[ome-users] Cannot import OpenLab images

[Curtis Rueden]

Hi Mario,

I was able to import your 120207_Image1.liff file into OME:

1) Download the loci_tools.jar from the Bio-Formats web site:
  http://www.loci.wisc.edu/ome/formats.html

2) Follow the instructions for "Using Bio-Formats in ImageJ,"
downloading and installing ImageJ if necessary, and dropping in the
loci_tools.jar file to the plugins folder.

3) Read your files into ImageJ using the Bio-Formats Importer, then
upload them to OME using the "Upload to OME" plugin. Both can be found
beneath the "LOCI" submenu of the "Plugins" menu.

This solution is not ideal, as it requires you have enough RAM to read
in the entire file, and the client-side upload performed by the
"Upload to OME" plugin is not perfect either, but it is functional --
I was able to browse through the image in the OME web interface.

We also have a command line uploader script called omeul that you can
get as part of the Bio-Formats command line tools, which should work
instead of the ImageJ route, though it has not been thoroughly tested
lately (if you try it and find bugs, let me know and I will fix).

Once OME 2.6.1 is released this sort of thing will hopefully no longer
be necessary.

-Curtis

On 5/14/07, Mario Valle <mvalle at cscs.ch> wrote:
> I'm evaluating OME for a project.
> Our biology partner laboratory will use OpenLab images.
> I read that Bioformats can read this format, but that it is not yet integrated in OME 2.6
> Could you suggest a method to import them into OME?
> If you need two examples:
> ftp ftp.cscs.ch
> <login as anonymous>
> cd in/put/abc/ftp/mvalle
>
> The files are:
> -rw-r--r--   1 ftp      30000    61632541 May 14 09:27 120207_Image1.liff
> -rw-r--r--   1 ftp      30000    90986545 May 14 09:28 523_1
>
> Thanks for your help!
>                                 mario
>
> --
> Ing. Mario Valle
> Visualization Group                              | http://www.cscs.ch/~mvalle
> Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91) 610.82.60
> v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91) 610.82.82
>
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