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Olympus OIR format

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Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

Olympus OIR format

Postby Lachie » Mon Oct 26, 2015 4:01 am

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
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Re: Olympus OIR format

Postby sbesson » Mon Oct 26, 2015 3:21 pm

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
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Re: Olympus OIR format

Postby Lachie » Tue Oct 27, 2015 12:15 am

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
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Re: Olympus OIR format

Postby sbesson » Tue Oct 27, 2015 12:41 pm

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
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Re: Olympus OIR format

Postby labriedion » Fri Feb 05, 2016 4:48 pm

Hi,

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

Thanks!
Étienne
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Re: Olympus OIR format

Postby sbesson » Mon Feb 08, 2016 11:18 am

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
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Re: Olympus OIR format

Postby Lachie » Wed Feb 17, 2016 11:22 pm

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
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Re: Olympus OIR format

Postby Lachie » Tue Apr 19, 2016 12:51 am

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.
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Re: Olympus OIR format

Postby jmoore » Tue Apr 19, 2016 7:57 pm

Updated the ticket with your link, Lachie. Thanks.
~Josh.
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Re: Olympus OIR format

Postby sbesson » Tue May 09, 2017 12:02 pm

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