The Filament Sensor for Near Real-Time Detection of Cytoskeletal Fiber Structures
Publication Date
May 21, 2015
Journal
PLOS ONE
Authors
Benjamin Eltzner, Carina Wollnik, Carsten Gottschlich, Stephan Huckemann, et al
Volume
10
Issue
5
Pages
e0126346
DOI
https://dx.plos.org/10.1371/journal.pone.0126346
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0126346
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/25996921
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4440737
Europe PMC
http://europepmc.org/abstract/MED/25996921
Web of Science
000356444000021
Scopus
84930665483
Mendeley
http://www.mendeley.com/research/filament-sensor-near-realtime-detection-cytoskeletal-fiber-structures
Events
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2078343"], "description"=>"<p>Subfigures are as in 15, now for simulated cells, with all axes linear. Data points corresponding to same methods in plots (a) and (c) are connected only for better visualization.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422729, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g021", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_R_fp_false_positive_ratios_and_R_fn_false_negative_ratios_/1422729", "title"=>"Comparison of <i>R</i><sub>fp</sub> (false positive ratios) and <i>R</i><sub>fn</sub> (false negative ratios).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078302"], "description"=>"<p>(a) an isotropic two dimensional Gaussian. Convolving the image with such a filter will lead to blurring of the image. (b) restriction of an isotropic Gaussian to a line. This filter locally homogenizes pixel brightness along lines that run in direction of the filter. It is computationally efficient as it only uses few pixels. (c) an elongated Gaussian. This filter also homogenizes lines, but it has much more Pixels and thus requires much longer computation.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422696, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustration_of_the_line_Gaussian_/1422696", "title"=>"Illustration of the line Gaussian.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078320"], "description"=>"<p>This illustration uses the simulated cell 05. Green pixels are false positives detected by the method, yellow are correctly identified pixels and red are missed pixels as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0126346#pone.0126346.g009\" target=\"_blank\">Fig 9</a>.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422709, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g010", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tracing_results_with_false_positives_and_missed_filaments_for_a_simulated_cell_/1422709", "title"=>"Tracing results with false positives and missed filaments for a simulated cell.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078305"], "description"=>"<p>FQS is determined in terms of line sharpness and contrast, size of the cell, and bright spots due to overexposure, where the latter decreases the score, while the line sharpness and contrast and cell size contribute positively. The blue lines indicate our separation of the images into qualitative classes. The classes were chosen to contain like numbers of images and only serve illustrative purposes as a rough quality label.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422699, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g008", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Filament_quality_scores_of_benchmark_database_images_/1422699", "title"=>"Filament quality scores of benchmark database images.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078323"], "description"=>"<p>It also contains several crossings of lines of different brightness at small angles. The image is used as a test case to qualitatively highlight the performance of the three methods compared here in terms of filament pixel detection and especially structure detection. As the FS is the only method that extracts line data, the notion of parallel or intersecting lines only makes sense for this method.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422712, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g011", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Simulated_test_case_image_featuring_many_parallel_lines_at_different_distances_some_very_close_/1422712", "title"=>"Simulated test case image featuring many parallel lines at different distances, some very close.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078339"], "description"=>"<p>The cell G1 used for this illustration is a fixed cell that has been immunofluorescently stained. The subfigures display: (a) ground truth, (b) FS results, (c) eLoG results, (d) Hough results. The black curves illustrate the result of kernel smoothing with a Gaussian of standard deviation <i>σ</i> = 10.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422725, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g018", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Angular_histograms_of_filament_mass_for_an_hMSC_/1422725", "title"=>"Angular histograms of filament mass for an hMSC.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078298"], "description"=>"<p>Subfigures: (a) <i>good quality</i> image G1 of an immunoflurescently stained fixed cell of large size with clearly visible stress fibers on gel with stiffness 10 kPa; (b) <i>medium quality</i> image M3 of an immunoflurescently stained fixed cell of moderate size with inhomogeneous brightness and slight blur on glass; (c) <i>poor quality</i> image B2 of a live cell of moderate size with considerable noise and excessive brightness due to overexposure on glass; (d) <i>very poor quality</i> image VB2 of a live cell of moderate size with very low contrast due to bleaching, considerable blur and hardly discernible stress fibers.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422692, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Varying_quality_images_of_human_mesenchymal_stem_cells_in_view_of_filament_expression_/1422692", "title"=>"Varying quality images of human mesenchymal stem cells in view of filament expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078332"], "description"=>"<p>Showing cell VB2. Green pixels are false positives detected by the method, yellow are correctly identified pixels and red are missed pixels as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0126346#pone.0126346.g009\" target=\"_blank\">Fig 9</a>. All methods produce some false positives but the eLoG method stands out by detecting almost all cell pixels as line pixels. CID produces a cobweb structure with a similar amount of oversegmentation as the FS.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422718, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g013", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Performance_comparison_in_the_presence_of_blur_/1422718", "title"=>"Performance comparison in the presence of blur.