A MATLAB-based software for extracting cytoskeletal filaments from single-molecule superresolution dataset


Super-resolution microscopy and contemporary scientific imaging generates huge amount of data.  The quantitative analysis of these datasets has been an ongoing challenge and major bottlenecks.  Check out our computational tools at our github:

  • ImaEdge for the segmentation and quantification of time-lapse movies of cell cortex.  See MATLAB-code on github. 

  • SFEX  MATLAB-based software for extracting actin stress fibers from fluorescence microscopy images. 

  • ZMAP  IDL-based software for the simulation and analysis of super-resolution microscopy by surface-generated structured illumination (VIAFLIC, SAIM), used for our previous studies (Liu et al., PNAS 2015; Bertocchi et al., Nature Cell Biology 2017).

  • SIFNE 1.0 A MATLAB-based software for extracting microtubules filaments from single-molecule-based superresolution microscopy datasets.  

  • Morphometry IDL-based software for automated and curated segmentation of cell area, and focal adhesion morphometrics. (Xia et al., ACS Biomaterials Sci. & Eng. 2019, Rafiq et al., Nature Materials 2019)

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