Olympus .oib Files Metadata


has anybody has any luck getting .oib files to load into the new v2.1? I can get it to read the file and get some metadata, but not get it quite right. It sees that there are three channels, as the SizeC is 3, but it doesn’t have any option that shows each channel number. Are there any special ways to split the channels out for analysis?

Also it shows the color format as Planar, and then after screwing around with ColorToGrey and GreyToColor and coming back it shows it as Monochrome. Any ideas if that means something?

Thanks in advance for your time.


Hi Neil,

I’ve confirmed this behavior for 2.1. However, the image reader schema has been overhauled a bit for the upcoming 2.1.1 patch, which I confirmed will show the proper information for .oib files. If you want a sneak preview, you can download the trunk build page (subject to the caveats therein).; 2.1.1 is our patch release candidate.


Thanks Mark, you’re a diamond!
When might we see the 2.1.1 patch? If it’s not too long I can hold off on playing with the trunk build…


I’d say within the next month; we’re finalizing code fixes now.

Hi Mark, I’m not sure where to correctly report this bug, but I noticed a problem with the smooth function in the release candidate I just installed (attached).


after playing with the Smooth functions, it appears that all of my EnhanceEdges functions are screwed up with the same effect too (not using the output of the smooth of course; Smooth input: chn2, Smooth output; chn2_smth; EnhanceEdges input: chn2).

restarting CP and reloading project fixes the issue.

It appears that after hitting Run in test mode the smooth function went funny again (see attached). Also, see attached project.
myocytes.cpproj (826 KB)

Would you be able to zip up and post the .oib file as well?