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. However, high-throughput analysis of SFM data is limited by the lack of versatile software tools accessible to SFM users. Most existing SFM software tools are aimed at broad general use: from material-surface analysis to visualization of biomolecules. Results: 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. Conclusion: Assembled 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. &Copy; Malm et al.; licensee BioMed Central.

dx.doi.org/10.1186/s12859-015-0457-8, hdl.handle.net/1765/84575
B M C Bioinformatics
This work was funded by the European Commission 7th Framework Programme; grant id fp7/276898 - Recombinational DNA repair analyzed by simultaneous scanning force and single molecule fluorescence microscopy: role of RAD54 in presynaptic and postsynaptic events (DNAREPAIR AT 3DETAIL)
Department of Radiation Oncology

Sanchez, H, & Wyman, C. (2015). SFMetrics: An analysis tool for scanning force microscopy images of biomolecules. B M C Bioinformatics, 16(1). doi:10.1186/s12859-015-0457-8