Gwyddion – Free SPM (AFM, SNOM/NSOM, STM, MFM, …) data analysis software


The following list contains publications that describe Gwyddion, its architecture, individual components, algorithms, and other parts of the ‘Gwyddion ecosystem’ or are related to the software in some other fundamental manner.

The goal is not to gather here all papers mentioning that Gwyddion was used for data analysis. Such papers, while gratifying and encouraging futher development of the software, are quite a few and you can get them Scopus, Web of Science or a similar database if you are interested. A list of publications where Gwyddion was utilised may be added in future if we figure out how to manage such thing reasonably.

Generally, the list contains publications by Gwyddion contributors about things inherently gwyddionic. But third party publications are not excluded. For instance papers describing a data analysis system built on top of Gwyddion libraries or third-party extension modules can be good candidates for inclusion. If you think your publication should be mentioned here please do not hesitate to contact us.

Books and book chapters

Quantitative Data Processing in Scanning Probe Microscopy, 2nd edition

Petr Klapetek et al.

Elsevier 2018, ISBN: 978-0-12-813347-7

Publisher's store link: Quantitative Data Processing in Scanning Probe Microscopy, 2nd edition

Table of contents:
1. Motivation
2. Instrumentation Principles
3. Data Models
4. Basic Data Processing
5. Dimensional Measurements
6. Force and Mechanical Properties
7. Friction and Lateral Forces
8. Electrostatic Fields
9. Magnetic Fields
10. Local Current Measurements
11. Thermal Measurements
12. Optical Measurements
13. Sample Data Files
14. Numerical Modeling Techniques

The book is accompanied with freely available sample data.

Quantitative Data Processing in Scanning Probe Microscopy

Petr Klapetek et al.

William Andrew 2012, ISBN: 978-1-4557-3058-2

Publisher's store link: Quantitative Data Processing in Scanning Probe Microscopy

Table of contents:
1. Motivation
2. Instrumentation Principles
3. Data Models
4. Basic Data Processing
5. Dimensional Measurements
6. Force and Mechanical Properties
7. Friction and Lateral Forces

Papers in scientific journals

Gwyddion: an open-source software for SPM data analysis

David Nečas and Petr Klapetek

Central European Journal of Physics 10 (2012) 181–188

DOI: 10.2478/s11534-011-0096-2

Abstract: In this article, we review special features of Gwyddion—a modular, multiplatform, open-source software for scanning probe microscopy data processing, which is available at We describe its architecture with emphasis on modularity and easy integration of the provided algorithms into other software. Special functionalities, such as data processing from non-rectangular areas, grain and particle analysis, and metrology support are discussed as well. It is shown that on the basis of open-source software development, a fully functional software package can be created that covers the needs of a large part of the scanning probe microscopy user community.

Determination of tip transfer function for quantitative MFM using frequency domain filtering and least squares method

David Nečas, Petr Klapetek, Volker Neu, Marek Havlíček, Robert Puttock, Olga Kazakova, Xiukun Hu and Lenka Zajíčková

Scientific Reports 9 (2019) 3880

DOI: 10.1038/s41598-019-40477-x

Abstract: Magnetic force microscopy has unsurpassed capabilities in analysis of nanoscale and microscale magnetic samples and devices. Similar to other Scanning Probe Microscopy techniques, quantitative analysis remains a challenge. Despite large theoretical and practical progress in this area, present methods are seldom used due to their complexity and lack of systematic understanding of related uncertainties and recommended best practice. Use of the Tip Transfer Function (TTF) is a key concept in making Magnetic Force Microscopy measurements quantitative. We present a numerical study of several aspects of TTF reconstruction using multilayer samples with perpendicular magnetisation. We address the choice of numerical approach, impact of non-periodicity and windowing, suitable conventions for data normalisation and units, criteria for choice of regularisation parameter and experimental effects observed in real measurements. We present a simple regularisation parameter selection method based on TTF width and verify this approach via numerical experiments. Examples of TTF estimation are shown on both 2D and 3D experimental datasets. We give recommendations on best practices for robust TTF estimation, including the choice of windowing function, measurement strategy and dealing with experimental error sources. A method for synthetic MFM data generation, suitable for large scale numerical experiments is also presented.

