OIF-Import

[Johannes Breu]

Hello,

while trying to import oif-files via loci_tools.jar
(C:\Programme\ImageJ\plugins) the best result I got was an import with
inverted colors.

Somehow I found the information it was helpful to add bio-formats.jar
(C:\Programme\ImageJ\jre\lib\ext) but then an exception window pops up,
starting with
java.lang.IllegalArgumentException: Metadata object cannot be null; use
loci.formats.meta.DummyMetadata instead

I would like to open the oif-file in a way that allows me to mark the
green-signal for measuring the red-signal (that overlaps with the
red-signal). My idea was that the picture looks quite similar to the one I
know from fluoview where I can decide if I can see both channels or just
one. I found no mode in image J that allows me to do so ( even if I open a
tiff-file).

Thank you very much.

Joh Breu

[ctrueden]

Hi Joh,

I would advise follow the directions from the official Bio-Formats web site:

http://www.loci.wisc.edu/ome/formats.html

In particular, see the page on using Bio-Formats with ImageJ:

http://www.loci.wisc.edu/ome/formats-imagej.html

All you need to download is the latest loci_tools.jar, which you
should place in the plugins folder. Do not put any other files into
the plugins folder or into jre/lib/ext.

If the colors are inverted, it is most likely a bug in Bio-Formats. If
you would be willing to send a sample dataset demonstrating the
problem, we can investigate a fix.

HTH,
Curtis

On Fri, Jul 4, 2008 at 4:09 PM, Johannes Breu <[hidden email]> wrote:

> Hello,
>
> while trying to import oif-files via loci_tools.jar
> (C:\Programme\ImageJ\plugins) the best result I got was an import with
> inverted colors.
>
> Somehow I found the information it was helpful to add bio-formats.jar
> (C:\Programme\ImageJ\jre\lib\ext) but then an exception window pops up,
> starting with
> java.lang.IllegalArgumentException: Metadata object cannot be null; use
> loci.formats.meta.DummyMetadata instead
>
> I would like to open the oif-file in a way that allows me to mark the
> green-signal for measuring the red-signal (that overlaps with the
> red-signal). My idea was that the picture looks quite similar to the one I
> know from fluoview where I can decide if I can see both channels or just
> one. I found no mode in image J that allows me to do so ( even if I open a
> tiff-file).
>
> Thank you very much.
>
> Joh Breu
>