Image SXM handles scanning microscope image files from more than 40 different instruments.

Image SXM was developed by S D Barret ( ) in 1993 based on the image analysis software NIH Image (now ImageJ). There are several open licensed software packages available for SFM. SPIP™ (Scanning Probe Image Processor- ImageMetrology) is a dedicated metrological tool for SFM that supports many formats but requires additional license payment. For example, ‘NanoScope Analysis’ from Bruker and ‘JPKSPM Data processing’ from JPK Instrument software packages open their own generated images, allowing some basic filtering operations like flattening, but also other metrological operations like point to point length measurements, or volume analysis from selected particles. Software analysis is generally provided as part of the microscope operating system software. Usually data analysis requires the use of different, sometimes multiple, software programs none specifically designed for DNA and protein analysis. However there is no single software platform that allows semi-automatic and high-throughput data analysis. Dozens of images with hundreds of molecules each can be routinely produced in one day. DNA and proteins are easily identified by SFM without staining procedures in conditions compatible with biochemical function (no vacuum, room temperature). Functional assemblies of biomolecules are inherently flexible, variable and irregular. Single-molecule imaging is a valuable tool in this sense because it reveals different stages of assembly and function. Quantification of structural features from individual molecular complexes is used to explain their mechanism of action. ConclusionĪssembled in a single user interface, SFMetrics serves as a semi-automatic analysis tool capable of measuring several geometrical properties (length, volume and angles) from DNA and protein complexes, but is also applicable to other samples with irregular shapes. We present SFMetrics as a metrology toolbox for SFM, specifically aimed at biomolecules like DNA and proteins, which features (a) semi-automatic high-throughput analysis of individual molecules (b) ease of use working within MATLAB environment or as a stand-alone application (c) compatibility with MultiMode (Bruker), NanoWizard (JPK instruments), Asylum (Asylum research), ASCII, and TIFF files, that can be adjusted with minor modifications to other formats.

Most existing SFM software tools are aimed at broad general use: from material-surface analysis to visualization of biomolecules. However, high-throughput analysis of SFM data is limited by the lack of versatile software tools accessible to SFM users. Scanning force microscopy (SFM) allows direct, rapid and high-resolution visualization of single molecular complexes irregular shapes and differences in sizes are immediately revealed by the scanning tip in three-dimensional images.

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