Im using the BigStitcher-Plugin in Fiji to stitch a mouse embryo imaged using light sheet microscopy. The tissue was recorded from two angels (0° and 180°). After successfully stitching tiles, I am having problems fusing the images acquired from the two different angles. If one compares the two images, they overlap completely in some parts (anterior part of the embryo) but others seem elongated (posterior part of the embryo). After fusing, the final stack is created as an average of the two images. This is particularly problematic in those parts, which do not align perfectly because the average then looks blury and has a halo effect.
To overcome this, I would rather like to chose the anterior part of the image from angle1 and the posterior part of the image acquired from angle2. In this way, I am hoping to fuse the high resolution parts of both images.
Is there a way to select/delete parts of the image along the z axis of the image stack? Or is it possible to deactivate one part of the image, let both overlap in the middle and switch to the other angle at the end of the image?
Thanks a lot in advance for any suggestions on this.