PhagoSight: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model
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{"title"=>"PhagoSight: An Open-Source MATLAB® Package for the Analysis of Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model", "type"=>"journal", "authors"=>[{"first_name"=>"Katherine M.", "last_name"=>"Henry", "scopus_author_id"=>"55843018200"}, {"first_name"=>"Luke", "last_name"=>"Pase", "scopus_author_id"=>"6506381192"}, {"first_name"=>"Carlos Fernando", "last_name"=>"Ramos-Lopez", "scopus_author_id"=>"55843349900"}, {"first_name"=>"Graham J.", "last_name"=>"Lieschke", "scopus_author_id"=>"7004160769"}, {"first_name"=>"Stephen A.", "last_name"=>"Renshaw", "scopus_author_id"=>"6603849831"}, {"first_name"=>"Constantino Carlos", "last_name"=>"Reyes-Aldasoro", "scopus_author_id"=>"55905527000"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84883380064", "pui"=>"369734543", "pmid"=>"24023630", "doi"=>"10.1371/journal.pone.0072636", "sgr"=>"84883380064", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203"}, "id"=>"13d290b2-7d25-34c8-aeef-3e4bd2aadda4", "abstract"=>"Neutrophil migration in zebrafish larvae is increasingly used as a model to study the response of these leukocytes to different determinants of the cellular inflammatory response. However, it remains challenging to extract comprehensive information describing the behaviour of neutrophils from the multi-dimensional data sets acquired with widefield or confocal microscopes. Here, we describe PhagoSight, an open-source software package for the segmentation, tracking and visualisation of migrating phagocytes in three dimensions. The algorithms in PhagoSight extract a large number of measurements that summarise the behaviour of neutrophils, but that could potentially be applied to any moving fluorescent cells. To derive a useful panel of variables quantifying aspects of neutrophil migratory behaviour, and to demonstrate the utility of PhagoSight, we evaluated changes in the volume of migrating neutrophils. Cell volume increased as neutrophils migrated towards the wound region of injured zebrafish. PhagoSight is openly available as MATLAB® m-files under the GNU General Public License. Synthetic data sets and a comprehensive user manual are available from http://www.phagosight.org.", "link"=>"http://www.mendeley.com/research/phagosight-opensource-matlab-package-analysis-fluorescent-neutrophil-macrophage-migration-zebrafish", "reader_count"=>44, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Student > Doctoral Student"=>1, "Researcher"=>14, "Student > Ph. D. Student"=>12, "Student > Master"=>6, "Student > Bachelor"=>5, "Professor"=>4}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Student > Doctoral Student"=>1, "Researcher"=>14, "Student > Ph. D. Student"=>12, "Student > Master"=>6, "Student > Bachelor"=>5, "Professor"=>4}, "reader_count_by_subject_area"=>{"Engineering"=>4, "Biochemistry, Genetics and Molecular Biology"=>2, "Materials Science"=>1, "Mathematics"=>1, "Agricultural and Biological Sciences"=>24, "Medicine and Dentistry"=>9, "Neuroscience"=>1, "Immunology and Microbiology"=>1, "Environmental Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>4}, "Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>9}, "Neuroscience"=>{"Neuroscience"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>24}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Mathematics"=>{"Mathematics"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Taiwan"=>1, "United Kingdom"=>2, "Germany"=>2}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1186048"], "description"=>"<p>The region described by low threshold (bright) will contain one or more regions described by the high threshold (dark); if segmented solely with a single high threshold several unconnected regions would arise. A single low threshold would in turn produce more regions of low intensity not shown here.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Immune physiology", "Immune cells", "Computational biology", "Biological data management", "developmental biology", "morphogenesis", "cell migration", "immunology", "immunity", "inflammation", "Immune response", "Model organisms", "Animal models", "zebrafish", "algorithms", "Programming languages", "software engineering", "Software tools", "thresholding", "segmentation", "neutrophil"], "article_id"=>784997, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Katherine M. Henry", "Luke Pase", "Carlos Fernando Ramos-Lopez", "Graham J. Lieschke", "Stephen A. Renshaw", "Constantino Carlos Reyes-Aldasoro"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0072636.