[ome-users] bio-formats problem reading ND2 files with several stage positions

[Melissa Linkert]

Hi Aaron,

> > we have ND2 files that contain several stage (XY) positions. At every stage position, a few stacks of a few tens of planes over a few channels and a few time points are acquired.
> >  
> > Bio-Formats (5.0.0) seems to get all dimensions correctly, but then it misinterprets the sequences of planes and redistributes them over the wrong axes.
> >  
> > Specifically, even though the number of series in the file match the number of stage positions, the T, C, and Z dimensions match the ones in each series, when you look at the opened stacks you see that it contains segments from different stage positions. Swapping dimensions while opening does not help, because you can do it for planes within a series; here the problem is that the planes are read “horizontally” over stage positions.
> >  
> > I have a good example file if you would like to have it (a.k.a. where can I upload it ;-) ?)
> >  

Thank you for uploading an example file.  We are reviewing a fix for
this now:

https://github.com/openmicroscopy/bioformats/pull/989

Any feedback you have there would be welcome, otherwise I would expect
this to be included in the upcoming 5.0.1 release of Bio-Formats.

Regards,
-Melissa

On Fri, Mar 21, 2014 at 02:06:47PM +0000, Will Moore wrote:
> Hi,
> 
> Thanks for the feedback,
> 
>  You can upload files at http://qa.openmicroscopy.org.uk/qa/upload/ 
> 
>  Cheers,
> 
>    Will.
> 
> 
> On 21 Mar 2014, at 14:00, Ponti Aaron wrote:
> 
> > Hi,
> >  
> > we have ND2 files that contain several stage (XY) positions. At every stage position, a few stacks of a few tens of planes over a few channels and a few time points are acquired.
> >  
> > Bio-Formats (5.0.0) seems to get all dimensions correctly, but then it misinterprets the sequences of planes and redistributes them over the wrong axes.
> >  
> > Specifically, even though the number of series in the file match the number of stage positions, the T, C, and Z dimensions match the ones in each series, when you look at the opened stacks you see that it contains segments from different stage positions. Swapping dimensions while opening does not help, because you can do it for planes within a series; here the problem is that the planes are read “horizontally” over stage positions.
> >  
> > I have a good example file if you would like to have it (a.k.a. where can I upload it ;-) ?)
> >  
> > Thanks a lot in advance
> > a2
> >  
> > ----
> > Dr. Aaron Ponti
> > Software and Data Management Engineer
> > Single Cell Unit
> > 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
> 

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