[ome-users] Problem reading czi files of line scans

[Ponti Aaron]

Dear list,

we run line scans on Zeiss hardware using Zen Black. I attach a czi file that contains an X = 2048, Y = 1, Z = 25 dataset. Bio-formats only reads the first 2048 pixels for Z = 1. I attach a TIFF export as well for comparison.

The OME metadata reports:

<Pixels DimensionOrder="XYCZT" ID="Pixels:0" PhysicalSizeX="0.10378322968147374" PhysicalSizeY="0.10378322968147374" PhysicalSizeZ="1.4733031502239864" SizeC="2" SizeT="1" SizeX="2048" SizeY="1" SizeZ="1" Type="uint16">

Note the SizeZ = 1 entry. Interestingly, however, deep into the ImageJ metadata one can find the correct Z value:

Information|Image|SizeZ|0        25

I tried overriding the value of Z in my loadGeneric.m MATLAB function that uses bio-formats (4.4.8) in the backhand but this causes bio-formats to fail with following error.

Error using loadGeneric (line 305)
Java exception occurred:
loci.formats.FormatException: Invalid image number: 2 (series=0, imageCount=2)
at loci.formats.FormatTools.checkPlaneNumber(FormatTools.java:737)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:167)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:159)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:143)

The problem is therefore NOT just a wrong interpretation of the Z value of the dataset.

You will also find loadGeneric.m attached to this email.

Thanks,
a2

----
Dr. Aaron Ponti
Software and Data Management Engineer
Department of Biosystems Science and Engineering (D-BSSE)
ETH Zürich
Office 2.24
Mattenstrasse 26
4058 Basel, Switzerland
aaron.ponti at bsse.ethz.ch<mailto:aaron.ponti at bsse.ethz.ch>
+41 61 387 33 74
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