Issue with Imagej Grid Stitching Image Output


I am getting different image outputs depending on whether or not I select “Fuse and Display” or “Write to Harddrive” options when using Grid Stitching in Fiji.

I am trying to fuse a number of image stacks based off xyz coordinates specified in a Log.registered text file. I am using virtual stacks when fusing. All Grid Stitching parameters are the same except for the image outputs.

When I run the fusion with the “Fuse and Display” option, the inserted stacks appear normal as shown below:

But when I run the fusion with the “Write to Harddrive” option, I get unusual blocking and a different placement of the stacks as seen below.

If anyone knows what might be causing this, please let me know.