Has anyone had a problem like this? It seem to appear during image fusion step. BigStitcher creates a black square in the middle of the image. I also stitched these tiles myself and the result didn’t show such an artifact.
This is the result from BigStitcher
This what I expect in terms of illumination
Could this be due to some sort of normalization?
The input data is uint16 and I also save it as uint16.
This is the fusion settings that I use
// fuse dataset, save as TIFF
run("Fuse dataset ...",
"select=/output/best_focus/Cyc002_Reg001_CH001/dataset.xml" +
" process_angle=[All angles]" +
" process_channel=[All channels]" +
" process_illumination=[All illuminations]" +
" process_tile=[All tiles]" +
" process_timepoint=[All Timepoints]" +
" bounding_box=[All Views]" +
" downsampling=1" +
" pixel_type=[16-bit unsigned integer]" +
" interpolation=[Linear Interpolation]" +
" image=[Precompute Image]" +
" interest_points_for_non_rigid=[-= Disable Non-Rigid =-]" +
" blend produce=[Each timepoint & channel]" +
" fused_image=[Save as (compressed) TIFF stacks]" +
" output_file_directory=/output/processed_images/Cyc002_Reg001_CH001");