https://github.com/ucl/bernabeuinterface2014
MATLAB files implementing the vascular geometry reconstruction algorithm in Bernabeu et al. "Computer simulations reveal complex distribution of haemodynamic forces in a mouse retina model of angiogenesis" J. R. Soc. Interface 2014
https://github.com/ucl/bernabeuinterface2014
Last synced: 4 months ago
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MATLAB files implementing the vascular geometry reconstruction algorithm in Bernabeu et al. "Computer simulations reveal complex distribution of haemodynamic forces in a mouse retina model of angiogenesis" J. R. Soc. Interface 2014
- Host: GitHub
- URL: https://github.com/ucl/bernabeuinterface2014
- Owner: UCL
- License: lgpl-3.0
- Created: 2014-07-03T09:19:56.000Z (about 12 years ago)
- Default Branch: master
- Last Pushed: 2014-11-06T15:22:21.000Z (over 11 years ago)
- Last Synced: 2025-03-28T20:19:59.196Z (over 1 year ago)
- Language: Matlab
- Size: 43.5 MB
- Stars: 6
- Watchers: 4
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
BernabeuInterface2014
=====================
MATLAB files implementing the vascular geometry reconstruction algorithm in Bernabeu et al. "Computer simulations reveal complex distribution of haemodynamic forces in a mouse retina model of angiogenesis" J. R. Soc. Interface 2014.
Available scripts
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**SkelotonizeTiffPlexus.m** computes the skeleton (and associated radii) of a binary image of a vascular plexus. It opens a dialog box to choose a .tif image and generates a .mat to be consumed by ReconstructSurfaceFromSkeleton.m. Note that the repository doesn't currently include any .tif image due to their size. The processed .mat have been included instead.
**ReconstructSurfaceFromSkeleton.m** takes computed skeleton and radii of a vascular plexus and reconstructs a 3D model of the luminal surface of the vessels
**compile_VTP_writer.m** compiles the MEX files needed to use certain VTK functionality from MATLAB in ReconstructSurfaceFromSkeleton.m
**UsageExamples.m** example of usage of previous scripts.
Variables stored in the .mat file generated by SkelotonizeTiffPlexus.m
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**plexusImg** is the mask for the plexus.
**plexusBoundary** is the edge of the mask, from the bwboundaries function in MATLAB
**voronoiSkeleton** is the skeleton produced by the voronoiSkel function
**vertices** is the xy data for the voronoi vertices from the voronoiSkel function
**edges** is the index data defining which vertices are connected by each edge (from voronoiSkel).
**radii** is the distance from each voronoi vertex to the edge of the plexus (i.e. the radius of the maximum inscribed circle at that point), calculated with knnsearch
**radiiIndex** is the index of the nearest point on plexusBoundary to the vertex (not sure if you need this), from knnsearch
**skeleton** is the skeleton produced by postprocessing voronoiSkeleton with MATLAB's bwmorph function
**branchpoints** is the data for the branchpoints of the plexus, produced with the bwmorph function