[ome-users] BioFormats CZI-Reader reads wrong sublocks of CZI file when an image pyramid was created during acquistion

[Sebastian Rhode]

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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