Thanks for your response. I am using Fiji that updates frequently and contains the Bioformats plugin. Would the command-line tools be more useful? Essentially, my problem is that have .lif files from a Confocal Microscope that I want to bring into Amira. But, I am running into problems with this process. I have been bringing the .lif files into Fiji and converting them to .ome-tiff to be read in Amira for reconstruction analysis. The reconstructions appear fine when I open 3D surface in Fiji for the .lif file. But, when I save the file as .ome-tif, the Fiji reconstruction does not display any recognizable surface. In Amira, the surface appears significantly stretched in the z-axis, even though the voxel information is entered when the file is opened in Amira. When opening the ome-tiff file in Fiji, the voxel information is changed. But even if I go to properties and save the proper voxel information, the reconstruction with the one-tiff file is the same. I am unable to share the .lif or .ome-tif file on this forum, but I can try sending it to you through email.