[ImageJ-bugs] [Bug 881] New: BioFormats CZI-Reader reads wrong sublocks of CZI file when an image pyramid was created

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=881

            Bug ID: 881
           Summary: BioFormats CZI-Reader reads wrong sublocks of CZI file
                    when an image pyramid was created
           Product: Fiji
           Version: unspecified
          Hardware: PC
                OS: Windows
            Status: NEW
          Severity: major
          Priority: P5
         Component: Bio-Formats
          Assignee: imagej-bugs at imagej.net
          Reporter: sebrhode at googlemail.com
                CC: sebrhode at googlemail.com

Hi guys,

I am not sure if this is actually or bug or a feature request. And here is the
problem.

In ZEN exits an option to create an image pyramid during acquisition (-->
Image_Pyramid_Option.png), which is usually checked, since the user will only
see the acquired images right away already during the acquisition, when this
option is activated.
The resulting file has some additional sublocks which contain scaled images
(--> WBa.ImagingTool_IMG_PYR.png)

Those sublocks have a scaling which is not = 1.0
Scaling is derived from StoredSize / Size (in the example = 0.5. Due the 10%
overlap for the tiles the size is not 2x the actual image size (640x640 pixel)

CZI-File: 2014_08_06_S=2_T=1_Z=1_CH=2_IMG_PYR.czi

When one tries to open this using BioFormats (--> Bio-Formats Import
Options.png) the result is strangle and contains black images. The OME-XML data
also contain the wrong dimensions SizeX and SizeY = 1216 (-->
IMG_PYR_OME_XML.png)

If the Image Pyramid option is not activated, the CZI data structure is
different (--> WBa.ImagingTool_NO_PYR.png). No additional subblocks for the
pyramid are present. All blocks have the scale = 1.0 and a size bof 640x640
pixels.

CZI-File: 2014_08_06_S=2_T=1_Z=1_CH=2_NO_PYR.czi

When this file is opened via BioFormats, the import works as expected. The
OME-XML are correct (--> NO_PYR_OME_XML.png)


The my question is, if it would be possible, that BioFormats can somehow skip
those pyramid blocks, which do not a scaling = 1.0? Those pyramid blocks are
not always the first ones (inside the WBa.ImagingTool View). Their order might
differ, so one needs to filter out those by some other tricks.

The image data and screenshots can be downloaded here:

https://dl.dropboxusercontent.com/u/623476/CZI_Image_Pyramid_Problem.zip

Cheers, Sebi

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