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GUI-Independent projection module from EpiTools

this repository contains the projection module from EpiTools-Matlab (/src/src_analysis/module_projection) with all the GUI dependencies removed.

The main projection function can be found in createProjection.m which calls the surface estimation routine gridfit.m from John D'Errico.

To know more about the projection routine check out our wiki page: epitools.github.io/wiki/Analysis_Modules/00_projection/ or the epitools article http://dx.doi.org/10.1016/j.devcel.2015.12.012

example execution

% @SmoothingRadius - gaussian blur to apply before estimating the surface [0.1 - 5]
s = 0.2;
% @depthThreshold - Cutoff distance in z-planes from the 1st estimated surface [1 - 3]
d = 2;
% @SurfSmoothness1 - Surface smoothness for 1st gridFit(c) estimation, the smaller the smoother [30 - 100]
ss1 = 50;
% @SurfSmoothness1 - Surface smoothness for 3nd gridFit(c) estimation, the smaller the smoother [20 - 50]
ss2 = 20;
% @ShowProcess - Boolean to output intermediate results
v = 0;

[ProjIm,DepthMap,xg2,yg2,zg2] = createProjection(time_point,s,d,ss1,ss2,v);

The complete example can be found in _Run_createProjection.m which uses mij.jar to interface with imageJ to load the test image test_image.tif.

Optionally the estimated surface can also be exported as VTK file using the included library vtkwrite.m or as x,y,z coordinate cloud like in the included gridfit_surface.vtk.