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

[Ponti Aaron]

Hi Melissa,

Just to confirm that issue 797 ("Zeiss CZI: fix image reading for linesman
images") is solved!

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 11/19/13 8:58 PM, "Melissa Linkert" <melissa at glencoesoftware.com> wrote:

>Hi Aaron,
>
>> 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):
>
>*snip*
>
>> 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.
>
>Thank you for catching that, and my apologies for not getting back to
>you sooner.  We have a fix for the problem under review here:
>
>https://github.com/openmicroscopy/bioformats/issues/797
>
>Once that shows as being merged, the trunk build should include the fix.
>
>> One more detail: metadata.nImagesInSeries is
>> 
>>loci.formats.ChannelSeparator(loci.formats.ChannelFiller()).getImageCount
>>()
>> : is it correct that it reports 50?.
>
>Yes, that's correct - one image for each Z and channel.
>
>Regards,
>-Melissa
>
>On Wed, Nov 13, 2013 at 10:41:59AM +0000, Ponti  Aaron wrote:
>> 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
>> >>
>> >>
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>>