Open Microscopy Environment

Hi All,

Apparently Olympus have come out with a new file format for their multi-photon microscope, the OIR format.
Trying to open with bioformats results in an "Unknown file format" error (perhaps unsurprisingly as it doesn't appear on the supported file type lists, I just thought it was worth a shot).

I'm just wondering if this filetype is being worked on, I can provide an example image if needed.

Thanks,
-Lachie

Hi Lachie,

looking at our Trac history, we currently do not have any ticket to add support for the new Olympus OIR format. I can create a new one if you want and add you to the cc list if you wish. Providing us with a sample file for this new format would be ideal. You can do so by uploading it at http://qa.openmicroscopy.org.uk/qa/upload/.

Best regards,
Sebastien

Hi Sebastien,

Thanks for the feedback. I've uploaded a file via that link, ID 16871.

Please do keep me informed of any progress.

Thanks again,
-Lachie

Thanks for the file upload,

I have created a ticket to capture this support request. Let me know if you want to be cc'ed on the ticket and if so which email address should be used.

Best regards,
Sebastien

Hi,

I also have this issue with reading oir files. Do you have an idea of the progress of this ticket?

Thanks!
Étienne

Hi Étienne,

thanks for uploading additional sample OIR files, I have linked them to the original ticket.

Regarding the support request, as we explained in our most recent blog post the work for Bio-Formats 5.2.0 is primarily aimed at upgrading our Data Model to improve the ROI usability.

This implies we will not be adding any ​more readers other than those currently scheduled to Bio-Formats 5.2.0 and the ticket mentioned currently remains unscheduled. If anyone in the community has the expertise to help with the development of this reader, we welcome their input via GitHub - some docs are available to write new format readers and contributing to Bio-Formats.

Best regards,
Sebastien

Just thought I'd add to this some new info in case it helps anyone.

The newest version of Imaris can read oir files. I'm aware that they aren't an open source option, but if you have access to it you can at least open your files and convert them to tif (though not using their batch converter unfortunately).

Thanks.
-Lachie

Sorry for bumping this thread again but in case it helps anyone, there is an Olympus plugin for imageJ that will allow reading of oir files. http://imagej.net/OlympusImageJPlugin

It has its downsides (it's not particularly compatible with the imageJ macro language for one), but at least it opens them. For the record I'd still love to see oirs supported in bioformats and omero but I'm aware it may not be a priority right now.

Updated the ticket with your link, Lachie. Thanks.
~Josh.

Thanks for all the input. Olympus OIR is now supported by Bio-Formats since the 5.5.0 release.