Table of contents
- Description, p1
- Collaborations - image (...), p1
- Installation, p2
- Documentation, p3
- Tutorial, p4
- Measurements, p5
- References, p6
- Code, p6
Tutorial:
This sequence of analysis was conceived to explore some of the functionalities and the functioning of this toolset.
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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.
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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.
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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.
- 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.
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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.