Problem with olympus file format

[Mickael Lefebvre]

Hi !

I use and recommend ImageJ to my customers for open and read olympus
microscope's image format (OIB and OIF). Nevertheless I encounter a
problem : my image has 3 channels, corresponding to DAPI, Alexa 488 and
mito tracker. When I visualise it with Olympus fluoview viewer, the colors
are correctly attributed to each channel, but when I use ImageJ to open
it, some colors are inverted, like DAPI appear red and mito tracker blue.
I have tried different plugins to solve this problem, but I haven't find
solution.

Could somebody help me ?

Thanks.

Mickaël Lefebvre
Olympus France

[Michael Weber-4]

Hi Mickaël,

same happens to other file formats such as Leica lif while using the
LOCI importer, the LUT cannot be assigned correctly. However, if you
want to analyze something, color doesn't matter, if you need the
overlay, RGB merge will assign the color you want. In any other case,
you can manually assign a LUT for a single channel.

Michael


Mickael Lefebvre wrote:

> Hi !
>
> I use and recommend ImageJ to my customers for open and read olympus
> microscope's image format (OIB and OIF). Nevertheless I encounter a
> problem : my image has 3 channels, corresponding to DAPI, Alexa 488 and
> mito tracker. When I visualise it with Olympus fluoview viewer, the colors
> are correctly attributed to each channel, but when I use ImageJ to open
> it, some colors are inverted, like DAPI appear red and mito tracker blue.
> I have tried different plugins to solve this problem, but I haven't find
> solution.
>
> Could somebody help me ?
>
> Thanks.
>
> Mickaël Lefebvre
> Olympus France

[ctrueden]

Hi Michael,

I just wanted to mention that we are aware of this LUT issue with the
Bio-Formats Importer, and have a ticket in our bug tracking system for it: <
https://skyking.microscopy.wisc.edu/trac/java/ticket/241>. It will be
addressed in a future release.

The bug only applies when each channel is supposed to be a predefined type
such as "red" or "green." For explicitly defined color tables (i.e., 8-bit
indexed color, embedded within the file), things should work correctly -- if
not, please let us know.

-Curtis

On Wed, Apr 16, 2008 at 6:24 AM, Michael Weber <[hidden email]> wrote:

> Hi Mickaël,
>
> same happens to other file formats such as Leica lif while using the LOCI
> importer, the LUT cannot be assigned correctly. However, if you want to
> analyze something, color doesn't matter, if you need the overlay, RGB merge
> will assign the color you want. In any other case, you can manually assign a
> LUT for a single channel.
>
> Michael
>
>
>
> Mickael Lefebvre wrote:
>
> > Hi !
> >
> > I use and recommend ImageJ to my customers for open and read olympus
> > microscope's image format (OIB and OIF). Nevertheless I encounter a problem
> > : my image has 3 channels, corresponding to DAPI, Alexa 488 and mito
> > tracker. When I visualise it with Olympus fluoview viewer, the colors are
> > correctly attributed to each channel, but when I use ImageJ to open it, some
> > colors are inverted, like DAPI appear red and mito tracker blue.
> > I have tried different plugins to solve this problem, but I haven't find
> > solution.
> >
> > Could somebody help me ?
> >
> > Thanks.
> >
> > Mickaël Lefebvre
> > Olympus France
> >
>