Selective Plane Projection for Z-Stacks


Summary

Creates a 2D projection from a Z-stack by selectively choosing from which plane to extract each pixel based on a surface estimation.

Selective Plane Projection


Assumptions

The input image is composed of several z planes representing a cohesive tissue which can be approximated by a 3D surface. In order to exclude another surface from being also projected the latter has to have a lower intensity or at least a smaller number of high intensity points than the region of interest (ROI).


Main algorithm steps:

  1. 1st Surface estimation [1] using the highest intensities in the sample (1st quartile)
  2. Application of a cutoff distance to confine the ROI
  3. 2nd Surface estimation [1] using the highest intensities in the confined ROI
  4. Projection of the Z-Stack on a 2D plane using (3)

Output files in the Analysis/ folder

File Description
ProjIm.mat Matlab matrix file containing the projected image for each frame
Surface.mat Matlab matrix file containing the original z-plane index for each pixel in ProjIm.mat
vtk/gridfit_frame_###.vtk Surface files for every frame containing the coordinates of the 2nd gridFit estimation in ASCII format (1 grid point per line: x,y,z) (see CellSurface plugin for further usage) [ ! output added starting from version 2.1.5 ]

Parameters

Parameter: Smoothing Radius

Parameter: Surface Smoothness 1

Parameter: Cutoff distance

Parameter: Surface Smoothness 2


Debugging


References


Do you think these informations are not enough to help you? Drop a line to the author and he will extend this tutorial asap!
This page was written by Davide Heller on 10.11.15@17:40