The Porto AFM Workshop 2019 has been announced. This is the sixth edition of the course!

 

The course will run from the 15th to 18th April. This is a training workshop, aimed at any researcher or scientist, who wants to learn about AFM, or increase their knowledge of the technique. Following the successful courses that have run since 2011, the course will includes several hours hands-on training in acquiring images with the atomic force microscope as well as AFM data processing.

 

Please click the image below to download the flyer with more details.

link to .pdf of flyer

 

  UPDATES:

  • More details of the course will be announced soon, meanwhile, as usual, pre-registration can be made by emailing me at This email address is being protected from spambots. You need JavaScript enabled to view it.Places on the course are very limited, so interested students should make enquiries or register as soon as possible.

  • There will be some guest scientists, talking about advanced applications in different areas. More details will be announced soon

 

 A blog with information and student feedback from the previous courses can be seen here:2017 course, 2014 course2013 course2011 course.


The course is supported by AFMWorkshop, The Faculty of Sciences of The University of Porto and my research institution, LAQV/Requimte

The Porto AFM Workshop 2019 has been announced. This is the sixth edition of the course!

 

The course will run from the 15th to 18th April. This is a training workshop, aimed at any researcher or scientist, who wants to learn about AFM, or increase their knowledge of the technique. Following the successful courses that have run since 2011, the course will includes several hours hands-on training in acquiring images with the atomic force microscope as well as AFM data processing.

 

Please click the image below to download the flyer with more details.

link to .pdf of flyer

 

  UPDATES:

  • More details of the course will be announced soon, meanwhile, as usual, pre-registration can be made by emailing me at This email address is being protected from spambots. You need JavaScript enabled to view it.Places on the course are very limited, so interested students should make enquiries or register as soon as possible.

  • There will be some guest scientists, talking about advanced applications in different areas. More details will be announced soon

 

 A blog with information and student feedback from the previous courses can be seen here:2017 course, 2014 course2013 course2011 course.


The course is supported by AFMWorkshop, The Faculty of Sciences of The University of Porto and my research institution, LAQV/Requimte. 

TT-AFM noise floor measurement

1. Place a clean silicon calibration sample on the scanner.
2. Place a new probe in the instrument.
3. For this comparison, use vibrating mode. Setup the optical  alignment and Tune frequency as normal.
4. Select parameters to test are listed below. note that for a fair comparison, you can use parameters relevant to your typical measurements. The parameters described here, will give you an “ideal” value, i.e the best result possible.

 

Suggested parameters 

Parameter

Suggested value

X Gain %

0

Y Gain %

0

XY HV Gain

Initially 1 (note it should be 0 for the actual measurement)

Z HV Gain

1

Image Add

Off

Z Feedback values

Values you typically  use, for example Gain 1.5, Proportional 150, Integral 1500

Lines

128

speed

1 Hz

Left Image

Z_DRIVE

Samples/Pixel

25

 

Note that you can use any different parameters you like for this, and they can and will alter the results that you get. Also, the instrument should be properly calibrated in z to allow comparison with any other values. Be aware that tip approach with Z HV gain at 1 will be very slow, and some post-approach adjustments might be necessary.(i.e Jog Down).

 

5. Go into feedback, and scan an image of a small area of the surface (XY HV Gain of 1). The image should be clean, with very few features visible. Ensure you end the scan with the probe on a flat part of the sample.

6. Withdraw probe.

7. Set scan size to 0, by using XY HV Gain = 0.

8. Approach surface again.

 

NOTE: It is important that you go into feedback on the surface in the same way as you did when you scanned an image. If you go into false feedback (probe almost but not quite, on the surface), you will not make a valid noise floor measurement.

9. Scan another image. No sample features should appear, as scan size is zero. The image may look something like the image below, or have some regular patterns in it.

noise-floor
1
0. Save the file, and open the Left image -  z piezo drive file (height image) in gwyddion.
11. Apply a 1st order polynomial levelling (fit linear).
12. Use “Statistical Quantities” and record the RMS average roughness (Sq). This is the noise floor

You should get a value of <1 angstrom (Gwyddion reports this in picometers, typically, so you expect to see a value of <100 pm).

If you do not get a satisfactory value, try removing sources of external vibration (other machinery, acoustic noise, unnecessary cables) from the instrument. Ensure probe and sample are grounded. Ensure that the vibration isolation system is setup properly.

