title: SFMetrics: an analysis tool for scanning force microscopy images of biomolecules.
abstract: BACKGROUND
  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.
  
  
  CONCLUSIONS
  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.
authors: Department of Genetics, Erasmus University Medical Center, Rotterdam 3000CA, The Netherlands. h.sanchezgonzalez@erasmusmc.nl.
authors: Humberto
authors: H
authors: Sánchez
authors: Claire
authors: C
authors: Wyman
mesh_terms: D000465:Algorithms; D004247:DNA / Q000032:analysis*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D020407:Internet; D018625:Microscopy, Atomic Force; D036103:Nanotechnology; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis*; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins; D004247:DNA
references: J Mol Biol. 1996 Dec 20;264(5):919-32
references: 9000621
references: Methods. 2013 Apr 1;60(2):113-21
references: 23454289
references: Rev Sci Instrum. 2007 Jan;78(1):013705
references: 17503926
references: Nucleic Acids Res. 2005;33(10):3292-302
references: 15944450
references: Chromosome Res. 2009;17(2):277-88
references: 19308707
references: Methods Mol Biol. 2011;783:213-31
references: 21909891
references: Nat Methods. 2012 Jul;9(7):671-5
references: 22930834
references: Opt Express. 2013 Apr 22;21(8):9862-74
references: 23609692
references: J Am Chem Soc. 2001 Jun 20;123(24):5632-5
references: 11403593
references: Ultramicroscopy. 2001 Mar;87(1-2):55-66
references: 11310542
references: Biochem Biophys Res Commun. 1996 Sep 24;226(3):645-9
references: 8831670
references: Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7581-6
references: 12805565
references: Nucleic Acids Res. 2009 Apr;37(5):1580-8
references: 19151086