I’m trying to use Ashlar to stitch together an ome-tif. BigStitcher in Fiji successfully aligns the tiles in my file but, Ashlar is outputting a strange, seemingly incomplete product.
I am starting with a czi file and use bftools to convert it to an ome-tif.
bfconvert -option zeissczi.autostitch false input.czi output.ome.tif
I get the same result if I use bioformats importer/exporter in Fiji.
I am running macOS 10.15.5. I installed pyfftw with conda as recommended on the github page.
I get the exact same result with my image if I run it through Ashlar in the docker container (see the Dockerfile on the github page).
Does anyone have any clue what is going on?