Deconvolution - Erosion

         Windows logo The MIDAS program for Windows by Markiewicz et al.

         Mac logo A recent paper by Torzo and Cerolini ("SFM Image Reconstruction Reducing Tip Artifacts", Amer. Microscopy and Analysis, May 2000, pg 23-24) suggests ImageSXM might soon have this feature.

         Java logo NIH Image is available in Java, so maybe ImageSXM could soon be JavaSXM?

Blind Reconstruction

         Windows logo The work of J.S. Villarrubia at N.I.S.T.
Enter the directory "pub/spm_morph" and use an "anonymous" login.

Erosion and Blind Reconstruction

         Windows logo Anton Efimov's "Deconvo" at Silicon MDT


Windows logo Complete AFM Software from Nanotec

WSxM (Windows Scanning X (Force, Tunneling, Near Optical, ...) Microscope) is a powerful and user-friendly Windows application for Data Acquisition and Processing in Scanning Probe Microscopy (SPM).

The goal of this FREE program is to provide a flexible tool that opens the doors to the nanoscience world to the scientific and technical community. The WSxM program allows them to easily operate these instruments providing new insights on the capabilities of this new microscopy technique.

The WSxM program is divided into two well defined parts. The first one is devoted to image rendering and data processing. Among other capabilities, the program allows the user to perform very general processes such as 3D rendering, pseudocolor image representation, Fourier and roughness analysis, data smoothing, cross section profiles... . In addition to that, more sophisticated operations including current vs voltage (I-V) curves normalization, Current Image Tunneling Specstroscopy (CITS) analysis, grain detection, ... . The program supports many of the most common data files used in SPM, including DI and Park Instruments.

The second part uses a Digital Signal Processor (DSP) to control the microscope, providing flexible and powerful operation in Real Time. The new windows user interface has been designed to take adventage of all the features commonly available in this operating system: windows, toolbars, menus, dialog boxes... . The WSxM program allows the user to easily interact with the SxM microscopes taking adventage of all their features.

The main features of the WSxM program are:

Data Process
  • Unlimited number of simultaneous processing images in your screen.
  • Friendly and powerful user interface.
  • Flexible and easy to use browser for all kind of data (Images, Movies, CITS, FZ, IZ,IV...).
  • All of the most common image processing filters: zoom, plane substraction, smooth, matrix convolution...
  • Sophisticated data analysis, including dI/dV normalization, hole detection, line removal, non-linear correction...
  • 2D profiles and 2D multiple image profiles.
  • Multiple dynamic zoom.
  • Tip convolution.
  • Surface and perimeter histograms with fractal analysis.
  • Roughness analysis.
  • FFT analysis, including window filtering.
  • Compatible with most of the SPM commercial file formats: Digital Instruments, Topometrix, Park Instruments, Omicron...
  • Powerful and intuitive 3d rendering based on OpenGL.

Windows logo Imagemet - Scanning Probe Image Proccesor(SPIP)

Formerly put out by the Danish Institute of Metrology, now commercially available through Imagemet.

The manufacturer states on their Web page:

  • Automatic and accurate unit cell measurements based on Fourier analysis.
  • Advanced Fourier analysis and filtering.
  • Automatic calculation of calibration data for x,y,z and lateral orthogonality.
  • Correction of images based on calibration data.
  • Correlation averaging for extraction of repeated features in images with low SNR. This is useful for analysis of, e.g., inner molecular structures.
  • Automatic calculation of hysteresis curves and subsequent image correction.
  • Evaluation and correction of lateral non linearities at sub pixel level. This tool is valuable even for systems having feed back loops on the lateral scanning elements. A correction facility is now also available on the Windows 95 version.
  • Full automated step height measurement and Z-calibration.
  • Roughness measurements of 20 roughness parameters.
  • Slope correction with choice of method and polynomial degree, linewise leveling based on histogram or mean value.
  • Measurement of coherent noise frequencies in Hz.
  • Grain Analysis, Detects and quantifies grains and particles. Invert the image and use it for pit and pore analysis as well.
  • Visualization in 2D,3D or 3D with light emulation, with easy color manipulation.
  • Context sensitive help in all menus (MS Windows Only). Tutorial files and instrutctions included.
  • It automatically recognizes and reads several image file format like NanoScope II and III, TopoMetrix, Park, RasterScope, RHK, Quesant, IBM, Omicron, Burleigh, Wyko, Zygo, BCR-SDF, Bitmap, Tiff and can be instructed to read most other topographic file formats.

Mac logo ImageSXM (U.K. site), (U.S. site) (Macintosh software)

This is a full version of NIH Image (see below) with a special patch written by Steve Barrett for microscopists. Miiror sites at Liverpool, U.K. (Univ. of Liverpool) and Pasadena, CA, U.S.A. (Caltech).

This is the version of interest to probe microscopists. See the NIH Image description below for details on the standard features of Image, and note that the ImageSXM version does much more:

  • Image SXM is a version of the public domain image analysis software NIH Image that has been extended to handle the loading, display and analysis of scanning microscope images. Image SXM supports SEM, SPM and SAM images from several systems.

Mac logo National Institutes of Health Image (Web site) (Macintosh software)

Here is general description of Image's features. It is NOT necessary to download this if one wishes to use ImageSXM, the version designed for Probe Microscopy (see above).

