I've recently updated the SPM software list, with a couple of new (to me) programs, after many years! The links to the programs can be found on the software page.

A request for help!

I am currently looking for one manual, and one piece of AFM control software:

  • Topometrix Discoverer manual
  • Nanocockpit software disc (CD-ROM?) This is the software to control a Nano-R AFM or similar from Pacific Nanotechology.

If you haveeither of these, please get in touch at This email address is being protected from spambots. You need JavaScript enabled to view it.


This page is intended to act as a repository for manuals for atomic force microscopes. At this time, there is relatively little information here (basically, the manuals I have .pdf copies of), but I hope that over time it will grow. If you have a manual for your instrument that you think could be useful for other AFM users, please send it to me at This email address is being protected from spambots. You need JavaScript enabled to view it..


I hope that this page is useful for AFM users, especially those who inherited older instruments that have become spearated.



  • TT2-AFM manual v2.3 - This .pdf file is the user manual for AFMWorkshop's 2nd gen TT-AFM , i.e. "Table-Top AFM"
  •  LS-AFM Manual v1.1 - This user manual is for AFMWorkshop's "Life Sciences AFM". This covers the AFM instrument, there may be a separate manual for the optical microscope from AFM Workshop if you have a copy of that one, please send it to me
  •  HR-AFM Manual - This .pdf file is the user manual for AFMWorkshop's "High Resolution AFM" instrument. Unlike the TT2 manual, it covers use of the v4.x software
  •  B-AFM Manual v1.0 - This is the user maual for the B-AFM from AFMWorkshop


Asylum Research (now  Oxford Instruments)

  • MFP 3D User Guide V13 - This is the .pdf file of the user guide for the MFP 3D Bio-AFM from Asylum which was since aquired by Oxford Instruments
  • Cypher User Guide -  This is the User guide for the Cypher "small sample AFM", from Asylum



  • NWS User guide - This is the .pdf file of the user g uide for the NWS (NanoWorkshop) softwar euse dby Nanonics
  • MV4000 user guide -  This is the user guide (pdf)  for theNanonics multiview 4000 AFM/SPM system. These systems are very unusual in supporting multiple probes scanning the sample at the same time (up to four I think).



  • Nanoscope Software 6.13 User Guide - This .pdf file is the user manual for the nanoscope software interface for any microscope using a nanoscope controller, i.e. the popular multimode and dimension instruments. This version is compatible with Windows XP latest.
  • Multimode Instruction Manual v4.31 - This is a .pdf version of the instruction manual for the multimode microscope. This is based on a rather old version of the software (in DOS windows). Note that for these DI instruments, the controller and microscope have spearate manuals.


JPK (now a part of Bruker)

  • Nanowizard User Manual - This .pdf file is the user manual for JPK (now Bruker) Nanowizard bio-AFM instruments. THis covers the version 6.0 software. As far as I know this means instruments up to Nanowizard 4. Covers hardware, control software and analysis functions.


 Molecular Imaging/Agilent/Keysight

  • Agilent 5500 User Guide revB - This .pdf is the user guide for the Agilent 5500 microscope, which I think used to be called the PicoPlus before it becasme an Agilent instrument


Other Documents

A Practical Guide to Scanning Probe Microscopy - This is a .pdf file of the SPM practical guide, which I beleive was first made by TopoMetrix, this is the Thermomicroscopes version. This is a very old document, but contains a lot of helpful information for AFM users, still. Not an instrument manual, it's a simple guide to the general principles of how an AFM works. If you read this and want something more in-depth, I reccomend this book!



Frequently Asked Questions about Atomic Force Microscopy

by Peter Eaton

This FAQ was originally created for clients of the AFM, i.e. those whose samples I scan.
However, it's grown a lot, and should also answer many questions of people planning to use the AFM themselves, or researching the technique. Its contents include a description of AFM suitability to various samples, sample preparation, tips for scanning and data processing, and a short bibliography. There is also a guide to recognising artifacts in AFM.

All the material here is discussed in greater detail in the book "Atomic Force Microscopy".


We will be running a two-day AFM course at The Bridge, at the University of Lincoln in June. Details can be found on the page linked below. You can also email me directly with questions.

My name is Peter Eaton, and I have been working with Atomic Force Microscopy for more than 20 years. I am currently an Instrument Scientist at The Bridge, in the University of Lincoln, UK. I am the co-author (with Paul West of AFMWorkshop) of the book Atomic Force Microscopy, published in 2010 by Oxford University Press. I have collaborated with researchers in the UK, France, Spain, Brazil, Argentina, Portugal, the USA and Germany in AFM. I have taught AFM around the globe, and am the coordinator of the well-known Porto AFM Training Workshop (running from 2011 onwards).

In addition to development of research and education in Atomic Force Microscopy, my interests include:

Antimicrobial peptides derived from amphibians

  • Nano particle preparation and characterisation
  • Natural Products
  • Biosensors
  • Antiviral and anticancer peptides
  • Scanning electron microscopy
  • Transmission electron microscopy

A complete list of my research papers can be found along with my academic CV here. I have co-authored more than 90 scientific works.

I am happy to collaborate scientifically in interesting projects or carry out scientific consultancy in the field of atomic force microscopy.