Visualizing Escherichia coli Sub-Cellular Structure Using Sparse Deconvolution Spatial Light Interference Tomography
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{"title"=>"Visualizing Escherichia coli sub-cellular structure using sparse deconvolution spatial light interference tomography", "type"=>"journal", "authors"=>[{"first_name"=>"Mustafa", "last_name"=>"Mir", "scopus_author_id"=>"24724877400"}, {"first_name"=>"S. Derin", "last_name"=>"Babacan", "scopus_author_id"=>"18041993800"}, {"first_name"=>"Michael", "last_name"=>"Bednarz", "scopus_author_id"=>"53981165400"}, {"first_name"=>"Minh N.", "last_name"=>"Do", "scopus_author_id"=>"34869347800"}, {"first_name"=>"Ido", "last_name"=>"Golding", "scopus_author_id"=>"6701314358"}, {"first_name"=>"Gabriel", "last_name"=>"Popescu", "scopus_author_id"=>"7103015520"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"365122131", "doi"=>"10.1371/journal.pone.0039816", "sgr"=>"84863001314", "scopus"=>"2-s2.0-84863001314", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"22761910"}, "id"=>"ed888364-861c-366c-bf4c-ea3e95baf6fb", "abstract"=>"Studying the 3D sub-cellular structure of living cells is essential to our understanding of biological function. However, tomographic imaging of live cells is challenging mainly because they are transparent, i.e., weakly scattering structures. Therefore, this type of imaging has been implemented largely using fluorescence techniques. While confocal fluorescence imaging is a common approach to achieve sectioning, it requires fluorescence probes that are often harmful to the living specimen. On the other hand, by using the intrinsic contrast of the structures it is possible to study living cells in a non-invasive manner. One method that provides high-resolution quantitative information about nanoscale structures is a broadband interferometric technique known as Spatial Light Interference Microscopy (SLIM). In addition to rendering quantitative phase information, when combined with a high numerical aperture objective, SLIM also provides excellent depth sectioning capabilities. However, like in all linear optical systems, SLIM's resolution is limited by diffraction. Here we present a novel 3D field deconvolution algorithm that exploits the sparsity of phase images and renders images with resolution beyond the diffraction limit. We employ this label-free method, called deconvolution Spatial Light Interference Tomography (dSLIT), to visualize coiled sub-cellular structures in E. coli cells which are most likely the cytoskeletal MreB protein and the division site regulating MinCDE proteins. Previously these structures have only been observed using specialized strains and plasmids and fluorescence techniques. Our results indicate that dSLIT can be employed to study such structures in a practical and non-invasive manner.", "link"=>"http://www.mendeley.com/research/visualizing-escherichia-coli-subcellular-structure-using-sparse-deconvolution-spatial-light-interfer", "reader_count"=>56, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>5, "Student > Doctoral Student"=>5, "Researcher"=>20, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>2, "Student > Master"=>7, "Other"=>4, "Student > Bachelor"=>1, "Professor"=>2, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>5, "Student > Doctoral Student"=>5, "Researcher"=>20, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>2, "Student > Master"=>7, "Other"=>4, "Student > Bachelor"=>1, "Professor"=>2, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>13, "Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>4, "Materials Science"=>1, "Agricultural and Biological Sciences"=>17, "Medicine and Dentistry"=>2, "Physics and Astronomy"=>15, "Chemistry"=>1, "Energy"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>13}, "Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Energy"=>{"Energy"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>15}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>17}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"South Korea"=>1, "United States"=>2, "Poland"=>1, "United Kingdom"=>1, "France"=>2, "Switzerland"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/617991"], "description"=>"<p>A) SLIM and dSLIT images at a variety of z-positions, with clearly visible coiled structures. B) Scattering maps corresponding to the images shown in A. The increase in resolution is clearly visible from the extra information at higher angles in the dSLIT maps.