  We develop a variational optimization method for crystal analysis in atomic
resolution images, which uses information from a 2D synchrosqueezed transform
(SST) as input. The synchrosqueezed transform is applied to extract initial
information from atomic crystal images: crystal defects, rotations and the
gradient of elastic deformation. The deformation gradient estimate is then
improved outside the identified defect region via a variational approach, to
obtain more robust results agreeing better with the physical constraints. The
variational model is optimized by a nonlinear projected conjugate gradient
method. Both examples of images from computer simulations and imaging
experiments are analyzed, with results demonstrating the effectiveness of the
proposed method.
