Super-Resolution 3D Reconstruction of Thick Biological Samples: A Computer Vision Perspective

In this paper we present a case-study about recent breakthroughs of three-dimensional (3D) super-resolution live-cell imaging through thick specimens (50 - 150um). This technology is enabling the deep understanding of cellular mechanism by obtaining very detailed 3D descriptions of cells. In particular, we discuss the image analysis problems related to the accurate localization of single molecules. This problem is hard because of the extreme noise conditions, the high and heterogeneous density of the cell molecules and the distortions induced by light-sample interactions on the imaging capabilities. For this reason, robust computational tools are required to obtain the localization of the photo-activated molecules and to enable the super-resolution accuracy. In such context, we show that a novel set of challenges exists and novel Computer Vision approaches are needed for delivering high-performing imaging systems for life science.

[1]  Michael W. Davidson,et al.  Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes , 2007, Proceedings of the National Academy of Sciences.

[2]  W. Webb,et al.  Precise nanometer localization analysis for individual fluorescent probes. , 2002, Biophysical journal.

[3]  Dylan T Burnette,et al.  Bayesian localisation microscopy reveals nanoscale podosome dynamics , 2011, Nature Methods.

[4]  Zeno Lavagnino,et al.  Two-photon excitation selective plane illumination microscopy (2PE-SPIM) of highly scattering samples: characterization and application. , 2013, Optics express.

[5]  Michael D. Mason,et al.  Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. , 2006, Biophysical journal.

[6]  Mark Bates,et al.  Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes , 2007, Science.

[7]  X. Zhuang,et al.  Statistical deconvolution for superresolution fluorescence microscopy. , 2012, Biophysical journal.

[8]  Christian Eggeling,et al.  Fluorescence Nanoscopy in Whole Cells by Asynchronous Localization of Photoswitching Emitters , 2007, Biophysical journal.

[9]  A. Diaspro,et al.  Live-cell 3D super-resolution imaging in thick biological samples , 2011, Nature Methods.

[10]  S. Hess,et al.  Three-dimensional sub–100 nm resolution fluorescence microscopy of thick samples , 2008, Nature Methods.

[11]  Travis J Gould,et al.  Nanoscale imaging of molecular positions and anisotropies , 2008, Nature Methods.

[12]  J. Lippincott-Schwartz,et al.  High-density mapping of single-molecule trajectories with photoactivated localization microscopy , 2008, Nature Methods.

[13]  Mike Heilemann,et al.  Three-Dimensional, Tomographic Super-Resolution Fluorescence Imaging of Serially Sectioned Thick Samples , 2012, PloS one.

[14]  Stanley R. Sternberg,et al.  Biomedical Image Processing , 1983, Computer.

[15]  X. Zhuang,et al.  Whole cell 3D STORM reveals interactions between cellular structures with nanometer-scale resolution , 2008, Nature Methods.

[16]  S. Hell,et al.  Nanoscale separation of molecular species based on their rotational mobility. , 2008, Optics express.

[17]  Lei Zhu,et al.  Faster STORM using compressed sensing , 2012, Nature Methods.

[18]  J. Lippincott-Schwartz,et al.  Imaging Intracellular Fluorescent Proteins at Nanometer Resolution , 2006, Science.

[19]  Andrew G. York,et al.  Confined Activation and Subdiffractive Localization Enables Whole-Cell PALM with Genetically Expressed Probes , 2011, Nature Methods.

[20]  H. Flyvbjerg,et al.  Optimized localization-analysis for single-molecule tracking and super-resolution microscopy , 2010, Nature Methods.

[21]  Michael J Rust,et al.  Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) , 2006, Nature Methods.