VSI Files duplicated channels as Slices

[Oli]

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

[dgault]

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

[Oli]

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

[dgault]

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.