A Computational Tool for Quantitative Analysis of Vascular Networks
Publication Date
November 16, 2011
Journal
PLOS ONE
Authors
Enrique Zudaire, Laure Gambardella, Christopher Kurcz & Sonja Vermeren
Volume
6
Issue
11
Pages
e27385
DOI
https://dx.plos.org/10.1371/journal.pone.0027385
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0027385
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22110636
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3217985
Europe PMC
http://europepmc.org/abstract/MED/22110636
Web of Science
000297555400041
Scopus
81155134376
Mendeley
http://www.mendeley.com/research/computational-tool-quantitative-analysis-vascular-networks
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Mendeley | Further Information

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CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/711912"], "description"=>"<p>The control allantois explants for the experiment shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0027385#pone-0027385-g005\" target=\"_blank\">Fig. 5</a> were overlaid according to the pre-set parameters (skeletons not optimised) or after careful optimisation. This lead to significantly different branching indices (B; p<0.001, Mann Whitney T-test). (A) shows an enlarged area of a stained explant; the same area is shown after skeletonisation using the pre-set parameters (C) or after optimisation (C'. A few examples of missed vessels and junctions in the non-optimised skeleton are highlighted by ringed areas and arrowheads.</p>", "links"=>[], "tags"=>["skeletons", "thorough"], "article_id"=>382272, "categories"=>["Physiology", "Biological Sciences", "Developmental Biology"], "users"=>["Enrique Zudaire", "Laure Gambardella", "Christopher Kurcz", "Sonja Vermeren"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0027385.g007", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Optimising_skeletons_for_a_thorough_analysis_/382272", "title"=>"Optimising skeletons for a thorough analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-11-16 00:37:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/711748"], "description"=>"<p>Allantois explants were cultured in the presence of inhibitor or its vehicle, fixed, stained and microscopic photographs taken as described. (A) Representative images of a control (top) and a Y-27632 treated (bottom) allantois explant (left), their skeletonised images (middle panels) and a representative, enlarged part of the skeletonised images shown in the middle panels. The vessels outlines are represented in yellow, the skeleton in red and the branching points in blue. (B) Graphical representations of the analysis with AngioTool performed on seven control and ten Y-27632 treated explants. Statistical analysis was by T-test (Mann Whitney) *, p<0.05; **, p<0.01.</p>", "links"=>[], "tags"=>["angiogenesis", "y-27632", "treated", "allantois"], "article_id"=>382113, "categories"=>["Physiology", "Biological Sciences", "Developmental Biology"], "users"=>["Enrique Zudaire", "Laure Gambardella", "Christopher Kurcz", "Sonja Vermeren"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0027385.g005", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_angiogenesis_in_Y_27632_treated_allantois_explants_/382113", "title"=>"Analysis of angiogenesis in Y-27632 treated allantois explants.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-11-16 00:35:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/711136"], "description"=>"<p>(A) AngioTool GUI for analysis of angiogenesis networks. A detailed quick analysis guide can be accessed through the help button. (B) Representation of the logical analysis flow performed by AngioTool which is based on identification of vessels using multiscale Hessian analysis and skeletonization. The analysis process is mostly automated (yellow boxes) with minimal user intervention required to select the test image and during the visual identification of vessels (green squares).</p>", "links"=>[], "tags"=>["gui"], "article_id"=>381505, "categories"=>["Physiology", "Biological Sciences", "Developmental Biology"], "users"=>["Enrique Zudaire", "Laure Gambardella", "Christopher Kurcz", "Sonja Vermeren"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0027385.g001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_AngioTool_s_GUI_and_analysis_flow_/381505", "title"=>"AngioTool's GUI and analysis flow.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-11-16 00:25:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/711628"], "description"=>"<p>Allantois explants were cultured in the presence of inhibitor or its vehicle, fixed, stained and microscopic photographs taken as described. (A) Representative images of a control (top) and a LY294002-treated (bottom) allantois explant (left), the resulting images after analysis (middle panels) and a representative, enlarged part of the result images shown in the middle panels. The vessel outlines are shown in yellow, the skeletons in red and the branching points in blue (B) Graphical representations of the analysis with AngioTool performed on eight control and eight LY294002-treated explants. Statistical analysis was by T-test (Mann Whitney) ***, p<0.001, **, p<0.01.