1. A computer-implemented method for determining a first quantification of a deformation of a sample, said method implemented using a computing device in communication with a memory, said method comprising: receiving, by the computing device, a first image of the sample, the first image comprising a two dimensional image, a three dimensional image, or a paired stereo image comprising a camera 1 image obtained by a first camera and a camera 2 image obtained by a second camera; receiving, by the computing device, a second image of the sample, the second image comprising a two dimensional image, a three dimensional image, or a paired stereo image comprising a camera 1 image obtained by a first camera and a camera 2 image obtained by a second camera; registering the first image to the second image using a warping function, wherein the warping function maps a plurality of pixels in the first image to a plurality of pixels in the second image and the warping function is selected from the group consisting of: [ 1 + p 1 p 3 p 5 p 2 1 + p 4 p 6 0 0 1 ] if the first and second images are two dimensional images, wherein p 1 , p 2 , p 3 , p 4 , p 5 , and p 6 are warping parameters; p s is a translation in the x direction; and p 6 is a translation in the y direction; [ ( 1 + p 1 ) p 4 p 7 p 10 p 2 ( 1 + p 5 ) p 8 p 11 p 3 p 6 ( 1 + p 9 ) p 12 0 0 0 1 ] if the first and second images are three dimensional images, wherein p 1 , p 2 , p 3 , p 4 , p 5 , p 6 , p 7 , p 8 , p 9 , p 10 , p 11 , and p 12 , are warping parameters; p 10 is a translation in the x direction; p 11 is a translation in the y direction; and p 12 is a translation in the z direction; and a first warping function W 1 (x; p) for the camera 1 image and a second warping function W 2 (x; p) for the camera 2 image if the first and second images are paired stereo images, W 1 (x; p) and W 2 (x; p) comprising W 1 ⁡ ( x ; p ) = [. .. T i , x. R i. T i , y. .. T i , x ] ⁢ Λ i ⁢ C i ⁢ R 1 ⁢ p ⁢ K 2 ⁡ [ X 2 Y 2 1 ] + T 1 ⁢ p ; and W 2 ⁡ ( x ; p ) = [. .. T i , x. R i. T i , y. .. T i , x ] ⁢ Λ i ⁢ C i ⁢ R 1 ⁢ p T ⁢ R 12 ⁢ K 1 ⁡ [ X 1 Y 1 1 ] + T 1 ⁢ p + T 12 , where: x is a 3D position within a world coordinate system; p is a set of shared warp parameters; [. .. T i , x. R i. T i , y. .. T i , x ] is a matrix containing a rotation matrix R i and a translation vector [ T i , x T i , y T i , x ] describing a translation and rotation from each first paired stereo image to each second paired stereo image; Λ i is any deformation tensor, scalar, or vector describing a deformation from each first paired stereo image to each second paired stereo image; C i is a normalization factor relating a normalized coordinate system to a world coordinate system; R 1p is a 3D rotation matrix describing a rotation from the world coordinate system to a coordinate system of the first camera; R 12 is a 3D rotation matrix describing a rotation from the coordinate system of the first camera to a coordinate system of the second camera; K 1 and K 2 are calibrations for the first camera and the second camera respectively; [ X 1 Y 1 1 ] ⁢ ⁢ and ⁢ [ X 2 Y 2 1 ] are positions within the coordinate systems of the first camera and the second camera, respectively; T 1p is a 3D translation matrix describing a translation from the world coordinate system to the coordinate system of the first camera; and T 12 is a 3D translation matrix describing a translation from the coordinate system of the first camera to the coordinate system of the second camera; determining a first deformation gradient tensor for the sample based on the warping function, the first deformation gradient tensor including at least a portion of the warping function, wherein the first deformation gradient tensor is selected from the group consisting of: [ 1 + p 1 p 3 p 2 1 + p 4 ] if the first and second images are two dimensional images; [ ( 1 + p 1 ) p 4 p 7 p 2 ( 1 + p 5 ) p 8 p 3 p 6 ( 1 + p 9 ) ] if the first and second images are three dimensional images; and Λ i if the first and second images are paired stereo images; and determining the first quantification of the deformation of the sample based at least in part on the first deformation gradient tensor.