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078301"], "description"=>"<p>The algorithm begins at the very top with a binary image and outputs an orientation field and line information, displayed to the bottom left of the chart. A detailed explanation is given in the text.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422695, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g004", "stats"=>{"downloads"=>0, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flow_chart_illustrating_the_algorithm_of_the_line_segment_sensor_/1422695", "title"=>"Flow chart illustrating the algorithm of the line segment sensor.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078342"], "description"=>"<p>Subfigures are as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0126346#pone.0126346.g014\" target=\"_blank\">Fig 14</a>, now for simulated cells, with all relative masses and distances now linear. Data points corresponding to same methods in plots (a) and (c) are connected only for better visualization.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422728, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g020", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_angular_histograms_/1422728", "title"=>"Comparison of angular histograms.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078304"], "description"=>"<p>Some connectivity lines (left) with detail (right) along which the segment sensor probes. The lines illustrated correspond to multiples of 10° to render the illustration legible. The algorithm uses multiples of 1°, which implies ten times as many paths. The detail shows that the lines are thin in the sense that pixels on diagonal lines touch only at the corner points.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422698, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g007", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustration_of_the_segment_sensor_8217_s_probing_paths_/1422698", "title"=>"Illustration of the segment sensor’s probing paths.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078338"], "description"=>"<p>Showing details from the simulated test image displayed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0126346#pone.0126346.g011\" target=\"_blank\">Fig 11</a>. The columns show, from left to right, the original detail, the results of the FS, the results of the eLoG method, and the results of CID. Green pixels are false positives detected by the method, yellow are correctly identified pixels and red are missed pixels as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0126346#pone.0126346.g009\" target=\"_blank\">Fig 9</a>. In the details shown the FS and eLoG method clearly outperform CID, which does poorly at detecting close parallel lines, as shown in the first three rows of the figure. Also for crossing lines as displayed in the fourth and fifth row, CID performs poorly. The eLoG method shows some weaknesses for close parallel lines and overshoots at the endings of lines. Overall, its line pixel detection capabilities in these synthetic test cases are comparable to those of the FS.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422724, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g017", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Performance_comparison_for_close_parallel_lines_and_lines_crossing_at_small_angles_/1422724", "title"=>"Performance comparison for close parallel lines and lines crossing at small angles.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078335"], "description"=>"<p>Subfigure (a) displays <i>R</i><sub>fp</sub> for individual cells, subfigure (b) the corresponding boxplots over all 10 cells. Subfigure (c) displays <i>R</i><sub>fp</sub> for individual cells, subfigure (d) shows the corresponding boxplots over all 10 cells. The plots are semi-logarithmic because scales vary widely. Data points corresponding to same methods in plots (a) and (c) are connected only for better visualization.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422721, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g015", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_R_fp_false_positive_ratios_and_R_fn_false_negative_ratios_/1422721", "title"=>"Comparison of <i>R</i><sub>fp</sub> (false positive ratios) and <i>R</i><sub>fn</sub> (false negative ratios).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078341"], "description"=>"<p>Subfigures and black line are as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0126346#pone.0126346.g018\" target=\"_blank\">Fig 18</a>.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422727, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g019", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Angular_histograms_of_filament_mass_for_a_simulated_cell_cell_05_/1422727", "title"=>"Angular histograms of filament mass for a simulated cell (cell 05).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078300"], "description"=>"<p>(a) original. The lines in question are discernible to the human eye but contrast is low. (b) normalized cross correlation. Contrast is greatly enhanced but faint lines are severed by crossing bright lines (c) line Gaussians. Contrast and overall brightness are enhanced. Especially, faint lines crossing bright lines are not suppressed. A line illustration these findings particularly well is running from the upper left to the lower right.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422694, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_cross_correlation_filter_suppresses_faint_lines_/1422694", "title"=>"The cross correlation filter suppresses faint lines.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078354"], "description"=>"<div><p>A reliable extraction of filament data from microscopic images is of high interest in the analysis of acto-myosin structures as early morphological markers in mechanically guided differentiation of human mesenchymal stem cells and the understanding of the underlying fiber arrangement processes. In this paper, we propose the filament sensor (FS), a fast and robust processing sequence which detects and records location, orientation, length, and width for each single filament of an image, and thus allows for the above described analysis. The extraction of these features has previously not been possible with existing methods. We evaluate the performance of the proposed FS in terms of accuracy and speed in comparison to three existing methods with respect to their limited output. Further, we provide a benchmark dataset of real cell images along with filaments manually marked by a human expert as well as simulated benchmark images. The FS clearly outperforms existing methods in terms of computational runtime and filament extraction accuracy. The implementation of the FS and the benchmark database are available as open source.