</p>", "links"=>[], "tags"=>["deconvolved"], "article_id"=>288481, "categories"=>["Physics", "Biotechnology", "Microbiology"], "users"=>["Mustafa Mir", "S. Derin Babacan", "Michael Bednarz", "Minh N. Do", "Ido Golding", "Gabriel Popescu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039816.g004", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_raw_and_deconvolved_data_from_two_cells_/288481", "title"=>"Comparison of raw and deconvolved data from two cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 03:20:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/617926"], "description"=>"<p>A) Comparison of raw and deconvolved. PSF in the x-y plane; the deconvolution process reduces the FWHM from 397 nm to 153 nm. B) Comparison of raw and deconvolved PSF in the x–z plane; the deconvolution process reduces the FWHM from 1218 nm to 357 nm. The dashed lines show the data and the circular markers indicate the Gaussian fit used to determine the FWHM.</p>", "links"=>[], "tags"=>["dimensional"], "article_id"=>288419, "categories"=>["Physics", "Biotechnology", "Microbiology"], "users"=>["Mustafa Mir", "S. Derin Babacan", "Michael Bednarz", "Minh N. Do", "Ido Golding", "Gabriel Popescu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039816.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Three_dimensional_point_spread_function_/288419", "title"=>"Three dimensional point spread function.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 03:20:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/617878"], "description"=>"<p>Images show the original phase image, and the output images obtained by applying first order directional derivatives in the x, y, and z directions, as labeled, scale bar is 1 µm. The plot shows the corresponding log-histograms, the increase in sparsity is clearly visible.</p>", "links"=>[], "tags"=>["microbiology", "biotechnology", "physics"], "article_id"=>288372, "categories"=>["Physics", "Biotechnology", "Microbiology"], "users"=>["Mustafa Mir", "S. Derin Babacan", "Michael Bednarz", "Minh N. Do", "Ido Golding", "Gabriel Popescu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039816.g002", "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sparsity_property_of_phase_images_/288372", "title"=>"Sparsity property of phase images.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 03:20:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/618058"], "description"=>"<p>In the x–y plane a coil structure is visible that has a period of approximately 0.43 µm and does not vary with the length of the cell. In the x-z plane another structure is visible that has a period of half the cell-length.</p>", "links"=>[], "tags"=>["structures", "26"], "article_id"=>288551, "categories"=>["Physics", "Biotechnology", "Microbiology"], "users"=>["Mustafa Mir", "S. Derin Babacan", "Michael Bednarz", "Minh N. Do", "Ido Golding", "Gabriel Popescu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039816.g005", "stats"=>{"downloads"=>4, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Measurement_of_prominent_structures_found_in_26_cells_/288551", "title"=>"Measurement of prominent structures found in 26 cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 03:21:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/617755"], "description"=>"<p>The SLIM module is attached to a commercial phase contrast microscope (AxioObserver Z1, Zeiss). The first 4-f system (lenses L1 and L2) expands the field of view to maintain the resolution of the microscope. The polarizer, P is used to align the polarization of the field with the slow axis of the Spatial Light Modulator (SLM). Lens L3 projects the back focal plane of the objective, containing the phase ring, onto the SLM which is used to impart phase shifts of 0, π/2, π and 3π/2 to the un-scattered light relative to the scattered light as shown in the inset. Lens L4 then projects the image plane onto the CCD for measurement. From the 4 intensity measurements a quantitative phase map is reconstructed as shown in the inset.</p>", "links"=>[], "tags"=>["microbiology", "biotechnology", "physics"], "article_id"=>288239, "categories"=>["Physics", "Biotechnology", "Microbiology"], "users"=>["Mustafa Mir", "S. Derin Babacan", "Michael Bednarz", "Minh N. Do", "Ido Golding", "Gabriel Popescu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0039816.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Experimental_setup_/288239", "title"=>"Experimental setup.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 03:19:16"}

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Relative Metric

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