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Hysteresis_thresholding_segmentation_of_a_single_neutrophil_at_five_time_points_/784997", "title"=>"Hysteresis thresholding segmentation of a single neutrophil at five time points.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-30 01:28:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1186052"], "description"=>"<p>(a,d) One slice of a 3D stack where one object (box) was considered as an outlier due to its volume. (b,e) A three-dimensional rendering of the object indicates that it is formed by two neutrophils that collided. (c,f) Two new objects after the segmentation.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Immune physiology", "Immune cells", "Computational biology", "Biological data management", "developmental biology", "morphogenesis", "cell migration", "immunology", "immunity", "inflammation", "Immune response", "Model organisms", "Animal models", "zebrafish", "algorithms", "Programming languages", "software engineering", "Software tools", "objects", "synthetic"], "article_id"=>784999, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Katherine M. Henry", "Luke Pase", "Carlos Fernando Ramos-Lopez", "Graham J. Lieschke", "Stephen A. Renshaw", "Constantino Carlos Reyes-Aldasoro"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0072636.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Segmentation_of_large_objects_in_synthetic_top_row_and_real_bottom_row_data_sets_/784999", "title"=>"Segmentation of large objects in synthetic (top row) and real (bottom row) data sets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-30 01:28:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1186054"], "description"=>"<p>(a) Three-dimensional plot of the tracks with time as the vertical axis. The DIC image of the fish is presented as a horizontal plane at time 0 and one fluorescent slice is shown at time 120. The black square over the DIC corresponds to the artificial wound region. (b) Description of the absolute, oriented and lateral neutrophil velocities with respect to the axis defined according to a manual delineation of the wound region.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Immune physiology", "Immune cells", "Computational biology", "Biological data management", "developmental biology", "morphogenesis", "cell migration", "immunology", "immunity", "inflammation", "Immune response", "Model organisms", "Animal models", "zebrafish", "algorithms", "Programming languages", "software engineering", "Software tools"], "article_id"=>785000, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Katherine M. Henry", "Luke Pase", "Carlos Fernando Ramos-Lopez", "Graham J. Lieschke", "Stephen A. Renshaw", "Constantino Carlos Reyes-Aldasoro"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0072636.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Orientation_of_the_movement_based_on_the_artificial_wound_region_/785000", "title"=>"Orientation of the movement based on the artificial wound region.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-30 01:28:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1186056"], "description"=>"<p>(a) One slice at t = 26 and the paths of six neutrophils shown as coloured lines. Vertical axis indicates time. (b) Five histograms for background (noise) and neutrophils (signal) for different levels of noise. The separability is indicated by the Bhattacharyya Distance (<i>BD</i>) values: highest <i>BD</i> corresponds to more separable classes (solid lines with no markers) and lowest <i>BD</i> corresponds to less separable classes (solid lines with circle markers). (c) One slice (<i>BD</i> = 1.61, SNR = 25.2 dB) shown as a mesh, intensity corresponds to the vertical axis. (d) One slice (<i>BD</i> = 0.45, SNR = 10.7 dB). The noise can be easily compared between the two data sets.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Immune physiology", "Immune cells", "Computational biology", "Biological data management", "developmental biology", "morphogenesis", "cell migration", "immunology", "immunity", "inflammation", "Immune response", "Model organisms", "Animal models", "zebrafish", "algorithms", "Programming languages", "software engineering", "Software tools", "synthetic"], "article_id"=>785002, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Katherine M. Henry", "Luke Pase", "Carlos Fernando Ramos-Lopez", "Graham J. Lieschke", "Stephen A. Renshaw", "Constantino Carlos Reyes-Aldasoro"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0072636.