[ome-users] Bio-Formats Zeiss ZVI Mosaix Issues

[Melissa Linkert]

Hi Pradeep,

Thank you for uploading a file.  I was able to reproduce the problem,
and we are now testing a fix:

https://github.com/openmicroscopy/bioformats/pull/2167

I would expect that fix to be included in the 5.2.0 release.

For now, you might try using the "Specify range for each series" option in the
"Bio-Formats Import Options" window to assemble all of the timepoints
for a single tile (likely by setting the "step" to the tile count).

Regards,
-Melissa

On Tue, Dec 15, 2015 at 06:00:11PM -0500, Pradeep Kota wrote:
> Hi Melissa,
> 
> Thanks for your e-mail. I was running Bio-Formats 5.1.5 when I wrote that
> e-mail. After your response I updated Bio-Formats to 5.1.7 and still saw
> the same behavior. I will try to upload the file tonight for you to have a
> look at.
> 
> Thanks again
> Pradeep
> 
> 
> On Tue, Dec 15, 2015 at 9:36 AM, Melissa Linkert <
> melissa at glencoesoftware.com> wrote:
> 
> > Hi Pradeep,
> >
> > > Now my problem is that the order of the images in each of these 16 stacks
> > > is messed up. They don't correspond to the same tile. The XYTCZ for
> > Mosaix
> > > seems to point to the order in which the tiles in the Mosaix are
> > arranged.
> > > i.e., starting with X=1, Y=1 (top left of 4x4), T should go from 1-1200
> > to
> > > give the stack for Tile 1. Instead, the tile stack output by Bio-Formats
> > > has the order - for T=1 to 1200, X=1 to 4 followed by Y=1 to 4 - and
> > hence
> > > puts time points n and n+1 for each tile at n and n+16 in each output
> > > series. Is this normal behavior? Am I missing an option that would help
> > me
> > > fix this? It already takes nearly 10 minutes to read one such file and I
> > > don't think it is practical to write each series as a separate tiff file
> > > and sort through it.
> >
> > Thank you for reporting this - it's definitely not expected behavior.
> >
> > Could you please confirm that you are using Bio-Formats 5.1.7?  "Help >
> > About Plugins > Bio-Formats Plugins" in Fiji should indicate which
> > version is installed.
> >
> > If you see this problem with 5.1.7, then we would likely need to see the
> > problematic file in order to diagnose and fix the problem.  I have sent
> > upload instructions for large files, if you are willing to send this
> > file.
> >
> > Regards,
> > -Melissa
> >
> > On Sat, Dec 12, 2015 at 11:19:02PM -0500, Pradeep Kota wrote:
> > > Dear OME Users,
> > >
> > > I am trying to read a large (~30 GB) Axiovision Mosaix ZVI file in Fiji
> > > using Bio-Formats. Obviously, I need to open this as a virtual stack.
> > Since
> > > the file is huge, (understandably) I cannot use the 'Concatenate series
> > > when compatible' option along with 'Use virtual stack'. So, I set 'Use
> > > virtual stack' and 'Open all series' options. The stack order in this
> > file
> > > is XYTCZ.  This file represents a 4x4 mosaic for ~1200 time points with 1
> > > channel and 1 Z-slice at each time point. When I open this file using
> > Fiji,
> > > I get 16 tif stacks, each (supposedly) corresponding to a tile in the 4x4
> > > mosaix, with each tif containing ~1200 slices. So far so good.
> > >
> > > Now my problem is that the order of the images in each of these 16 stacks
> > > is messed up. They don't correspond to the same tile. The XYTCZ for
> > Mosaix
> > > seems to point to the order in which the tiles in the Mosaix are
> > arranged.
> > > i.e., starting with X=1, Y=1 (top left of 4x4), T should go from 1-1200
> > to
> > > give the stack for Tile 1. Instead, the tile stack output by Bio-Formats
> > > has the order - for T=1 to 1200, X=1 to 4 followed by Y=1 to 4 - and
> > hence
> > > puts time points n and n+1 for each tile at n and n+16 in each output
> > > series. Is this normal behavior? Am I missing an option that would help
> > me
> > > fix this? It already takes nearly 10 minutes to read one such file and I
> > > don't think it is practical to write each series as a separate tiff file
> > > and sort through it.
> > >
> > > Any help is much appreciated.
> > >
> > > Thanks a lot
> > > Pradeep
> > >
> > > --
> > > -------------------------------------------------
> > > --My tongue, so voluble and kind,
> > >   It always runs before my mind.--
> > > ------------------------------------------------
> >
> > > _______________________________________________
> > > ome-users mailing list
> > > ome-users at lists.openmicroscopy.org.uk
> > > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> >
> 
> 
> -- 
> -------------------------------------------------
> --My tongue, so voluble and kind,
>   It always runs before my mind.--
> ------------------------------------------------