Re: Grid Stitching - Can't OK image selection when >50 Images to stitch

Posted by asullivan on Apr 13, 2017; 10:05pm
URL: http://imagej.273.s1.nabble.com/Grid-Stitching-Can-t-OK-image-selection-when-50-Images-to-stitch-tp5018541p5018544.html

Thanks Mike,

I wonder what operating system you use?  I'm using Windows 10 and for me it doesn't matter if I use sequential or unknown.  I don't see a difference in the popup window when choosing either option. I'm still stuck not being able to process all my images. I don't know if a Mac or Linux box would make things different.  My screen resolution is 1920x1080 BTW.

As to separating them out. I find when stitching together nearly 300 images it becomes very tedious.  I then need to break down the images into folders of 40-50 with overlap, run  Grid Stitching on each folder, then run the folder with the stitched images (pairwise works better if I don't have enough overlap, but much slower). And then do that again for another 20 data-sets.  It's what I have been doing, but I was hoping for a better solution.

I recorded a macro for Grid Stitching using only 10 images as the basis of my macro.  

The recorded macro looked like this:

run("Grid/Collection stitching", "type=[Unknown position] order=[All files in directory] directory=[D:\\Users\\Aaron\\UCSF\\Pancreas 7665\\Fused Pics - Copy] confirm_files output_textfile_name=TileConfiguration.txt fusion_method=[Linear Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50 absolute_displacement_threshold=3.50 ignore_z_stage display_fusion computation_parameters=[Save computation time (but use more RAM)] image_output=[Fuse and display] fused_001_to_050.tif fused_051_to_100.tif fused_090_to_110.tif fused_101_to_150.tif fused_140_to_160.tif fused_151_to_200.tif fused_190_to_220.tif fused_201_to_250.tif fused_240_to_260.tif fused_251_to_289.tif");

saveAs("Tiff", "D:\\Users\\Aaron\\UCSF\\Pancreas 7665\\Fused Pics - Copy\\Fused_test.tif");

Then I created variables for both the file path (inDir) and the file names (str) and used them to replace the appropriate areas in the recorded macro.  The file path variable (inDir) seems to input correctly, but the image names (str) are not being counted as selected and the Stitching plugin is generating the error in my first post.

Thanks for your help again.

Aaron