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Angiogenesis Analyzer for ImageJ

Saturday 20 October 2012, by Gilles Carpentier

  Table of contents  

 Tutorial:


This sequence of analysis was conceived to explore some of the functionalities and the functioning of this toolset.
  • Analyze the demo images with the default settings

    • Download a demo image of HUVEC acquired in phase contrast. Then save the image in a well identified folder.
    • Launch the analysis The next picture (zoomable slide show) shows the results : green = branches; cyan = twigs; magenta = segments; orange = master segments; blue sky = meshes ; red surrounded by blue = nodes surrounded by junctions symbol; junctions surrounded by red = master junctions; blue = isolated elements; cyan = small isolated elements ; red surrounded by yellow = extremities. See "Documentation" section for more informations about these elements.
      Below: phase contrast analysis - slide show:
      HUCEV cells network - initial image HUVEC cells network analyzed
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  • Explore documents available for a single image analysis at the "segment level"

    • Set parameters to make a basic network analysis. This settings will return analysis at the "segments and junction level". 3 iterations of the pruning will be performed. In the settings dialog box, unchek the "Remove small master segments" and the "Analyze master tree" options, and select "Show maps of elements (single analysis)".
    • Start the analysis of the phase contrast demo image. You will obtain all analysis documents (overlay of elements, binary maps of elements, etc...) available for a single analysis. The slide show below, shows the resulting images; binary map of extremities, nodes, final binary pruned tree, and elements of network. With these options, the segments (magenta on the last slide) are peaces of tree with a junction at their extremities, regardless the elements connected by these junctions (branch or segment). Note that the meshes (blue sky) bypasses the branches (slide 5) in the below slide show.
      Below, binary elements, segments and junctions analysis - slide-show:
      HUVEC cells network - initial image HUVEC cell network - map of nodes of binary tree HUVEC cell network - final binary tree HUVEC cell network - final tree analysis
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  • Explore documents available for a single image analysis at the "master segment level"

    • Start the analysis of the phase contrast demo image.
    • Set parameters with the "Analyze master tree" option. From the previous settings, check the "Analyze master tree" option. Here again you will obtain all analysis documents (overlay of elements, binary maps of elements, etc...) available for a single analysis. Some new maps, show master junctions and master tree composed from master segments. See the "Documentation" section for the definition of these elements. Master segments are in yellow-orange, and master junction are junctions surrounded by a red selection (last slide) in the following slide show.
      • Note that the meshes (blue sky) now ignore the branches.
      • Note that some junctions are too close to correspond to a real junction at the cellular tube scale.
        Below: binary elements, master segments and master junctions analysis - slide-show:
        HUVEC cell network - initial image HUVEC cell network - map of extremities HUVEC cell network - map of nodes HUVEC cell network - map of master segments HUVEC cell network - master tree HUVEC cell network - final tree HUVEC cell network - final analysis with master segments and master junctions
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    • Fuse the close master junctions. Return to the defaults settings; check "Remove small master segments" and deselect "Show maps of elements (single analysis)". Then start the analysis of the phase contrast demo image as previously. The next slide show, compares results with and without the "Remove small master segments" option used.
      Below: small master segment removal - slide-show:
      HUVEC cell network - final analysis with master segments and master junctions HUVEC cell network with fused too close master junctions
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  • Get some custom map elements"

    Map of some elements can be convenient for presentation or further analysis.

    • Start the analysis of the phase contrast demo image as previously.
    • Select the "Get Maps of Selections" function from the "Tuning Functions menu tool" and check functions as follows. Below, the obtained map.
logoij ImageJ (http://rsb.info.nih.gov/ij/) is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.1 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux. The author, Wayne Rasband (wayne@codon.nih.gov), is at the Research Services Branch, National Institute of Mental Health, Bethesda, Maryland, USA.
Gilles Carpentier, Faculte des Sciences et Technologie,
Universite Paris Est Creteil Val-de-Marne, France.

Special thanks to Alessandra Albano for the English correction of these sites.
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