[ome-users] Fiji / ImageJ Bio-Formats PlugIn: Two open issues with CZI image format

[Roger Leigh]

On 06/12/13 13:08, Martin Huettinger wrote:

> - Bio Formats 5.0.0-beta1 plugin - Zeiss CZI Reader with / on
> - Fiji / ImageJ v1.48i
> - Java RE x64 1.7.0 U25
> - Win7 SP1 x64
>
> Please see screenshot. Fiji-ImageJ-BioFormats-VersionInfo.jpg:

The version info in this dialogue is definitely suspect.  Thanks for
pointing this out.  I'll look at whether this is fixed or still present.

> There are two basic and obvoius issues - at least the first one has been
> reported before:
>
> 1) First issue is with BGR48 (36 valid bits) color images -  a common
> pixel format with Zeiss AxioCam models.
>
> These images are displayed either with wrong size and therefore somehow
> compressed, shifted, overlayed,  pixelated or blackened - please see
> screenshots below:

> I uploaded a couple of sample images a few month ago to the omero.qa server:
>
> BGR48:
> - AxioCamICc5_bgr48_36ValidBits_1C_8Z.czi
> - AxioCamMRc_bgr48_36ValidBits_1C_9Z.czi
>
> BGR24:
> - AxioCamICc5_bgr24_24ValidBits_1C_8Z.czi
>
> Gray16:
> - AxioCamMRc_Gray16_12ValidBits_1C_9Z.czi
> - AxioCamICc5_Gray16_12ValidBits_1C_8Z.czi
>
> Unfortunately I did not manage to create a functional account there so I
> wasn't able to track, if these images were usefull anyhow.
>
> Please let me know If you need these images again and where to deposit
> them - thanks in advance!

Thanks for mentioning this.  These images were indeed uploaded as QA
#7601, but without any context of who uploaded them or why, and as a
result they may have been overlooked.  There was a mention of checking
if they were from Matthias Pospiech, but no followup that I can see.  So
there's no need to re-upload these images--we still have a copy, and can
look at them in more detail.  It would certainly be useful to have
screenshots of how each of the above images appear in Zen though, so
that we have a reference for what they are supposed to look like, if
that's possible?

> 2) Second issue is with tile images, which were processed somehow along
> the way in ZEN. The resolution pyramid is recalculated in this case (so
> called offline pyramid) and Bio Formats importer seems to be unable to
> handle these images properly. Either import fails with a java exception
> (please find exception test below) or the display is scrambled / chopped.

>
> I can provide sample images as well. as theses are tile images of 100MB
> file size each, please let me know where to upload them - Thanks in advance!
>
> In case you need additional information, please let me know!

For the tiling case, it would certainly be useful to have a copy of the
image, plus a Zen screenshot as a reference.  We did encounter a tiling
issue last week, but it's not clear without an example image if it's a
separate issue or an instance of the issue we already know about.  If
you could upload a copy, that would be much appreciated.  You can do so
here:

   http://qa.openmicroscopy.org.uk/qa/upload/


Many thanks,
Roger Leigh

--
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