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VSI Files duplicated channels as Slices

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Please note:
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.

VSI Files duplicated channels as Slices

Postby Oli » Tue Mar 28, 2017 12:10 pm

Hi all,

Again we return with BioFormats and the VSI files.
Since a couple of versions, we are having the issue that our VSI files are opened incorrectly

The files are mutichannel lfuorescence 3 channel images, but bioformats opens them as 3 channel, 3 Z slices, making the final file 3x larger...

Opening in the original VSI software causes no issues...

I submitted a sample dataset
http://qa.openmicroscopy.org.uk/qa/feedback/17658/

So you can hopefully replicate the problem.

Best

Oli
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Re: VSI Files duplicated channels as Slices

Postby dgault » Wed Mar 29, 2017 3:43 pm

Hi Oli,

Thank you for providing the sample dataset. I was able to test and reproduce the issue as your reported with the latest Bio-Formats 5.4.0.

It appears from debugging that when the reader is parsing the dimension order that both the Z and C end up being the same for some of the series. I believe this is related to the DIMENSION_MEANING tag which we added to the parsing last year.

I have created a new Trello card on our Bio-Formats inbox to further investigate and prioritise this issue.

With Thanks,
David Gault
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Re: VSI Files duplicated channels as Slices

Postby Oli » Fri Mar 02, 2018 11:12 am

Dear David,

We have further datasets that still exhibit this issue with the latest BioFormats plugin.
Do you know if anything was done in this respect?
Just in case I uploaded another dataset
https://www.openmicroscopy.org/qa2/qa/f ... efebc15018


All the best

Oli
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Re: VSI Files duplicated channels as Slices

Postby dgault » Mon Mar 05, 2018 1:13 pm

Hi Oli,

Unfortunately as of the latest release 5.8.0, we have not yet been able to put in place a fix for this particular issue. We appreciate your patience and thank you for providing an additional dataset, these are always extremely helpful for our testing and debugging. I will update the existing Trello card (https://trello.com/c/LXfwDnlK/126-vsi-issues) with the latest QA file.
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