</p></div>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422740, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Filament_Sensor_for_Near_Real_Time_Detection_of_Cytoskeletal_Fiber_Structures_/1422740", "title"=>"The Filament Sensor for Near Real-Time Detection of Cytoskeletal Fiber Structures", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078331"], "description"=>"<div><p>Showing a detail of cell M3. The subfigures represent (a) the original detail, (b) the results of the FS, (c) the results of the eLoG method and (d) the results of CID. Green pixels are false positives detected by the method, yellow are correctly identified pixels and red are missed pixels as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0126346#pone.0126346.g009\" target=\"_blank\">Fig 9</a>.</p>\n<p>The FS produces a fair amount of false positives but fares quite well both in the dark region on the left as well as the bright region with crossing lines on the right. The eLoG method also find parts of the lines in the dark region albeit at the expense of significant oversegmentation in the bright region. CID detects lines almost exclusively in the higher contrast bright region, where it produces a cobweb structure with an amount of oversegmentation similar to the FS.</p></div>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422717, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g012", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Performance_comparison_for_inhomogeneous_brightness_and_crossing_lines_/1422717", "title"=>"Performance comparison for inhomogeneous brightness and crossing lines.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078344"], "description"=>"<p>Checkmarks in parentheses indicate that for lack of documentation and source code availability the FibreScore method is not portable in terms of full configurability and usability to a generic system.</p><p>Data collected by various methods and comparison of runtime.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422730, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.t001", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Data_collected_by_various_methods_and_comparison_of_runtime_/1422730", "title"=>"Data collected by various methods and comparison of runtime.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078303"], "description"=>"<p>These are examples of the circular masks used by the segment sensor algorithm to determine line width. The circles displayed here correspond to diameters of 2, 4, 6 and 8 pixels. The masks are squares with an odd number of pixels as they are centered at a unique pixel.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422697, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g006", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Some_circle_masks_/1422697", "title"=>"Some circle masks.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078337"], "description"=>"<p>Showing cell B2. Green pixels are false positives detected by the method, yellow are correctly identified pixels and red are missed pixels as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0126346#pone.0126346.g009\" target=\"_blank\">Fig 9</a>. For this image the FS fares much better than both other methods. The eLoG method as well as CID both find a large amount of spurious features, where the eLoG method detects large contiguous areas and CID produces a cobweb structure, covering nearly the whole cell. Especially in the left, lower, and central parts of the image the FS is the only method that does not detect a large amount of spurious line pixels.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422723, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g016", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Performance_comparison_in_the_presence_of_noise_/1422723", "title"=>"Performance comparison in the presence of noise.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078314"], "description"=>"<p>The cell G1 used for this illustration is a fixed cell that has been immunofluorescently stained. The subfigures display: (a) ground truth, (b) FS results, (c) eLoG results, (d) CID results. Green pixels are false positives detected by the method, yellow are correctly identified pixels and red are missed pixels. A pixel is correctly identified, if it corresponds to a ground truth labeled pixel within an 8-neighborhood. A ground truth labeled pixel is considered missing, if no pixel was detected within an 8-neighborhood.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422703, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g009", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tracing_results_with_false_positives_and_missed_filaments_for_an_hMSC_/1422703", "title"=>"Tracing results with false positives and missed filaments for an hMSC.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078299"], "description"=>"<p>(a) blur (detail from image VB2) The overall contrast of the cell body is very low and lines are hardly discernible. (b) overexposure and noise (B2) The extensive regions of maximal brightness hide any structure that may be present in those regions. Salt and pepper noise is clearly visible as dark spots in bright areas and bright spots in dark areas. (c) filament crossings (M3). A bundle of roughly vertical filaments of varying brightness crosses a bundle of roughly horizontal filaments with varying brightness.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422693, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Challenges_for_filament_extraction_/1422693", "title"=>"Challenges for filament extraction.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/2078333"], "description"=>"<p>Log-scales and logs of earth movers distances are compared independently. Subfigure (a) shows the log-scaled relative mass of the histograms with respect to the histogram from filaments marked by a human expert for individual cells. In subfigure (b) boxplots of the log-scaled relative masses each over all 10 cells are displayed. Subfigure (c) shows the logs of earth movers distance between normalized histograms of the evaluation method and the ground truth; subfigure (d) displays the corresponding boxplots each over all 10 cells. The plots are semi-logarithmic because scales vary widely. Data points corresponding to same methods in plots (a) and (c) are connected only for better visualization.</p>", "links"=>[], "tags"=>["fs", "cell images", "filament data", "Filament Sensor", "filament extraction accuracy", "fiber arrangement processes", "benchmark database", "benchmark dataset", "method", "term", "benchmark images", "analysis", "processing sequence", "records location", "Cytoskeletal Fiber Structures"], "article_id"=>1422719, "categories"=>["Biological Sciences"], "users"=>["Benjamin Eltzner", "Carina Wollnik", "Carsten Gottschlich", "Stephan Huckemann", "Florian Rehfeldt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0126346.g014", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_angular_histograms_/1422719", "title"=>"Comparison of angular histograms.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-05-21 03:25:41"}

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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