Uploading .JP2 files through Bio-formats extension results in blue tinged images?

I’am currently using the MBF Bioscience stereological microscope to analyze H&E stained slides and take scans of them as .JP2 files (I cannot save them in any other file format). As such, I can only open these .JP2 files through the Bio-Formats Importer, however when I do so they come up with a blue tinge as you can see here: .

I suspected that it may be the way the microscope program saves the files however whenever I open up the .JP2 file on the microscope’s computer program (MBF biosciences) there is no blue tinge and looks just as I scanned it -an H&E stain with a white background.

Any suggestions for why this might be and how I could fix it or recommendations for software/programs that open up .JP2 files and allow or conversion to other file types would be much appreciated!

Hi @Rania, what Color Mode are you using in the Bio-Formats Importer. If you select Composite mode does the image display as expected? If not would you be able to upload the file to https://www.openmicroscopy.org/qa2/qa/upload/ for testing?

Hello @dgault, I have tried out the colour modes, both composite and default result in the same blue tinged image as you see above, unfortunately. Sounds great, I will upload the image for testing . Thank you!

Hi Rania

I opened the file using preview on Mac and the image looks exactly like the one in the screenshot you posted.
It does not seen to be a problem with Bio-Formats but more likely how the file was saved

Cheers
jmarie

Hello JMarie,

Thank you for clarifying this, I had suspected that it was in the file saving process but was not too sure.

In this case, to further clarify -I am currently using the MBF Biosciences microscope and software to image my H&E stain histology slides and thus save them before transferring images to be opened up on imageJ.

I am not sure if you are familiar with the program or have seen this problem before but if you have any recommendations on potential solutions I would greatly appreciate any ideas!

Thank you.

Cheers,

Rania

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Hi Rania

I am not familiar with the program and we do not have access to such microscope in our facility.
Will the vendor able to help?

Cheers
Jmarie

Hello Jmarie,

I have been in touch with the vendor of the microscope and have ran through a couple sessions with them on the processes I use to obtain the .JP2 files, which is has been found to be done properly.

When the vendor opened the .JP2 files on their own Fiji application via Bioformats Importer Plug-In, they too obtained a blue tinged image. We think it might be because the Bioformats Importer plug-in may be making certain assumptions it shouldnt make in
the process of importing the .JP2 files onto Fiji. Do you know if there are settings/parameters for the Bioformats Importer Plug-in that I can access and change?

Cheers,

Rania

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Unlike @j.burel I am not on a Mac. I tried using the OpenJPEG-based opj_decompress to decompress your image to PNG. (This is also what ffmpeg uses.) When I view that it is still very blue in every viewer I try, just as you show above. Certainly this “blue” interpretation of the file isn’t particular to Bio-Formats or to the Mac. Aside from the vendor’s proprietary software is there some standard reference viewer that does show your *.jp2 file as you expect? Maybe we can find out from that what the difference is. Does the vendor believe they’ve encoded some color information in a standard way that’s being ignored?

Hello @mtbc,

Unfortunately I havent been able to find any software aside from the vendor’s that does show the .jp2 file as expected. When I was in contact with the vendor, they did mention that it seems like certain assumptions might be made by the Bioformats plugin and other .jp2 file viewing software that might be causing the resulting image, however what these assumptions are I’am not sure.

It sounds as if certain assumptions might be being made by the vendor’s software but nobody else’s. :smiley: Can you provide a screenshot from that software of what the slide is expected to look like?

I tried adjusting the rendering settings in OMERO (switching the red and blue channels and boosting the levels a bit) but I don’t know if this is much of an improvement.

You say you can only save from the microscope as JP2, but is there an option in any other viewer software (where it looks correct) to export as any other format?

Will

Having looked briefly at some documentation, MBF internally uses a extended variant of the JP2 file format - see for example here or this image.sc thread.

As mentioned here, one of the drawbacks is the potential lack of compatibility with third-party applications. This seems to be the case for openjpeg and is certainly the case for Bio-Formats which is driven by community submissions as we had received no sample files representative of this extended format so far.

As discussed in OME’s position regarding file formats, the responsibility of adding support for new file formats or new variant file formats can no longer fall exclusively on academically funded projects. We have multiple example of successful partnerships with vendors that delivered improved imaging support for the entire bioimaging community and we would welcome another such interaction.

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Aha, thank you @s.besson for the detective work, that third link’s note about " MBF JPEG2000" does rather suggest that their *.jp2 files may be a variant that doesn’t open in some third-party applications. It would be great if MBF could extend Bio-Formats (we could advise and review) to extract their “additional information” or if they could simply offer a compliant OME-TIFF export too, that should allow to control color, preserve much metadata, etc.

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I’ve sent MBF’s support the URL link of this thread.

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