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ComplexOrganizationOfLivingMatter / Epithelia3D

"Scutoids are a geometrical solution to three-dimensional packing of epithelia" - https://www.nature.com/articles/s41467-018-05376-1.
https://www.scutoids.es/
GNU General Public License v3.0
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how to create scutoids shape #1

Open leeleolay opened 2 years ago

leeleolay commented 2 years ago

hi, I have read some codes and test some codes such as pipeline in the directory InSilicoModels/TubularModel/. by these codes, i can achieve voronoi diagram in different plane between apical and basal surface. But I can't create tubular 3d model. I don't which code could achieve this function and how to extract a cell model from tubular model. could you give me some suggestion about this problem or point out which scripts could achieve this target?

pedgomgal1 commented 2 years ago

Hi @leeleolay, you could develop an interpolation between the different cell apico-basal slices. You must correlate the 2D planar coordinates to 3D ones, and then use "alphaShape" in Matlab to join each slice.

We did it into the function -> create3DCylinder.m _

Epithelia3D -> correlationMain.m -> correlationVolumeAreaSidesSurfaceRatio.m -> create3DCylinder.m

_

In case your RAM memory is not too high, you must use a reductionFactor>1 to get your tube with a lower resolution.

Moreover, at this moment I am working on developing a 3D .stl/.ply model directly. This is a new project that will be hosted in "https://github.com/ComplexOrganizationOfLivingMatter/StructuralAnalysis". I do not know when I would finish. If you have any specific doubt, write me -> pgomez-ibis@us.es.