[ome-users] Bugreport - BioFormats CZIReader gets Dimension Order of CZI wrong

[William Moore]

Hi Sebastian,

 Thanks for the bug report.
I've downloaded and opened your images.
Do they look correct to you when you open them with Bio-Formats?
For both images I see 2 channels (DAPI, EGFP) with 5 Z-slices and 3 Time-points, although to me the images don't look like they're moving through Z and T (they all look quite unrelated to each other).
Is it only the metadata that seems wrong to you, or are the planes actually ordered incorrectly?

  Cheers,

   Will.


On 11 Mar 2015, at 09:43, Sebastian Rhode <sebrhode at gmail.com> wrote:

> Hi,
> 
> here you can find 2 CZI sample data sets:
> 
> https://dl.dropboxusercontent.com/u/623476/XYCZT_CH%3D2_Z%3D5_All_CH_per_Slice.czi
> 
> https://dl.dropboxusercontent.com/u/623476/XYZCT_Z%3D5_CH%3D2_Z%3D5_FullStack_per_CH.czi
> 
> The 1st CZI file was acquired with the option "All Channels per Slice" --> XYCZT
> 
> The 2nd  CZI file was acquired with the option "Full Stack per Channel" --> XYZCT
> 
> When I open both files via BioFormats the original Metadata show:
> 
> "All Channel per Slice" --> DimensenOrder = XYCZT -- > OK
> "Full Stack per Channel" --> DimensionOrder = XYCZT --> NOK
> 
> The DimensionOrder seems to be always XYCZT, no matter what it actaully was.
> 
> Inside the CZI File the "officail" dimension order is:
> 
> "All Channel per Slice" --> BTCZYX0 --> corresponds to XYZCT
> "Full Stack per Channel" --> BTCZYX0 --> corresponds to XYZCT
> 
> Would be nice to get this fixed soon ...
> 
> Cheers
> 
> Sebi
> 
> 
> 
> 
> 
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