This macro will manage images stitching IMSRC will generate black images with the proper size and will call image J plug-in for stitching. (S Preibisch, S Saalfeld, P Tomancak G. Bioinformatics 25 (11), 1463-1465).
The result will appear in the second scan acquisition folder.
This process can take long time depending of the amount of images to be processed.
- setBatchMode(true);
- dir = "#DIR#";
- inixgrid=#INIXGRID#;
- iniygrid=#INIYGRID#;
- size_xgrid=#SIZEXGRID#-#INIXGRID#+1;
- size_ygrid=#SIZEYGRID#-#INIYGRID#+1;
- run("Grid/Collection stitching", "type=[Filename defined position] order=[Defined by filename] grid_size_x="+size_xgrid+" grid_size_y="+size_ygrid+" tile_overlap=10 first_file_index_x="+inixgrid+" first_file_index_y="+iniygrid+" directory=["+dir+"] file_names=Field-X{xx}-Y{yy}.tif output_textfile_name=TileConfiguration.txt fusion_method=[Linear Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50 absolute_displacement_threshold=3.50 subpixel_accuracy computation_parameters=[Save memory (but be slower)] image_output=[Fuse and display]");
- saveAs("Tiff", "#tiffOutput#");