Typical values found in a TT-AFM in an acoustically shielding box, with bungee-cord type isolation, in vibrating mode would be 0.3 to 0.6 angstrom.

You should be able to achieve at least the value specified by AFM workshop on the instrument specification sheet which was delivered with your instrument.


All materials on this website are copyright 2010-2018 Peter Eaton.

While many other procedures are important for full determination of the performance of an AFM instrument, the Z noise floor is often used as a simple parameter to quantify instrument performance, since it indicates the lower limit of the precision that can be reached in the z axis in that instrument, and is also simple to measure.noise-floor

It can be essential to know the noise floor of the AFM instrument to assure that high resolution measurements are meaningful. This can be particularly important for measurements of very small features (i.e. < 5nm), and for high resolution force spectroscopy. Measuring the noise floor can also help in optimizing instrument setup and vibration isolation. It is important to know the noise floor when using only the z piezo in the z feedback loop, as well as the noise floor of the z calibration sensor if there is one in the instrument. In most instruments, the noise floor of the z calibration sensor will be much higher than that of the z piezo.

In order to get reproducible results, all scan parameters should be maintained the same when comparing two results. Some factors, such as the PID values vary greatly from instrument to instrument, so the specific values to use cannot be suggested here. In each case, standard values should be established such that a fair comparison can be made.

Note that the procedure below is adapted from general guidelines given in Appendix B, page 195 of Eaton and West “Atomic Force Microscopy”. For a outline of a procedure that’s generally applicable to any model of AFM, take a look at the procedure below. Click here to find a specific procedure for measuring the z noise floor on a TT-AFM from AFM workshop.

 

Measuring noise floor in the z piezo signal

a) Place a flat, clean sample in the instrument. Use a new probe.

b) Do a probe approach and scan a small image on the sample to verify cleanliness and optimize the PID parameters.

c) Set the instrument to make a zero size scan such that the probe does not move in the x and y axis. Some instruments do not seem to have the option to do this (I have found that the JPK Nanowizard software does not allow this). In this case, make the smallest size scan you are able to , such as 1nm, or even less if possible).

 

d) Measure an image without probe motion in x or y, i.e. an image with a scan size of 0 nm, at a 1 Hz scan rate. A 128 x 128 pixel image is adequate. The data from the z piezo voltage should be used. This may be labelled height, or topography. The z scale should be in nanometers.

 

e) It may be necessary to flatten the data before the measurement, e.g. by a 1st order horizontal line levelling routine.

 

f)  Calculate the RMS roughness (Rq, see chapter 5) of the image, this value is the noise floor.

If you get some transient noise in the image, from e.g. a person talking, or slamming a door, you can repeat the image.


The achievable noise floor varies from one instrument to another, as well as depending on the noise in the environment, the measurement parameters, and the vibration isolation, but typically a sub-Ångström noise floor can be achieved. An example of type of image you should get is shown in the image above. it's important that you scan a small image before doing the "zero size" image, as the instrument must be in feedback for the noise floor to be measured.

 


All text and images copyright Peter Eaton 2014-2018

Introduction

This article contains a list of all the software freely available to manipulate data from Scanning Probe Microscopy (SPM), that is, Atomic Force Microscopy (AFM), and Scanning Tunnelling Microscopy (STM). It does not include software designed only to load one particular format, i.e. the software provided by the instrument manufacturers, unless they are able to open other formats. It is intended to summarise the third party software available. It does not compare the quality of the software, and the order is entirely arbitrary. If you know of other software available, let me know.  I do know there are two other lists of SPM software[This one and This one], although neither seem to be updated.

 

This list is an updated version of that which appeared in my book:"Atomic Force Microscopy", OUP, 2010, with Paul West.

