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

[Ponti Aaron]

Hi,

Bug #11513 (CZI linescan dimensions incorrect) was reported as fixed a
couple of days ago. I tried the latest trunk build (yesterday) and indeed
the dimensions of the files are now correctly read. Unfortunately, there
still seems to be a problem with the actual reading of the pixel data. If
I read the same test file I sent you I get (loadGeneric() is my MATLAB
wrapper around loci_tools.jar):

>> [dataset, metadata] = loadGeneric('/Users/pontia/Desktop/001 post.czi')
dataset = 
     [1x2048x25 uint16]    [1x2048x25 uint16]

metadata = 
     width: 2048
     height: 1
     nPlanes: 25     ## This used to be 1. It is now correct
     nChannels: 2
     nTimepoints: 1
     seriesNumber: 1
     nImagesInSeries: 50
     voxelX: 0.103783229681474
     voxelY: 0.103783229681474
     voxelZ: 1.47330315022399
     datatype: 'uint16'
     stagePosition: []
     acquisitionDate: '2013-09-20T16:33:26'
     timeInterval: []
     timestamps: NaN
     color: []

If I take a look at the loaded dataset, all rows (planes) for z > 1 are
zero and only the first plane (z = 1) contains signal. Loading the scans
in the ZEN software shows that there is however signal at all a values.
>> [y, x, z] = ind2sub(size(d{1}), find(d{1}>0)); unique(z)
ans =
     1

>> [y, x, z] = ind2sub(size(d{2}), find(d{2}>0)); unique(z)
ans =
1


One more detail: metadata.nImagesInSeries is
loci.formats.ChannelSeparator(loci.formats.ChannelFiller()).getImageCount()
: is it correct that it reports 50?.
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
+41 61 387 33 74






On 10/11/13 3:42 AM, "Melissa Linkert" <melissa at glencoesoftware.com> wrote:

>Hi Aaron,
>
>> >Just to confirm, am I correct that the correct channel count of the
>> >image is 2, and both channels are 16-bit greyscale?
>>
>>
>> Indeed: 2 channels, 16-bit each (12-bit actual dynamic range).
>
>Fantastic - thank you for clarifying!
>
>Regards,
>-Melissa
>
>On Thu, Oct 10, 2013 at 07:08:02AM +0000, Ponti  Aaron wrote:
>> Hi,
>>
>>
>> >Many thanks for providing the sample image.  I have tested with our
>>most
>> >current 4.4 development version, and this also shows exactly the same
>> >behaviour you observed above.  I have opened a ticket for the issue in
>> >our bug tracker (https://trac.openmicroscopy.org.uk/ome/ticket/11513)
>> >and you should be CC'd on any changes to it.
>> >
>> >Just to confirm, am I correct that the correct channel count of the
>> >image is 2, and both channels are 16-bit greyscale?
>>
>>
>> Indeed: 2 channels, 16-bit each (12-bit actual dynamic range).
>>
>> 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
>> +41 61 387 33 74
>>
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users