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

[Pradeep Kota]

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

-- 
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--My tongue, so voluble and kind,
  It always runs before my mind.--
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