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

Fri Dec 6 13:08:08 GMT 2013

Dear LOCI Dev Team,

I'm currently testing 

- 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:

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:

They should be displayed like this:

Please find the metadata for both images 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!

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. 

Should look like this:

Metadata of both images:

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!

Mit freundlichen Gruessen / with best regards

Martin Huettinger

______________________________

Carl Zeiss Microscopy GmbH
Geschäftsbereich BioSciences / BioSciences Division
Imaging Software München / Imaging Software Munich
Systemingenieur / Systems Engineer

M a r t i n   H u e t t i n g e r

Kistlerhofstr. 75, 81379 München
Telefon / Phone: +49 89 90 9000-413
Fax: +49 89 90 9000-555
mailto:martin.huettinger at zeiss.com
http://www.zeiss.com/microscopy
______________________________

Carl Zeiss Microscopy GmbH
Vorsitzender des Aufsichtsrates: Dr. Michael Kaschke
Geschäftsführung: Dr. Ulrich Simon, Wilhelm Nörthemann, Dr. Bernhard 
Ohnesorge, 
Dr. Frank Stietz
Sitz der Gesellschaft: 07740 Jena, Deutschland
Amtsgericht Jena, HRB 210.536, USt-IdNr: 814 503 774

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