The manufacturer states on their Web page:

  • NIH Image is a public domain image processing and analysis program for the Macintosh. It was developed at the Research Services Branch (RSB) of the National Institute of Mental Health (NIMH), part of the National Institutes of Health (NIH).
  • A free PC version of Image, called Scion Image for Windows, is available from Scion Corporation. There is also Image/J, a Java program inspired by Image that "runs anywhere".
  • Image can acquire, display, edit, enhance, analyze and animate images. It reads and writes TIFF, PICT, PICS and MacPaint files, providing compatibility with many other applications, including programs for scanning, processing, editing, publishing and analyzing images. It supports many standard image processing functions, including contrast enhancement, density profiling, smoothing, sharpening, edge detection, median filtering, and spatial convolution with user defined kernels.
  • Image can be used to measure area, mean, centroid, perimeter, etc. of user defined regions of interest. It also performs automated particle analysis and provides tools for measuring path lengths and angles. Spatial calibration is supported to provide real world area and length measurements. Density calibration can be done against radiation or optical density standards using user specified units. Results can be printed, exported to text files, or copied to the Clipboard.
  • A tool palette supports editing of color and gray scale images, including the ability to draw lines, rectangles and text. It can flip, rotate, invert and scale selections. It supports multiple windows and 8 levels of magnification. All editing, filtering, and measurement functions operate at any level of magnification and are undoable.
  • Image directly supports Data Translation and Scion frame grabber cards for capturing images or movie sequences using a TV camera. Acquired images can be shading corrected and frame averaged. Other frame grabbers are supported via plug-in modules.
  • Image can be customized in three ways: via a built-in Pascal-like macro language, via externally compiled plug-in modules and on the Pascal source code level. Example macros, plug-ins and complete source code can be downloaded from the Download page.
  • More information about NIH Image can be found in the Overview section of the manual.
  • Image requires a color capable Macintosh and at least 4MB of free RAM. 32MB or more of RAM is recommended for working with 3D images, 24-bit color or animation sequences. System 7.0 or later is required. Image directly supports, or is compatible with, large monitors, flatbed scanners, film recorders, graphics tablets, PostScript laser printers, photo typesetters and color printers.

Windows logo ImagePC (PC software)

ImagePC is a PC port for NIH Image package from ScionCorp.

Manufacturers claims (from their Web site):

  • Windows 95/98/NT port of Scion Image for MacOS
  • Extensive support of all Scion frame grabbers
  • Display of 24 bit color images
  • Control of on-chip integrating cameras
  • Extensive image analysis capabilities
  • Image enhancement and annotation support
  • Full macro language for task automation
  • Scion Image for Windows is the Windows version of Scion Image, which is in turn a version of the popular Macintosh program, NIH Image, written at the National Institutes of Health. Scion Image may be used to capture, display,analyze, enhance, measure, annotate, and output images.
  • Scion Image extensively supports all Scion frame grabber boards, and provides a powerful and complete imageacquisition environment.
  • Scion Image for Windows supports color and grayscale image capture with Scion frame grabbers. It includes advancedcapturing capabilities such as frame averaging and summation, frame sequence capture, and on-chip integrationsupport. All current features of NIH Image have been included.
  • Scion Image is available free of charge. Scion provides full technical support to users of Scion Image. Please note thatScion Image for Windows is currently in beta release and cannot be considered bug free. Scion Image for Windows is available in Windows 95, Windows 98 and Windows NT versions.
  • Scion Image requires a PC compatible computer with a Pentium processor. The Windows 95, Windows 98 or Windows NT operating system isrequired. MicroSoft DirectX operating system extensions must be installed. At least 32 Mb of RAM in the computer isrecommended. Scion Image works best with a display system that supports thousands or millions of colors.

Windows logo SPM Image Magic (PC software)

SPM Image Magic is a image processing and analysis application written for Microsoft Windows95 and Windows NT. The original aim of the author is for SPM Image Magic to be an intuitive and self-explanatory tool, for work with STM and AFM image data.

The advice to the user is hence to open the program as soon as possible, import the most typical image she wants to manipulate and start playing with it. Don't be shy, dissect it in particles, measure and count them and evaluate their properties. You will discover that with SPM Image Magic you can do more than you could even dream. :)

Overview of SPM Image Magic:

    General functions:
  • Line Profile Analysis.
  • Contrast modification by selected area of image.
  • Flatten image (line by line and substraction of a mean plane or parabola from image).
  • Copy image to clipboard.
  • Import DI file.
  • Import image in any binary format from SPM file .

    Analysis functions:

  • Automatically counting and measuring particles.
  • Calculation autocorrelation function for image.

Other sources for various AFM software

         Height Calibration program from Silicon-MDT
         Scanner Calibration software from Silicon-MDT
         Advanced Surface Microscopy's scanner calibration software
         DualScope and Rasterscope from Danish Micro Engineering
         SFM analysis tools for IGOR Pro
         Force curve analysis by Prof. Dr. Harald Fuchs at Westfälische Wilhelms-Universität
         SPMCON95 Force Curve Analysis at Prof. Ward's Web site (Minnesota)
         Pacific Scanning Corp. links to other software

Also see the Web pages of SPM systems manufacturers

         Asylum Research
         Digital Instruments
         Molecular Imaging
         Pacific Scanning Corporation
         RHK Technology, Inc.
         Surface Imaging Systems
         ThermoMicroscope (formerly Park Scientific Instruments and TopoMetrix Corporation)

To Main Page Hand

How the AFM works | Con/deconvolution | Blind Reconstruction | Available Tip Characterizers | What These Look Like
Spot the Artifacts | Deconvolution Examples | Helicity | Available Software | MIDAS98 | MIDAS Instructions | File formats | Related links

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   Last revised on 02-06-2001 by Peter Markiewicz