</p>", "links"=>[], "tags"=>["angiogenesis", "ly294002", "treated", "allantois"], "article_id"=>381993, "categories"=>["Physiology", "Biological Sciences", "Developmental Biology"], "users"=>["Enrique Zudaire", "Laure Gambardella", "Christopher Kurcz", "Sonja Vermeren"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0027385.g004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_angiogenesis_in_LY294002_treated_allantois_explants_/381993", "title"=>"Analysis of angiogenesis in LY294002 treated allantois explants.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-11-16 00:33:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/712013"], "description"=>"<p>*A vessel is defined after segmentation as a segment between two branching points or a branching point and an end point.</p>", "links"=>[], "tags"=>["angiogenesis", "parameters", "computed"], "article_id"=>382378, "categories"=>["Physiology", "Biological Sciences", "Developmental Biology"], "users"=>["Enrique Zudaire", "Laure Gambardella", "Christopher Kurcz", "Sonja Vermeren"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0027385.t001", "stats"=>{"downloads"=>5, "page_views"=>38, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_angiogenesis_related_parameters_computed_by_AngioTool_/382378", "title"=>"Summary of angiogenesis related parameters computed by AngioTool.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-11-16 00:39:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/711321"], "description"=>"<p>Hindbrains were dissected, stained and microscopic photographs were taken and assembled as described. (A) Representative E11 hindbrain. (B) Result image after analysis of the hindbrain shown in (A). (C) Enlarged area from skeleton shown in (B). The outline of the vasculature is shown in yellow, the skeleton representation of vasculature in red and branching points are blue. (D) Graphical representation of the analysis performed on three individual hindbrains.</p>", "links"=>[], "tags"=>["embryonic"], "article_id"=>381689, "categories"=>["Physiology", "Biological Sciences", "Developmental Biology"], "users"=>["Enrique Zudaire", "Laure Gambardella", "Christopher Kurcz", "Sonja Vermeren"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0027385.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Angiogenesis_in_the_embryonic_hindbrain_/381689", "title"=>"Angiogenesis in the embryonic hindbrain.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-11-16 00:28:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/711837"], "description"=>"<p>The eight images of control DMSO- and LY294002-treated allantois explants (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0027385#pone-0027385-g004\" target=\"_blank\">Fig. 4</a>) were analysed independently by two investigators. The results obtained are plotted. White bars, analysis performed by person 1, grey bars, analysis performed by person 2. Results obtained were subjected to statistical analysis by 2-way ANOVA. This showed highly significant differences for LY294002 treatment under all conditions tested (p<0.001) whilst there were no significant differences between the results obtained by the two investigators (p>0.66).</p>", "links"=>[], "tags"=>["physiology", "Computational biology", "developmental biology"], "article_id"=>382196, "categories"=>["Physiology", "Biological Sciences", "Developmental Biology"], "users"=>["Enrique Zudaire", "Laure Gambardella", "Christopher Kurcz", "Sonja Vermeren"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0027385.g006", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reproducibility_of_image_analysis_using_AngioTool_/382196", "title"=>"Reproducibility of image analysis using AngioTool.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-11-16 00:36:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/363102", "https://ndownloader.figshare.com/files/363138", "https://ndownloader.figshare.com/files/363173", "https://ndownloader.figshare.com/files/363206", "https://ndownloader.figshare.com/files/363271", "https://ndownloader.figshare.com/files/363326", "https://ndownloader.figshare.com/files/363366", "https://ndownloader.figshare.com/files/363423", "https://ndownloader.figshare.com/files/363495", "https://ndownloader.figshare.com/files/363541", "https://ndownloader.figshare.com/files/363591", "https://ndownloader.figshare.com/files/363660", "https://ndownloader.figshare.com/files/363716", "https://ndownloader.figshare.com/files/363754", "https://ndownloader.figshare.com/files/363779", "https://ndownloader.figshare.com/files/363812", "https://ndownloader.figshare.com/files/363841", "https://ndownloader.figshare.com/files/363893", "https://ndownloader.figshare.com/files/363946", "https://ndownloader.figshare.com/files/363974", "https://ndownloader.figshare.com/files/364010", "https://ndownloader.figshare.com/files/364051", "https://ndownloader.figshare.com/files/364095", "https://ndownloader.figshare.com/files/364127", "https://ndownloader.figshare.com/files/364177", "https://ndownloader.figshare.com/files/364220", "https://ndownloader.figshare.com/files/364292", "https://ndownloader.figshare.com/files/364355", "https://ndownloader.figshare.com/files/364401", "https://ndownloader.figshare.com/files/364449", "https://ndownloader.figshare.com/files/364513", "https://ndownloader.figshare.com/files/364537", "https://ndownloader.figshare.com/files/364596", "https://ndownloader.figshare.com/files/364642", "https://ndownloader.figshare.com/files/364693", "https://ndownloader.figshare.com/files/364745", "https://ndownloader.figshare.com/files/364791", "https://ndownloader.figshare.com/files/364836", "https://ndownloader.figshare.com/files/364876", "https://ndownloader.figshare.com/files/364914"], "description"=>"<div><p>Angiogenesis