Skeleton only

Only takes care of the cells contour, doesn't take into account the junction network

Signed-off-by: sebherbert <sherbert@pasteur.fr>

Overwrites and gets rid of the contourPo2D for the cellContour2D

adapted fields of the dataCells variable to match the later requirements.
Improved the output readability of the cell2face function

dataSeg.cellIdx replaces dataSeg.numbers

Elevation map input function is now a pure imread()
Fixes warning: "Warning: TIFF library warning - 'TIFFReadDirectory:  Unknown field with tag50838 (0xc696) encountered.'"

Currently only runs until the findContour line

Error introduced in commit 46c3e745 about parallelization

GUI was made with the app designer of MATLAB R2019a (or R2017a for the temp version).
It has not been tested again under Ubuntu because of freezing issues when interacting with the GUI. Mathworks has been contacted

Signed-off-by: sebherbert <sherbert@pasteur.fr>

improved speed but only by a marginal value (~20%)

Signed-off-by: sebherbert <sherbert@pasteur.fr>

Now accepts a 2D elevation map in .tif format (z is the height of the tissue)

Signed-off-by: sebherbert <sherbert@pasteur.fr>

Added the angular transformation of the ellipses to create a 3D orientation of the ellipses
Refactoring the code for new variable names easier to handle.
Last non nuclear commit!

Signed-off-by: sebherbert <sherbert@pasteur.fr>