[ome-users] problem opening .oif

[Melissa Linkert]

Hi Christian,

> I'm trying to open Olympus FV1000 .oif files in ImageJ using the
> Bio-Formats importer. However, after I make my settings in the
> Bio-Formats Import Options window I get the following error message:
> File is not in a supported format, a reader plugin is not available
> or was not found.
> I have the latest stable version of the LOCI plugins installed, the
> problem comes up in MBF ImageJ and Fiji, on Windows XP and 7, on a
> 32-bit and a 64-bit machine.
> Attached you will find a sample file.

The problem here appears to be a result of the .oif file and .oif.files
directory being renamed after acquisition.  We will make an effort to
fix this in Bio-Formats (see this ticket:
http://trac.openmicroscopy.org.uk/ome/ticket/9851), but the simple solution for
now is to rename those files back to Image0019.oif and Image0019.oif.files.

> I also have problems with the correct syntax when calling
> Bio-Formats from an ImageJ macro, especially how to open and save
> files. Is there a comprehensive documentation for that available?

If you are using the Bio-Formats macro extensions, then there is
documentation available by clicking "Plugins > LOCI > Bio-Formats Macro
Extensions" in addition to examples here:

https://github.com/openmicroscopy/bioformats/tree/develop/components/loci-plugins/utils/macros

Otherwise, the best way to find the correct syntax is by starting the
ImageJ macro recorder, manually going through the steps that you want
the macro to perform, and then pasting the recorded macro into your own
code.

Regards,
-Melissa

On Tue, Nov 06, 2012 at 09:22:48AM +0100, Christian Liebig wrote:
> Hi,
> 
> I'm trying to open Olympus FV1000 .oif files in ImageJ using the
> Bio-Formats importer. However, after I make my settings in the
> Bio-Formats Import Options window I get the following error message:
> File is not in a supported format, a reader plugin is not available
> or was not found.
> I have the latest stable version of the LOCI plugins installed, the
> problem comes up in MBF ImageJ and Fiji, on Windows XP and 7, on a
> 32-bit and a 64-bit machine.
> Attached you will find a sample file.
> 
> I also have problems with the correct syntax when calling
> Bio-Formats from an ImageJ macro, especially how to open and save
> files. Is there a comprehensive documentation for that available?
> 
> Thanks for your help,
> 
> Christian
> 
> -- 
> Christian Liebig, PhD
> 
> Light Microscopy Facility
> Max-Planck-Institute for Developmental Biology
> Spemannstrasse 35
> D-72076 Tuebingen
> Germany
> 
> Phone:  +49 7071 601 443
> e-mail: christian.liebig at tuebingen.mpg.de
> 


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