I’m trying to perform a 3D reconstruction for serial sections using the Elastic Alignment and Montage plugin (http://imagej.net/Elastic_Alignment_and_Montage). What I’d like to do, is to apply the estimated transformations to another image stack consisting of masks that define the tissue regions in the actual images.
There appears to be a plugin called Transform Virtual Stack Slices (http://imagej.net/Transform_Virtual_Stack_Slices) which does this for transformations estimated and saved using Register Virtual Stack Slices (http://imagej.net/Register_Virtual_Stack_Slices). Is it possible to similarly somehow store and reapply the transformations in the case of Elastic Alignment and Montage plugin? If not, is it possible to circumvent the issue by storing the mask as some kind of separate channel (e.g. as an alpha channel), which does not influence the reconstruction process but still gets aligned along with the actual image?