converter for Olympus *.oib or *.oif image files?

Share icon

Tue, 10/25/2011 - 07:18 am

Hello! We are wondering if anyone out there has developed a routine for importing Olympus Fluoview image files into Igor. We like Igor more than Fluoview, and want to do the analysis there. The analysis part we can handle, but we don't know how to load the images in. Anybody have any insights?

Matthew Xu-Friedman

I have no experience with this file format, but a Google search did turn up a command line utility that claims to be able to read .oib files and write them as TIFF files. See https://bioimage.ucsb.edu/bisque/bioimage-convert

Igor can of course load TIFF files. I don't know how much metadata you'd be able to retain if you did it that way.

See https://www.wavemetrics.com/code-snippet/using-executescripttext-get-li… for a code snippet that gives an example of how to call a command line utility and get the text output back in Igor. In this case you would probably be saving as new files.

You might also be able to export your data as TIFF files from the Olympus software. I used the Zeiss LSM5, and I would export my images as TIFF files (usually one file per layer, not as a full Z stack in one file) and then load them into Igor to do analysis.

October 25, 2011 at 08:30 am - Permalink