Dear Aaron,
the positions are available in 2 different locations. When collecting multi-area images in the OIF format the Olympus Fluoview software creates a directory for the imaging session containing sub-folders for each stage position.  Within the session folder will be a text file "MATL_Mosaic.log". This will contain the x,y coordinates of each field. 

For any individual image, the XY position of the stage for each image resides the .pty parameter file associated with each TIFF.  Open any .pty file (simple text file) and look for this block of text:

[Axis 7 Parameters]
AbsPositionUnitName="mm"
AbsPositionUnitNameX="nm"
AbsPositionUnitNameY="nm"
AbsPositionValue=0.0
AbsPositionValueX=2652600.0
AbsPositionValueY=-704200.0
Number=1

Note the XY positions in the mosaic.log file are in microns, the AbsPositionValueX and AbsPositionValueY are in nm.  

Open an OIF image from LOCI with 'Display OME-XML metadata' and search for  AbsPositionValueX and AbsPositionValueY to get the positions.
The stage positions are also in the LOCI Original Meta data window. 

The meta data in the OIF is written into plain text files, the filename.oif covers the set of images, and the filename.pty is associated with each image.  The .oif does not contain the stage positions, since its possible to have different stage positions within an image series.  So far, I've found very optical parameter is available.  I've not used the OIB format very much, but I'm sure that LOCI will read the stage positions from it. 

Regards,
Glen

Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
(206) 616-4156
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On Nov 16, 2009, at 1:32 AM, Ponti, Aaron wrote:

> Hello
> 
> We are investigating the purchase of one of the following confocals: Zeiss LSM 710, Olympus FluoView 1000, and Leica SP/SP5. One of the criteria for the choice is the possibility to read stage positions from the files (using the loci/ome-xml tools). With loci_tools 4.1 it seems that reading the stage positions into the OME schema is supported for the Leica, but is not for the other two. Can anybody confirm this? Does anybody know if stage positions are stored at all in .lsm and .oib files? How is reading metadata information in general for these file formats (like optical parameters)?
> 
> Thanks
> 
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> | Dr. Aaron C. Ponti
> | Friedrich Miescher Institute for Biomedical Research
> | Facility for Advanced Microscopy and Imaging
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