apply an affine matrix to the data in the viewer on the fly #89
Description
When the brain is cut into slices, the tissue gets slightly deformed. So, usually, researchers either do an MRI scan preceding the cutting so that there would be an MRI reference volume, or they would take a picture of the remaining tissue before every single cut, and use these so called blockface images to reconstruct a 3D reference volume.
The cut sections are then registered to the reference volume (best: MRI; blockface also possible) in order to align the slices with each other.
Output: for each section, there will be a 2D affine transformation matrix (including everything from rotation, stretch, shear, translation... everything)
Can we deal with that in the viewer? How can we add an affine matrix to the viewer? So that we can keep track of all transformations, adding up affine matrices, and just apply them to the slice in viewer!
OpenSeadragon has slider to rotate the image --> that could be an option!! :)