Gwyscan: a library to support non-equidistant Scanning Probe Microscope measurements

Petr Klapetek, Andrew Yacoot, Petr Grolich, Miroslav Valtr and David Nečas

Measurement Science and Technology 28 (2017) 034015

DOI: 10.1088/1361-6501/28/3/034015

Abstract: We present a software library and related methodology for enabling easy integration of adaptive step (non-equidistant) scanning techniques into metrological scanning probe microscopes or scanning probe microscopes where individual x, y position data are recorded during measurements. Scanning with adaptive steps can reduce the amount of data collected in SPM measurements thereby leading to faster data acquisition, a smaller amount of data collection required for a specific analytical task and less sensitivity to mechanical and thermal drift. Implementation of adaptive scanning routines into a custom built microscope is not normally an easy task: regular data are much easier to handle for previewing (e.g. levelling) and storage. We present an environment to make implementation of adaptive scanning easier for an instrument developer, specifically taking into account data acquisition approaches that are used in high accuracy microscopes as those developed by National Metrology Institutes. This includes a library with algorithms written in C and LabVIEW for handling data storage, regular mesh preview generation and planning the scan path on basis of different assumptions. A set of modules for Gwyddion open source software for handling these data and for their further analysis is presented. Using this combination of data acquisition and processing tools one can implement adaptive scanning in a relatively easy way into an instrument that was previously measuring on a regular grid. The performance of the presented approach is shown and general non-equidistant data processing steps are discussed.

Study of user influence in routine SPM data processing

David Nečas and Petr Klapetek

Measurement Science and Technology 27 (2017) 034014

DOI: 10.1088/1361-6501/28/3/034014

Abstract: The quantitative results obtained using scanning probe microscopy (SPM) are influenced not only by instrumentation factors, but also humans—the SPM users that perform the data processing and the evaluation of statistics, dimensions and other parameters from the images. We investigate this user influence empirically by performing several experiments in which real humans process SPM data in different settings using the same software, and statistically characterise the results. Two types of experiments are conducted: one in a well-defined laboratory setting where prescribed procedures requiring user input are applied by experienced users to large ensembles of similar data; the other in an open setting in which a large group of SPM users evaluate the same images to obtain specified parameters but without external guidance. The open study in particular brings about results that should be alarming for the SPM community and SPM metrology in particular. We also attempt to derive some guidance for the design of SPM data processing software functions from the results and classify the amount of user input in the data processing functions.

Independent analysis of mechanical data from atomic force microscopy

Petr Klapetek and David Nečas

Measurement Science and Technology 25 (2014) 044009

DOI: 10.1088/0957-0233/25/4/044009

Abstract: Present atomic force microscopes are capable of acquiring large data volumes by point using point force-distance spectroscopic measurements. Even if different trade names and different technical implementations are used, for most of these techniques a force-distance curve in every image pixel is measured, this curve is immediately fitted by some theoretical dependency and results are displayed as a mechanical properties channel (Young modulus, adhesion, etc.). Results are processed during the measurement directly in the SPM controller or, after it, by manufacturer provided software. In this article we present a software tool for independent numerical processing of such data, including more numerical models for force distance curves evaluation and including a simple estimate of uncertainties related with fitting procedure. This can improve the reliability and the analytical possibilities of mechanical properties mapping methods in atomic force microscopy.

One-dimensional autocorrelation and power spectrum density functions of irregular regions

David Nečas and Petr Klapetek

Ultramicroscopy 124 (2013) 13-19

DOI: 10.1016/j.ultramic.2012.08.002

Abstract: Scanning probe microscopy (SPM) can be effectively used for evaluation of nanoscale roughness of surfaces obtained by different technological processes. Spectral properties of surface roughness can be evaluated using algorithms based on Fast Fourier Transform (FFT). For data that are not rectangular, this approach, however fails. In this article we describe a modification of SPM data evaluation algorithms enabling to use FFT based approach even for irregular and non-continuous data. This opens novel possibilities in analysis of local surface roughness in many fields, e.g. on nanoparticles, semiconductor structures or any other nanostructured samples prepared using nanotechnology methods. Together with theoretical description of proposed method we present benchmarks for its performance and typical results of its application on different samples.

Methods for determining and processing 3D errors and uncertainties for AFM data analysis

Petr Klapetek, David Nečas, Anna Campbellová, Andrew Yacoot and Ludger Koenders

Measurement Science and Technology 22 (2011) 025501

DOI: 10.1088/0957-0233/22/2/025501

Abstract: This paper describes the processing of three-dimensional (3D) scanning probe microscopy (SPM) data. It is shown that 3D volumetric calibration error and uncertainty data can be acquired for both metrological atomic force microscope systems and commercial SPMs. These data can be used within nearly all the standard SPM data processing algorithms to determine local values of uncertainty of the scanning system. If the error function of the scanning system is determined for the whole measurement volume of an SPM, it can be converted to yield local dimensional uncertainty values that can in turn be used for evaluation of uncertainties related to the acquired data and for further data processing applications (e.g. area, ACF, roughness) within direct or statistical measurements. These have been implemented in the software package Gwyddion.

1.24 (yeti, 2019-05-07 08:45:39)
© David Nečas and Petr Klapetek

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