REVISITED: flattening a layer from z-stacks of thick uneven tissue

[Mark Krebs]

Hi All,

I'm still trying to "flatten" a layer of cell nuclei from a deconvoluted,
confocal z-stack of a thick uneven tissue.  The problem is not out-of-
plane fluorescence, but rather that the tissue is slightly curved and
bumpy in places, and therefore does not lie parallel to the slices of the
z-stack.  In most slices, nuclei of interest are flanked by nuclei from
other layers.  

https://list.nih.gov/cgi-bin/wa?A1=ind0910&L=imagej#55

I thought it might be possible to define a surface that could be used to
capture pixels defining the layer of nuclei.  Using the PointPicker plugin
on the z-stack, I collected xyz points in the layer of interest (data at
the end of this message).  Now I would like to fit a surface to these
points and use that surface to collect the corresponding layer from the z-
stack.  Once the layer is isolated, z projection can be used to flatten
the layer.

I haven't yet found a solution among the many excellent plugins for
ImageJ.  Any ideas?

I've tried exporting the xyz points to SigmaPlot10 for fitting with a
limited number of 3D curves, but these have been inadequate.  I think I
need a 3D spline curve to fit the data smoothly.  Alternatively, a Voronoi
diagram in 3D may work.  Does the Delaunay Voronoi plugin in Fiji work on
3D data, and can it be used to generate a surface?

http://pacific.mpi-cbg.de/wiki/index.php/Delaunay_Voronoi

Thanks for any help.

Cheers,
Mark

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