Bug 523 – BioFormats ignores Z-Position Information of current CZI-Files

Bug 523 - BioFormats ignores Z-Position Information of current CZI-Files


Summary:	BioFormats ignores Z-Position Information of current CZI-Files

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	Bio-Formats
Version:	unspecified
Hardware:	PC Windows

Importance:	P3 major
Assigned To:	Melissa Linkert

URL:

Depends on:
Blocks:

Reported:	2012-11-05 15:21 CST by Sebastian Rhode
Modified:	2012-11-13 20:33 CST
CC List:	1 user (show)

See Also:

Description Sebastian Rhode 2012-11-05 15:21:07 CST

Hi,

I just tested the BioFormats within Fiji library with some CZI file (2 Channels, 15 Z-Planes and 20 Time Points) --> see METADATA).

In principle the image stack is imported correctly, but if one has closer look at the XML-file (I checked this option upon the import via the LOCI plugin), you will see, that the Z-Postion for every image is missing.

But this information is present inside the original CZI File. There every image data SubBlock (the complete CZI file has 2x30x20 = 600 SubBlocks) contains the following informations:

<METADATA><Tags><StageXPosition>36.44761904761905</StageXPosition><StageYPosition>41.361904761904761</StageYPosition><AcquisitionTime>2006-07-20T12:54:29.474</AcquisitionTime><FocusPosition>2738.7428571428572</FocusPosition></Tags><DataSchema><ValidBitsPerPixel>16</ValidBitsPerPixel></DataSchema></METADATA>

Do you have any idea, why the "FocusPosition" is skipped? Maybe we gave you the wrong docu (hopefully not ...) or some typo is involved? Do not hesitate to contact me, if you need more information.

And here is the link to the data from my dropbox:

http://dl.dropbox.com/u/623476/CZI-Z-Bug_OME.zip

Cheers,

Sebi

Comment 1 Melissa Linkert 2012-11-13 20:33:29 CST

Fix to be reviewed for inclusion in Bio-Formats 4.5.0:

https://github.com/openmicroscopy/bioformats/pull/214

Parsing of the "FocusPosition" tag was originally missing because the latest .czi specifications that I have make no mention of the FocusPosition tag.

For the future, it is better to report this sort of problem to the ome-users mailing list:

https://www.openmicroscopy.org/site/community/mailing-lists

That is the official place to discuss Bio-Formats problems, especially things like metadata parsing which don't really have anything to do with Fiji or ImageJ.