# = "Output directory", style = "directory") dstFile # = "Input directory", style = "directory") srcFile So after inspection of the plugin jar I came up with the following based on the batch processing examples (you may simply ignore the string manipulation for the output destination). The Olympus plugin “Drag and drop” did that but the macro recorder did not unveil the details. oir file which spans over multiple physical files. oir, such as Zeiss or Nikon or Leica file formats.Īlthough the thread is already a bit dated I add my solution below as so far I could not find a solution in the forum or the cited locations. through Viewer, I discovered that the batch processing took an average of 54 seconds.
#Olympus viewer 3 batch processing upgrade
I feel this feature will be useful for other file formats as well, in addition to. So was yesterdays upgrade to Olympus Viewer 3 worth the effort. oir files in one go to TIFF files? Is there a macro feature or special button somewhere in ImageJ that I can press that will assist with the above procedure? Once converted it will take a few buttons to then set up the stitching procedure and get myself what I hope will be a really nice image.Īlternatively is there a stitch plugin with ImageJ that can stitch alternative file formats?
Once in TIFF format I go ahead with the stitch pluginsĪs it is a bit of a cumbersome procedure, is there anyway that I can ‘mass save’ or ‘mass convert’ or ‘batch save’ or ‘batch convert’ all of these. oir to TIFF before I can do any stitching and I do so via the ‘save as’ feature. However, I have to convert the files from. Now I want to stitch the files (as all 986 images are of one single sample) and it comes out really nicely with the ImageJ plugins when I did a test stitch with a few of the files. Eager to see how my images came out, I installed the Olympus plugin on ImageJ (technically I am running FIJI, version 1.51g) and was able to open the files and play around with them. Our institute got the chance to play around with a new Olympus confocal and I do not have access to their software. I hope someone will be able to help me with my question.įor my work I have 986 files that are in the.
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