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Description_of_the_synthetic_data_sets_/785002", "title"=>"Description of the synthetic data sets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-30 01:28:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1186058"], "description"=>"<p>In all cases the sets were automatically tracked with <i>PhagoSight</i>; input thresholds were automatically determined and then modified from 40% to 140% of the original values to test the robustness against variation of that input parameter. (a) Distance from the automatically generated tracks to the gold standard (D<sub>AG</sub>) for the synthetic data set, <i>BD</i> corresponds to the Bhattacharyya distance between background and neutrophils. (b) Distance from the gold standard to the automatically generated tracks (D<sub>GA</sub>) for the synthetic data set. (c) D<sub>AG</sub> for the real data set, (d) D<sub>GA</sub> for the real data set. High distances for the synthetic sets are due to low thresholds that interpret noise as neutrophils. The increase in D<sub>GA</sub> in (d) is caused by higher levels that do not detect faint neutrophils, this in turn will reduce D<sub>AG</sub> as with the higher threshold, the neutrophils which are detected are the brightest and thus the tracking is more precise.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Immune physiology", "Immune cells", "Computational biology", "Biological data management", "developmental biology", "morphogenesis", "cell migration", "immunology", "immunity", "inflammation", "Immune response", "Model organisms", "Animal models", "zebrafish", "algorithms", "Programming languages", "software engineering", "Software tools", "synthetic"], "article_id"=>785004, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Katherine M. Henry", "Luke Pase", "Carlos Fernando Ramos-Lopez", "Graham J. Lieschke", "Stephen A. Renshaw", "Constantino Carlos Reyes-Aldasoro"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0072636.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Validation_of_the_algorithms_with_synthetic_and_real_data_sets_/785004", "title"=>"Validation of the algorithms with synthetic and real data sets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-30 01:28:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1186064"], "description"=>"<p>A synthetic data set is shown in (a) whilst (b,c) are real data sets. In (a,c) the thresholds are 140% of the automatically detected values, while for (b) they are 60% of the detected values. The automatic tracks are displayed as thick solid lines and the gold standard as thin dashed lines, and one slice of the intensity data sets is presented with the tracks. In the real data set, the high thresholds prevented the low intensity neutrophils from being detected (solid arrows) and therefore no tracks were generated for these neutrophils with corresponding high D<sub>GA</sub>. With lower thresholds, the faint neutrophils were detected, and other neutrophils were also tracked (dashed arrow), this track could have been generated by noise or could have been missed during the manual tracking. It should be noticed that where <i>PhagoSight</i> detected the neutrophils, the tracks are very close to the gold standard.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Immune physiology", "Immune cells", "Computational biology", "Biological data management", "developmental biology", "morphogenesis", "cell migration", "immunology", "immunity", "inflammation", "Immune response", "Model organisms", "Animal models", "zebrafish", "algorithms", "Programming languages", "software engineering", "Software tools", "tracks"], "article_id"=>785009, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Katherine M. Henry", "Luke Pase", "Carlos Fernando Ramos-Lopez", "Graham J. Lieschke", "Stephen A. Renshaw", "Constantino Carlos Reyes-Aldasoro"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0072636.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Comparison_of_automatic_tracks_against_the_gold_standard_/785009", "title"=>"Comparison of automatic tracks against the gold standard.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-30 01:28:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1186065"], "description"=>"<p>In ICY, “size filter” was used with increasing values of size; <i>PhagoSight</i> input thresholds were automatically determined and then modified from 40% to 140% of the original. (a) Synthetic data set tracked with ICY, (b) Synthetic data set tracked with <i>PhagoSight</i>, (c) Real data set tracked with ICY, (d) Real data set tracked with <i>PhagoSight</i>. Solid line and circle markers corresponds to distance from the automatically generated tracks to the gold standard (D<sub>AG</sub>) and dotted line with square markers corresponds to the distance from the gold standard to the automatically generated tracks (D<sub>GA</sub>).