3D Motion Analysis of Embryos acquired with Lightsheet Microscopy (Unpublished, work in progress)

Python 2.7 (only the print functionality)
RealTITracker (3D optical flow), http://bsenneville.free.fr/RealTITracker/
SIFT3D, https://github.com/bbrister/SIFT3D.git (3D feature-based registration)
Mayavi
Matlab (rigid/similarity + nonrigid registration)
czifile
tifffile

[x] 3D rigid/similarity + nonrigid alignment using MATLAB registration toolbox

• this removes growth/translation + surface deformation artifacts to create fixed geometrical reference shape for unwrapping

[x] 3D optical flow estimation of cellular motion patterns following alignment (Requires RTTtracker Scripts)
[x] 3D segmentation of embryos using thresholding
[x] 3D tracks
[x] 3D->2D unwrapping module: given an embryo, automatically transform to surface cartesian or distal polar coordinates and unwrap the surface. Intensity is projected based on either local maximum surface depth projection or pullback.