Open Microscopy Environment

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

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

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

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.