Features

Gwyddion is a modular multiplatform software for SPM data analysis. The main idea behind Gwyddion developement is to provide modular program for 2D data analysis that could be easily extended by modules and plug-ins. Moreover, the status of free software enables to provide source codes to developers and users, which makes the further program improvement easier.

Data visualization and processing

The current version Gwyddion provides at least the following visualization and processing functions (this list is updated occasionally):

• visualization: false color representation with different types of mapping
• shaded, logarithmical, gradient- and edge-detected, local contrast representation, Canny lines
• OpenGL 3D data display: false color or material representation
• easily editable color maps and OpenGL materials
• basic operations: rotation, flipping, inversion, data arithmetic, crop, resampling
• leveling: plane leveling, profiles leveling, three-point leveling, facet leveling, polynomial background removal, leveling along user-defined lines
• value reading, distance and angle measurement
• profiles: profile extraction, measuring distances in profile graph, profile export
• filtering: mean, median, conservative denoise, Kuwahara, minimum, maximum, checker pattern removal
• general convolution filter with user-defined kernel
• statistical functions: Ra, RMS, projected and surface area, inclination, histograms, 1D and 2D correlation functions, PSDF, 1D and 2D angular distributions, Minkowski functionals, facet orientation analysis
• statistical quantities calculated from area under arbitrary mask
• row/column statistical quantities plots
• ISO roughness parameter evaluation
• grains: threshold marking and unmarking, watershed marking
• grain statistics: overall and distributions of size, height, area, volume, boundary length, bounding dimensions
• intergral transforms: 2D FFT, 2D continuous wavelet transform (CWT), 2D discrete wavelet transform (DWT), wavelet anisotropy detection
• fractal dimension analysis
• data correction: spot remove, outlier marking, scar marking, several line correction methods (median, modus)
• removal of data under arbitrary mask using Laplace or fractal interpolation
• automatic xy plane rotation correction
• arbitrary polynomial deformation on xy plane
• 1D and 2D FFT filtering
• fast scan axis drift correction
• mask editting: adding, removing or intersecting with rectangles and ellipses, inversion, extraction, expansion, shrinking
• simple graph function fitting, critical dimension determination
• force-distance curve fitting
• axes scale callibration
• merging and immersion of images
• tip modelling, blind estimation, dilation and erosion

Features

Thanks to the Free Software/Open Source nature of Gwyddion, all formulas, methods and algorithms are public and open. Anyone wishing to study or compare the fine calculation details that are beyond the scope of the user guide can read the actual implementation.

All calculations are performed in double precision, and Gwyddion native data format (.gwy) stores data in double precision too. Under normal circumstances, no information is ever lost due to the limited precision or range of values.

Gwyddion uses a fairly general physical unit system, there are no built-in limitations on the types of physical quantities data (and lateral dimensions) can represent. Units of slopes, areas, volumes, and other derived quantities are correctly calculated. SI unit system is used whenever possible.

Tools and other dialogs remeber their parameters, not only between tool invocations within one session, but also across sessions. Gwyddion native file format (.gwy) supports saving all data specific settings: false color palette, masks, presentations, selections, associated 3D view parameters, graphs associated with that data and their settings, etc.

Most Gwyddion library functions are available in the Python interface pygwy. Gwyddion can be extended by file and processing modules written in Python.

Gwyddion is well integrated to free desktop environments such as GNOME, XFce or KDE, including e.g. menus, file type associations and automated SPM file thumbnailing. Certain integration to non-free environments also exists, although not to such level.

Data formats supported

We would like to support as many AFM, STM, …, profilometer and general height-field formats as possible, of course. If you want your own format to be supported, please read the file format situation description.