 

List of Third Party SPM Software

Gwyddion

Freely available, open source software for manipulation of SPM files; supports very many formats, contains many analysis tools. Available for Linux, Windows and MAC OS. Frequently updated. Available here. (http://www.gwyddion.net)

 

SPIP (Scanning Probe Image Processor)

Commercial software for manipulation of SPM files; supports very many formats, contains many analysis tools. Also allows analysis of force curves in several formats. Has a purchase price, but a time-limited demonstration version is available. Frequently updated. Following acquisition of imagemet by digital surf, SPIP is being merged with the MountainsMap package (see below) . Details, purchase, and demo version here.  (http://www.imagemet.com)

 

MountainsMap SPM Image

This package loads all of the major formats of SPM files. I have recently tried this software, and it has most of the functions required, including an unusual "report" format of data analysis. Commercial software, but a downloadable demo version is available. Recently merged with SPIP into MountainsSPIP 8.
More details here. (https://www.digitalsurf.com/software-solutions/scanning-probe-microscopy/)

 

WSxM

Freely available software that supports many SPM file formats; and has many analysis tools. I personally like a lot the 3D rendering results from WSxM. It was originally developed by an AFM manufacturer for use with their instrument, but is now completely independent and supports very many other file formats. Unlike many third party programs, has support for force curves as well. Frequently updated. Available here. (http://wsxmsolutions.com/)

 

FemtoScan Online

Commercial software from a manufacturer, but loads lots of (about 20) other formats. 30-days trial has no functional limitations. English and Russian user interface. It seems to be quite capable software, if a little cryptic. Available here. (http://www.nanoscopy.net/en/Femtoscan-D.php)

 

PUNIAS (Protein Unfolding and Nanoindenation Analysis Software)

Commercial software, dedicated to analysis of force curves, supports several formats. Implements several of the common analysis techniques used for force spectroscopy, and nanoindentation data. Also supports force volume images. A licence must now be purchased to use it. Available here.  (http://punias.free.fr/)

 

AtomicJ

Freely available, open-source software, with versions for Windows, Mac and Linux. Like PUNIAs, this software concentrates on batch processing of force curves. Opens a small number of common file formats. Seems quite complete, and delivers thoroughly summarised results. Available here, and described in this paper.

 

Carpick Lab’s Software Toolbox

Some Matlab scripts to help with nanotribology research - i.e. friction measurements with the AFM. They are for Nanoscope files only. Available here. (http://nanoprobenetwork.org/software-library/welcome-to-the-carpick-labs-software-toolbox) (last time I checked this page had been "temporarily" taken down)


Image SXM

A version of NIH Image that has been extended to handle the loading, display and analysis of scanning microscope images. Seems to be able to open lots of file formats, but only works on MAC, so I've never tried it. Available here. (http://www.liv.ac.uk/~sdb/ImageSXM/)


ImageJ

Cross-platform image analysis program, not specifically designed for SPM images, but there are plugins to load MI or Nanoscope files here. I don't find it's often very useful, but some people use it, and it does have some useful functions, for e.g. particle counting. Available here. (http://rsb.info.nih.gov/ij/)

 

GXSM

This is a cross-platform (Linux, with a Windows port) open-source package that not only analyses data, but runs hardware, too. I haven't tried it. More details here.

 

 TrueMap and TrueSurf

True Map is an analysis and display program. TrueSurf is a surface roughness analysis program. These are extensions of profiler software packages, now offering some AFM format support. Commercial software, a licence must be bought for extended use. More details here. (http://www.truegage.com)

 

OpenFovea

OpenFovea is a program for analysis of force-volume files, i.e. AFM files containing spatially-resolved force curves. It is a Linux-native program with a Windows verison also available. I have not tried this software. More details here. (http://www.freesbi.ch/en/openfovea)

 

Pycroscopy

New (2016) package that aims to allow analysis of data from a very wide range of different microscopy methods including AFM / SPM. The program is available as a package for the Pythn programming language, meaning it's necesssary to install a verison of Python before you can use it. More details here: (https://pycroscopy.github.io/pycroscopy/about.html)

 

 

Software that's no longer maintained

MIDAS 98

Program for deconvolution of AFM files. No longer updated. Appears to only open nanoscope files. Available here.

n-Surf

Freeware program to open display and manipulate SPM files. It seems to have most of the common functions, but opens Veeco and NT-MDT only, and appears to be still in beta, and last updated in 2005. The website is  available at www.n-surf.com.

 SPM Image Magic

This program seems to be no longer updated, it is designed for Windows95 or NT. Opens just a few SPM image formats, and has relatively few analysis options. At the same place is SPM Image Voyager, which seems to be an image browser utility. AFAIK, no longer available, since the old website at Geocities disappeared.

Note: I welcome comments/suggestions for these lists, please contact me via the "contact" page.

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