodetector translation thumbscrews. Get the T-B and L-R signals as close to zero as you can (ideally within 0.1V), without jeopardising the T+B signal to do so.


 This is all that is required, see the scanning protocol for beginning to scan.

[1] If either laser or motor does not respond, you need to turn of the software and ebox, then turn the ebox, then the software back on.


 2. Shutdown Procedure

  1.  Ensure disengaged from surface
  2. Lift head ca. 1cm.
  3. Exit Software (e.g. AFM Workshop 1.4.1.exe)[1]
  4. Turn off EBox
  5. Shutdown PC and turn off monitor
  6. Remove your sample, and probe if appropriate.
  7. Remove video camera to USB
  8. Turn off video camera light source
  9. Fit dust cap to video microscope
  10. 10.   Place dust sheet over AFM

[1] BUG ALERT: Some versions of the software do not shutdown if you use the red box with a cross in the upper right of the window. Instead exit with the “Exit” button on the Topo Scan Tab. If the software won’t close, use windows task manager to close it.)

  1. Scan (Vibrating Mode)
    • Automated tip approach should have finished with the yellow line in the middle of the range , in the Z drive display. If not, approach again. If this never works, ensure the sample is not moving, and try reselecting the operation frequency.
    • Go to “topo scan” tab.
    • The table below has some suggested initial operating parameters. Some of these may be inappropriate for your sample. For example, you may only be interested in larger or smaller scans than 15 µm.


Suggested initial value



Scan rate


Scan lines


Scan size





0 degrees


X and Y = 25 µm ( for 50 µm range)









Left image, Right Image

Z_drive, Z_ampl

  • Click “start” to begin scanning.
  • If your images show NOTHING (except laser interference in the amplitude channel), there are several things to try: reduce setpoint, approach again, and / or increase amplitude in prescan (in this order). Typically, the initial setpoint will be too high, so a reduction of 10 to 20% maybe required. Be cautious, and do not reduce setpoint below 60% of it’s initial value.
  • Adjust parameters (especially scan speed, gain, Proportional, integral and Setpoint as required while scanning, watching the effect on the line scan and image. For more on this see chapter 4 of Eaton and West.


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