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Morphology Reconstruction

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Marwan Abdellah edited this page Oct 5, 2021 · 41 revisions

Morphology Visualization

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.

Morphology Visualization Methods


VessMorphoVis implements different algorithms for visualizing vascular networks. The outline of the morphology is sketched in (A) using thin polylines and tiny spheres to represent the sections and samples of the morphology respectively. In (B), the morphology is illustrated by a list of points showing only the individual samples without any connectivity. The morphology is visualized as a disconnected set of segments and sections using the same color in (C) and (F), with alternating colors in (D) and (G) and also using transparent shaders in (E) and (H) respectively.

The current version of VessMorphoVis has support to reconstruct (or draw) vascular morphologies using there principal methods:

  • Sections
  • Segments
  • Samples

Drawing Morphology using Sections

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.


Drawing the morphology as a set of individual sections, where each section is represented by a polyline.

Drawing Morphology using Segments

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.


Drawing the morphology as a set of individual segments, where each segment is composed of two points or vertices.

Drawing Morphology using Samples

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.


Drawing the morphology as a set of individual samples (or vertices), where each sample is represented by a sphere.

Morphology Color Coding Schemes

Color Coding Schemes for Sections

  • Default (Single Color)
  • Alternate Coloring
  • Short Sections
  • Section Length
  • Section Surface Area
  • Section Volume
  • Number of Samples
  • Section Index

Default Coloring


The default coloring scheme (Default) applied to a sample morphology.

Alternate Coloring


The alternating coloring scheme (Alternating Colors) applied to a sample morphology to easily visualize the different sections in the morphology.

Short Sections


The short sections coloring scheme (Short Sections) applied to a sample morphology to visualize the short sections in the morphology in a different colors to be able to easily spot them. A short sections is defined to be a section where its length is shorter than the sum of the radii of its two terminal samples.

Color-coding based on Section Length

                 

Color-coding the sections of a sample morphology skeleton based on the length of the sections in the morphology. Note that the colormap is drawn as a linear list of colors and the range of each element in the colormap.

Color-coding based on Section Surface Area


Color-coding the sections of a sample morphology skeleton based on the surface area of the section in the morphology.

Color-coding based on Section Volume


Color-coding the sections of a sample morphology skeleton based on the volume of the section in the morphology.

Color-coding based on Number of Samples in the Section

                 

Color-coding the sections of a sample morphology skeleton based on the number of samples of the sections in the morphology. Note that the colormap is drawn as a linear list of colors and the range of each element in the colormap.

Color-coding based on Section Index

                 

Color-coding the sections of a sample morphology skeleton based on the number of indices of the sections in the morphology. Note that the colormap is drawn as a linear list of colors and the range of each element in the colormap.

Color Coding Schemes for Segments

  • Default (Single Color)
  • Alternate Coloring
  • Segment Length
  • Segment Surface Area
  • Segment Volume
  • Segment Index
  • Segment Alignment

Default Coloring


The default coloring scheme (Default) applied to a sample morphology.

Alternate Coloring


The alternating coloring scheme (Alternating Colors) applied to a sample morphology to easily visualize the different segments in the morphology.

Color-coding based on Segment Length


Color-coding the segments of a sample morphology skeleton based on the length of the segment in the morphology.

Color-coding based on Segment Surface Area


Color-coding the segments of a sample morphology skeleton based on the surface area of the segment in the morphology.

Color-coding based on Segment Volume


Color-coding the segments of a sample morphology skeleton based on the volume of the segment in the morphology.

Color-coding based on Segment Index

                 

Color-coding the segments of a sample morphology skeleton based on the number of indices of the segments in the morphology. Note that the colormap is drawn as a linear list of colors and the range of each element in the colormap.

Color-coding based on Segment Alignment with respect to XYZ coordinates

                 

Color-coding the segments of a sample morphology skeleton based on their alignment with respect to the XYZ coordinates.

Color Maps

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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