</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Immune physiology", "Immune cells", "Computational biology", "Biological data management", "developmental biology", "morphogenesis", "cell migration", "immunology", "immunity", "inflammation", "Immune response", "Model organisms", "Animal models", "zebrafish", "algorithms", "Programming languages", "software engineering", "Software tools", "segmentation", "tracking", "icy", "synthetic"], "article_id"=>785011, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Katherine M. Henry", "Luke Pase", "Carlos Fernando Ramos-Lopez", "Graham J. Lieschke", "Stephen A. Renshaw", "Constantino Carlos Reyes-Aldasoro"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0072636.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Comparison_of_the_segmentation_and_tracking_results_against_ICY_for_one_synthetic_and_one_real_data_set_/785011", "title"=>"Comparison of the segmentation and tracking results against ICY for one synthetic and one real data set.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-30 01:28:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1186066"], "description"=>"<p>The field of view was split into 25 adjacent regions each containing 20 MATLAB® columns, with higher numbers denoting neutrophils closer to the wound region. The volume was averaged in each band and normalised to the mean of the data set for each larva, which were then pooled in the final analysis. Two sets of thresholds were used. Analysis A uses higher thresholds than analysis B.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Immune physiology", "Immune cells", "Computational biology", "Biological data management", "developmental biology", "morphogenesis", "cell migration", "immunology", "immunity", "inflammation", "Immune response", "Model organisms", "Animal models", "zebrafish", "algorithms", "Programming languages", "software engineering", "Software tools", "neutrophil", "anterior"], "article_id"=>785012, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Katherine M. Henry", "Luke Pase", "Carlos Fernando Ramos-Lopez", "Graham J. Lieschke", "Stephen A. Renshaw", "Constantino Carlos Reyes-Aldasoro"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0072636.g009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Mean_neutrophil_volume_relative_to_its_position_in_an_area_anterior_to_the_wound_region_/785012", "title"=>"Mean neutrophil volume relative to its position in an area anterior to the wound region.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-30 01:28:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1186067"], "description"=>"<p>Computationally derived measurements used to assess neutrophil migration following wounding.</p>", "links"=>[], "tags"=>["Anatomy and physiology", "Immune physiology", "Immune cells", "Computational biology", "Biological data management", "developmental biology", "morphogenesis", "cell migration", "immunology", "immunity", "inflammation", "Immune response", "Model organisms", "Animal models", "zebrafish", "algorithms", "Programming languages", "software engineering", "Software tools", "derived", "neutrophil"], "article_id"=>785013, "categories"=>["Biological Sciences", "Information And Computing Sciences"], "users"=>["Katherine M. Henry", "Luke Pase", "Carlos Fernando Ramos-Lopez", "Graham J. Lieschke", "Stephen A. Renshaw", "Constantino Carlos Reyes-Aldasoro"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0072636.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Computationally_derived_measurements_used_to_assess_neutrophil_migration_following_wounding_/785013", "title"=>"Computationally derived measurements used to assess neutrophil migration following wounding.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-30 01:28:40"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
  • {"unique-ip"=>"12", "full-text"=>"11", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"7", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"11"}
  • {"unique-ip"=>"9", "full-text"=>"8", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"12"}
  • {"unique-ip"=>"10", "full-text"=>"9", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"2"}
  • {"unique-ip"=>"11", "full-text"=>"13", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2017", "month"=>"3"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Developmental biology", "average_usage"=>[275, 472, 605, 720, 822, 921, 1013, 1106, 1200, 1289, 1378, 1459, 1531]}, {"subject_area"=>"/Computer and information sciences/Information technology", "average_usage"=>[265, 446, 547, 656, 751, 809, 898, 978, 1077, 1216, 1295, 1357, 1403, 1469]}, {"subject_area"=>"/Medicine and health sciences/Immunology", "average_usage"=>[262, 463, 587, 693, 790, 882, 965, 1051, 1135, 1218, 1300, 1376, 1438]}]}
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