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

[Melissa Linkert]

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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