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Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
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LIF: Incorrect channel colours #3655

Open dgault opened 3 years ago

dgault commented 3 years ago

Issue was raised on forum thread https://forum.image.sc/t/bioformats-and-lif-files/46700/5 A sample file has been provided which reproduces the issue. The file Images for James - RGB and BGR.lif has 2 series, one which appears to be RGB and the other BGR, interleaved. This mixture of RGB vs BGR may be the issue, however further debugging is needed to identify the root cause of the problem.

imagesc-bot commented 3 years ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/bioformats-and-lif-files/46700/10

XLEFReaderForBioformats commented 1 year ago

hi @dgault, I'm currently working on this issue and I have a more general question, I hope it's okay that I use the thread of this issue for this discussion. If not, please let me know which place would be better.

In the past, we've briefly discussed the idea that I adapt the LIFReader so it can be included in our LMSMetadata package. In the long term, having the LIFReader in our metadata package that also includes XLEF and LOF reader, we could save a lot of time for bug fixes (especially for the metadata issues).

So I did this locally and created a LIFReader2 from LIFReader that uses our classes. But it would be essential to have this LIFReader2 thoroughly tested.

What are your thoughts on this? Is it realistic to test and integrate this adapted LIFReader for one of the next upcoming releases? And what kind of commit would you prefer? Should I adapt the LIFReader directly or rather go with the LIFReader2? (though I'm not sure how to officially handle these two readers then, I locally adapted LIFReader.isThisType() and the readers.txt so the LIFReader2 is always used instead of LIFReader)

happy to hear your thoughts!

dgault commented 1 year ago

Hi @XLEFReaderForBioformats, long term that would be great to have a new LIFReader that is easier to maintain and update. The initial testing and switch over to the new reader though is likely to a large effort and there is a possibility that it will cause test failures with some of the legacy sample files that we have in our test repository.

One possible solution for this that we have used in the past is to create a DelegateReader which would allow both readers simultaneously and the users can select between the current reader LIFReader and a new LIFReader2 (naming to decided later, perhaps LeciaLIFReader?). This would be the quickest way for us to release the new reader, enabling users to access any new fixes in the new LIFReader2 while ensuring that we still have backwards compatibility and not breaking any existing functionality. It would then give us more time to further test the new reader and have confidence in transitioning fully to the new reader.

If that sounds like a potential solution then and I would suggest going ahead and opening a PR with the new reader, I will then follow up to add the suggested DelegateReader.

XLEFReaderForBioformats commented 1 year ago

hi @dgault , thanks for your message. I think this sounds like a good solution! Then I will continue working on the new LIFReader and prepare everything for the PR.