I hope someone will be able to help me with my question.
For my work I have 986 files that are in the .oir (Olympus) format. Our institute got the chance to play around with a new Olympus confocal and I do not have access to their software. 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.
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. However, I have to convert the files from .oir to TIFF before I can do any stitching and I do so via the ‘save as’ feature.
Basically what I do is:
-Plugins --> Olympus viewer --> DragDrop
-I then Drag/Drop some .oir files in DragDrop box
-File --> Save as --> TIFF
-Once in TIFF format I go ahead with the stitch plugins
As 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 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.
Alternatively is there a stitch plugin with ImageJ that can stitch alternative file formats?
I feel this feature will be useful for other file formats as well, in addition to .oir, such as Zeiss or Nikon or Leica file formats.
Thank you for your help.