Re: Stitching in batch

Posted by jmatthews on Feb 22, 2017; 5:11pm
URL: http://imagej.273.s1.nabble.com/Stitching-in-batch-tp5017365p5018168.html

I am trying to do the same thing as the OP. I have a folder of png files that I want to stitch together in batch. The files are 99 fields of view from each well of a 96-well plate.
My file name format is {xx}f{yy}.png where xx = well number (01 - 96) and yy = field of view.
I have recorded a macro for the stitching of a single well, and subsequent resizing and saving of a tiff output, but I am having a hard time figuring out how to modify it so it will stitch the entire set of 96 well x 99 FOV into 96 well images, as the OP was trying to do.
I'm sure this is relatively simple but this is my first foray into batch processing in ImageJ so any help would be greatly appreciated. Thanks.

Macro to date:

run("Grid/Collection stitching", "type=[Grid: row-by-row] order=[Right & Down]
grid_size_x=9 grid_size_y=11 tile_overlap=2
first_file_index_i=1
directory=[F:\\13-02-16-Acinar-Day0 BF__2017-02-13T16_16_18-Measurement2\\Stitching\\Objects]
file_names=r01c01f{ii}.png
output_textfile_name=TileConfiguration.txt
fusion_method=[Linear Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50 absolute_displacement_threshold=3.50
computation_parameters=[Save computation time (but use more RAM)] image_output=[Fuse and display]");
run("Size...", "width=2000 height=1840 constrain average interpolation=Bilinear");
saveAs("Tiff", "F:\\13-02-16-Acinar-Day0 BF__2017-02-13T16_16_18-Measurement2\\Stitching\\Objects\\Stitched Images\\r01c01.tif");
close();