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

[Pradeep Kota]

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.--
------------------------------------------------
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