File Format	Extensions	Supported By	Read	Write
APE Research	.dat	apefile module	Yes	No
ASCII data (raw)		rawfile, asciiexport modules	Yes	Yes(1)
Assing AFM	.afm	assing-afm module	Yes	Yes
Image Metrology BCR, BCRF	.bcr, .bcrf	bcrfile module	Yes	No
Binary data (raw)		rawfile module	Yes	No
Burleigh v2.1	.img	burleigh module	Yes	No
Burleigh BII	.bii	burleigh_bii module	Yes	No
Burleigh export	.txt, .bin	burleigh_exp module	Yes	No
Createc	.dat	createc module	Yes	No
DME Rasterscope	.img	dmefile module	Yes	No
ECS	.img	ecsfile module	Yes	No
Gwyddion native	.gwy	gwyfile module	Yes	Yes
PSI HDF4	.hdf	hdf4file module	Yes	No
Hitachi AFM	.afm	hitachi-afm module	Yes	No
Intematix SDF	.sdf	intematix module	Yes	No
JEOL SPM	.tif	jeol module	Yes	No
JPK Instruments	.jpk	jpkscan module	Yes	No
ADE Phase Shift MapVue	.map	mapvue module	Yes	No
Zygo binary MetroPro	.dat	metropro module	Yes	No
MicroProf FRT	.txt	microprof module	Yes	No
Micromap	.sdfa	sdfile module	Yes	No
Molecular Imaging MI	.mi	mifile module	Yes	No
Molecular Imaging STP	.stp	stpfile module	Yes	No
Nanonis	.sxm	nanonis module	Yes	No
Nanoscope		nanoscope, nanoscope-ii modules(2)	Yes	No
Nanosurf	.ezd, .nid	ezdfile module	Yes	No
Nanotop	.spm	nanotop module	Yes	No
GXSM netCDF	.nc	netcdf module	Yes	No
NT-MDT	.mdt	nt-mdt module	Yes	No
Olympus LEXT OLS3000	.ols	ols module	Yes	No
Omicron Scala	.par + data	omicron module	Yes	No
Omicron MATRIX	.mtrx + data	omicronmatrix module	Yes	No
Wyko Vision OPD and ASC	.opd, .asc	opdfile module	Yes	No
Pacific Nanotechnology PNI	.pni	pnifile module	Yes	No
Pixmap images	.png, .jpeg, .ppm, .tga(3)	pixmap module	Yes	Yes(4)
PSIA	.tiff	psia module	Yes	No
Quesant	.afm	quesant module	Yes	No
RHK Technology SM2	.sm2	rhk-spm32 module	Yes	No
RHK Technology SM3	.sm3	rhk-sm3 module	Yes	No
Seiko	.xqd	seiko module	Yes	No
Sensofar	.plu	sensofar module	Yes	No
Sensolytics	.dat	sensolytics module	Yes	No
Scanning Probe Microscopy Markup Language	.xml	spml module	Yes	No
Shimadzu		shimadzu module	Yes	No
IonScope SICM	.img	sicmfile module	Yes	No
SPIP ASCII export	.asc	spipasc module	Yes	No
Surfstand Surface Data File	.sdf	sdfile module	Yes	Yes
CSM Surf	.sur	surffile module	Yes	No
Surface Imaging Systems	.sis	sis module	Yes	No
STMPRG		stmprg module	Yes	No
Unisoku	.hdr + .dat	unisoku module	Yes	No
Veeco Instruments	.zfr, .trf, .zfp, …	spmlab module	Yes	No
Veeco Instruments FLT	.flt	spmlabf module	Yes	No
WITec	.wit	witfile module	Yes	No
WSxM (Nanotec)	.tom, .stp	wsxmfile module	Yes	No

(1) Only a simple data-matrix format si currently supported.

(2) Nanoscope II and Nanoscope III (and newer) are two distinct file formats, nanoscope loads the newer files while nanoscope-ii loads the old version II files.

(3) And others, namely for import. The exact list depends on formats supported by libraries on particular platforms.

(4) Though this is usually lossy. Export to pixmap graphics is intended for presentational purpose mainly.

Modularity

The data processing abilities depend on loaded modules abilities. There are already quite a few modules present in the package. However it is possible to add more data processing capabilities to your Gwyddion installation simply by installing new data processing modules, even from third parties.

In a similar way, you can write your own modules, test them on your Gwyddion installation and then send them to other Gwyddion users.

The same statements are valid also for plug-ins that represent other way how to improve Gwyddion. Writing plug-ins can be little bit easier (you can use any programming language, for example). However, you can not use existing Gwyddion data processing functions and widgets when writing plug-ins.

There is documentation on module and plug-in writing available as a part of libgwymodule documentation, sample plug-ins in C/C++, Perl, Python, Ruby, and Pascal are distributed directly with Gwyddion source code, and there is also a sample standalone module available.

An on-line version of module browser is available, in two forms: dynamic, with description pop-ups (needs a modern WWW browser) and a plain expanded table.

If you have any problems or questions concerning module or plug-in developement, do not hesitate to ask us.