is the generation of mature vascular networks from pre-existing vessels. Angiogenesis is crucial during the organism' development, for wound healing and for the female reproductive cycle. Several murine experimental systems are well suited for studying developmental and pathological angiogenesis. They include the embryonic hindbrain, the post-natal retina and allantois explants. In these systems vascular networks are visualised by appropriate staining procedures followed by microscopical analysis. Nevertheless, quantitative assessment of angiogenesis is hampered by the lack of readily available, standardized metrics and software analysis tools. Non-automated protocols are being used widely and they are, in general, time - and labour intensive, prone to human error and do not permit computation of complex spatial metrics. We have developed a light-weight, user friendly software, AngioTool, which allows for quick, hands-off and reproducible quantification of vascular networks in microscopic images. AngioTool computes several morphological and spatial parameters including the area covered by a vascular network, the number of vessels, vessel length, vascular density and lacunarity. In addition, AngioTool calculates the so-called “branching index” (branch points / unit area), providing a measurement of the sprouting activity of a specimen of interest. We have validated AngioTool using images of embryonic murine hindbrains, post-natal retinas and allantois explants. AngioTool is open source and can be downloaded free of charge.</p> </div>", "links"=>[], "tags"=>["computational", "quantitative", "vascular", "networks"], "article_id"=>131769, "categories"=>["Physiology", "Biological Sciences", "Developmental Biology"], "users"=>["Enrique Zudaire", "Laure Gambardella", "Christopher Kurcz", "Sonja Vermeren"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0027385.s001", "https://dx.doi.org/10.1371/journal.pone.0027385.s002", "https://dx.doi.org/10.1371/journal.pone.0027385.s003", "https://dx.doi.org/10.1371/journal.pone.0027385.s004", "https://dx.doi.org/10.1371/journal.pone.0027385.s005", "https://dx.doi.org/10.1371/journal.pone.0027385.s006", "https://dx.doi.org/10.1371/journal.pone.0027385.s007", "https://dx.doi.org/10.1371/journal.pone.0027385.s008", "https://dx.doi.org/10.1371/journal.pone.0027385.s009", "https://dx.doi.org/10.1371/journal.pone.0027385.s010", "https://dx.doi.org/10.1371/journal.pone.0027385.s011", "https://dx.doi.org/10.1371/journal.pone.0027385.s012", "https://dx.doi.org/10.1371/journal.pone.0027385.s013", "https://dx.doi.org/10.1371/journal.pone.0027385.s014", "https://dx.doi.org/10.1371/journal.pone.0027385.s015", "https://dx.doi.org/10.1371/journal.pone.0027385.s016", "https://dx.doi.org/10.1371/journal.pone.0027385.s017", "https://dx.doi.org/10.1371/journal.pone.0027385.s018", "https://dx.doi.org/10.1371/journal.pone.0027385.s019", "https://dx.doi.org/10.1371/journal.pone.0027385.s020", "https://dx.doi.org/10.1371/journal.pone.0027385.s021", "https://dx.doi.org/10.1371/journal.pone.0027385.s022", "https://dx.doi.org/10.1371/journal.pone.0027385.s023", "https://dx.doi.org/10.1371/journal.pone.0027385.s024", "https://dx.doi.org/10.1371/journal.pone.0027385.s025", "https://dx.doi.org/10.1371/journal.pone.0027385.s026", "https://dx.doi.org/10.1371/journal.pone.0027385.s027", "https://dx.doi.org/10.1371/journal.pone.0027385.s028", "https://dx.doi.org/10.1371/journal.pone.0027385.s029", "https://dx.doi.org/10.1371/journal.pone.0027385.s030", "https://dx.doi.org/10.1371/journal.pone.0027385.s031", "https://dx.doi.org/10.1371/journal.pone.0027385.s032", "https://dx.doi.org/10.1371/journal.pone.0027385.s033", "https://dx.doi.org/10.1371/journal.pone.0027385.s034", "https://dx.doi.org/10.1371/journal.pone.0027385.s035", "https://dx.doi.org/10.1371/journal.pone.0027385.s036", "https://dx.doi.org/10.1371/journal.pone.0027385.s037", "https://dx.doi.org/10.1371/journal.pone.0027385.s038", "https://dx.doi.org/10.1371/journal.pone.0027385.s039", "https://dx.doi.org/10.1371/journal.pone.0027385.s040"], "stats"=>{"downloads"=>8, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Computational_Tool_for_Quantitative_Analysis_of_Vascular_Networks/131769", "title"=>"A Computational Tool for Quantitative Analysis of Vascular Networks", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-11-16 00:29:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/711488"], "description"=>"<p>Retinas were dissected, stained, flat mounted and microscopic photographs were taken and assembled as described. (A) Representative P6 retina and (B) the resulting image after analysis (C) Graphical representation of the analysis performed on four individual retinas. (D) Enlarged area from (B). Vessels outlines are shown in yellow, the skeleton in green and branching points in blue.</p>", "links"=>[], "tags"=>["angiogenesis", "murine"], "article_id"=>381849, "categories"=>["Physiology", "Biological Sciences", "Developmental Biology"], "users"=>["Enrique Zudaire", "Laure Gambardella", "Christopher Kurcz", "Sonja Vermeren"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0027385.g003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Post_natal_angiogenesis_in_the_murine_retina_/381849", "title"=>"Post-natal angiogenesis in the murine retina.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-11-16 00:30:49"}

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