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

[Melissa Linkert]

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.--
> ------------------------------------------------

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