On 29/01/2013 17:16, Klaus Michel wrote:
> Dear all,
>
> today I tried to read Zeiss Axiovision files (zvi) with the Bio-Formats plugin (using a freshly
> installed and updated Fiji). The files that I tried were all image stacks of 27 images which
> were generated during calcium imaging experiments. Generally this worked very well (many
> thanks for this very helpful plugin!!).
> But I noticed that sometimes ROIs were correctly imported while sometimes the ROIs did not
> show up at all. Is this already known or is there some kind of workaround?
> If necessary I can provide more information or sample files.
Dear Klaus,
The Bio-Formats plugin should read the ROIs from the ZVI file. However,
the Zeiss AxioVision software supports a very large number of different
ROI types, while the OME Data Model supports most, but not all of these
types. If you are using one of the more esoteric ROI types, then it's
possible that these may not be imported since we can't represent them
internally.
When ROIs are not showing up, is this with specific files, or at random?
I'll be happy to take a closer look into this. If I could possibly have
an example image file containing these ROIs, I'll be able to investigate
in a bit more detail. You can upload it privately here:
http://qa.openmicroscopy.org.uk/qa/upload/ If the problem lies with
specific files, then an example good and bad file would be useful,
otherwise if it's random than any file which shows the problem will be fine.
Kind regards,
Roger
--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK Tel: (01382) 386364
The University of Dundee is a registered Scottish Charity, No: SC015096
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