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Morphology Reconstruction
This panel gives access to the parameters of the Morphology Visualization Toolbox. Note that visualization and reconstruction are used interchangebly in this context, where we draw a three-dimensional tubular skeleton from a morphology file that was originally segmented from an optical microscopy stack. The segmentation task could be implemented manually relying on a highly skilled operator or using semi-automated reconstruction methods. Unfortunately, and till now, fully automated segmentation methods are not yet available.
The current version of VessMorphoVis has support to reconstruct (or draw) vascular morphologies using there principal methods:
- Sections
- Segments
- Samples
If this mode is selected, the morphology will be drawn as a set of sections, or strands, where every section is visually represented by a polyline composed of multiple vertices and interpolated with a circular cross section using a bevel object.
If this mode is selected, the morphology will be drawn as a set of segments, where each segment is composed of two points (or vertices). This visualization method is helping when we need to analyze and verify the structure of a section, for instance to visualize its sampling rate or overlapping segments.
If this mode is selected, the morphology will be drawn as a set of spheres, where each sphere represents one sample or vertex in the morphology. Note that this method is only used to visualize the distribution of the samples in the morpholgy. However, it cannot be used for large datasets.
- Default (Single Color)
- Alternate Coloring
- Short Sections
- Section Length
- Section Surface Area
- Section Volume
- Number of Samples
- Section Index
- Default (Single Color)
- Alternate Coloring
- Segment Length
- Segment Surface Area
- Segment Volume
- Segment Index
- Segment Alignment
The current version of vessMorphoVis supports 16 different colormaps and their inverted ones including the following ones:
- GNU Plot
- Gnu Plot 2
- Rainbow
- Jet
- Turbo
- Magma
- Virvidis
- Plasma
- Blues
- Reds
- Greens
- Spectral
- Terrain
- Tab 10
- Dark 2
- Gray Scale
These colormaps are derived from matplotlib
.
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