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LSM Split Channels Broken

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Rebecca Keller

LSM Split Channels Broken

Dear Imagers,

Two things have recently happened with my LSM files:

-I now need to import rather than just opening them

-Split channels does not work; complains with "multichannel image
required." (But my images are multichannel, and I can see both with the
slider.)

Neither of these was a problem before--any thoughts as to what's going on?

JPK

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Rebecca Keller

Re: LSM Split Channels Broken

A follow-up to this problem: for some reason, FIJI thinks my images are
interleaved rather than separate channels, even though they appear with a
channel-slider--I've been able to separate the channels by using
"deinterleave" rather than "split channels." I think this is probably a
bona fide bug...

JPK

On Tue, Mar 31, 2015 at 9:51 PM, Rebecca Keller <[hidden email]>
wrote:

> Dear Imagers,
>
> Two things have recently happened with my LSM files:
>
> -I now need to import rather than just opening them
>
> -Split channels does not work; complains with "multichannel image
> required." (But my images are multichannel, and I can see both with the
> slider.)
>
> Neither of these was a problem before--any thoughts as to what's going on?
>
> JPK
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Ignacio Arganda-Carreras-2

Re: LSM Split Channels Broken

Hello Rebecca,

I observed the same problems.

The channel splitting can be fixed if you convert the image first to a
Composite (in a macro run("Make Composite", "display=Composite"); ). But I
agree it shouldn't be like this.

ignacio

On Thu, Apr 2, 2015 at 1:35 AM, Rebecca Keller <[hidden email]> wrote:

> A follow-up to this problem: for some reason, FIJI thinks my images are
> interleaved rather than separate channels, even though they appear with a
> channel-slider--I've been able to separate the channels by using
> "deinterleave" rather than "split channels." I think this is probably a
> bona fide bug...
>
> JPK
>
> On Tue, Mar 31, 2015 at 9:51 PM, Rebecca Keller <[hidden email]>
> wrote:
>
> > Dear Imagers,
> >
> > Two things have recently happened with my LSM files:
> >
> > -I now need to import rather than just opening them
> >
> > -Split channels does not work; complains with "multichannel image
> > required." (But my images are multichannel, and I can see both with the
> > slider.)
> >
> > Neither of these was a problem before--any thoughts as to what's going
> on?
> >
> > JPK
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Ignacio Arganda-Carreras, Ph.D.
Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
Bâtiment 2
INRA Centre de Versailles-Grignon
Route de St-Cyr (RD10)
78026 Versailles Cedex France

Tel : +33 (0)1 30 83 30 00 - fax : +33 (0)1 30 83 33 19
Website: http://sites.google.com/site/iargandacarreras/
<http://biocomp.cnb.csic.es/~iarganda/index_EN.html>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

ctrueden

Re: LSM Split Channels Broken

Hi Jacob, Ignacio & everyone,

> Two things have recently happened with my LSM files:
>
> -I now need to import rather than just opening them
>
> -Split channels does not work

I cannot reproduce on my system:

* Download dataset from http://loci.wisc.edu/sample-data/2chzt
* Unzip it
* Launch Fiji, File > Open, choose 2chZT.lsm

If 2chZT.lsm works for you, but you have data which does not, please upload
a non-working file using the Help > Upload Sample Image command, then reply
back with the name of the file you uploaded.

Regards,
Curtis

On Thu, Apr 2, 2015 at 3:20 AM, Ignacio Arganda-Carreras <
[hidden email]> wrote:

> Hello Rebecca,
>
> I observed the same problems.
>
> The channel splitting can be fixed if you convert the image first to a
> Composite (in a macro run("Make Composite", "display=Composite"); ). But I
> agree it shouldn't be like this.
>
> ignacio
>
> On Thu, Apr 2, 2015 at 1:35 AM, Rebecca Keller <[hidden email]>
> wrote:
>
> > A follow-up to this problem: for some reason, FIJI thinks my images are
> > interleaved rather than separate channels, even though they appear with a
> > channel-slider--I've been able to separate the channels by using
> > "deinterleave" rather than "split channels." I think this is probably a
> > bona fide bug...
> >
> > JPK
> >
> > On Tue, Mar 31, 2015 at 9:51 PM, Rebecca Keller <[hidden email]>
> > wrote:
> >
> > > Dear Imagers,
> > >
> > > Two things have recently happened with my LSM files:
> > >
> > > -I now need to import rather than just opening them
> > >
> > > -Split channels does not work; complains with "multichannel image
> > > required." (But my images are multichannel, and I can see both with the
> > > slider.)
> > >
> > > Neither of these was a problem before--any thoughts as to what's going
> > on?
> > >
> > > JPK
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>
> --
> Ignacio Arganda-Carreras, Ph.D.
> Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
> Bâtiment 2
> INRA Centre de Versailles-Grignon
> Route de St-Cyr (RD10)
> 78026 Versailles Cedex France
>
> Tel : +33 (0)1 30 83 30 00 - fax : +33 (0)1 30 83 33 19
> Website: http://sites.google.com/site/iargandacarreras/
> <http://biocomp.cnb.csic.es/~iarganda/index_EN.html>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Ignacio Arganda-Carreras-2

Re: LSM Split Channels Broken

Sorry for the late answer. I think this problem got fixed with the updates
of bioformats during the last week.

Cheers!

ignacio

On Mon, Apr 6, 2015 at 5:42 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Jacob, Ignacio & everyone,
>
> > Two things have recently happened with my LSM files:
> >
> > -I now need to import rather than just opening them
> >
> > -Split channels does not work
>
> I cannot reproduce on my system:
>
> * Download dataset from http://loci.wisc.edu/sample-data/2chzt
> * Unzip it
> * Launch Fiji, File > Open, choose 2chZT.lsm
>
> If 2chZT.lsm works for you, but you have data which does not, please upload
> a non-working file using the Help > Upload Sample Image command, then reply
> back with the name of the file you uploaded.
>
> Regards,
> Curtis
>
> On Thu, Apr 2, 2015 at 3:20 AM, Ignacio Arganda-Carreras <
> [hidden email]> wrote:
>
> > Hello Rebecca,
> >
> > I observed the same problems.
> >
> > The channel splitting can be fixed if you convert the image first to a
> > Composite (in a macro run("Make Composite", "display=Composite"); ). But
> I
> > agree it shouldn't be like this.
> >
> > ignacio
> >
> > On Thu, Apr 2, 2015 at 1:35 AM, Rebecca Keller <[hidden email]>
> > wrote:
> >
> > > A follow-up to this problem: for some reason, FIJI thinks my images are
> > > interleaved rather than separate channels, even though they appear
> with a
> > > channel-slider--I've been able to separate the channels by using
> > > "deinterleave" rather than "split channels." I think this is probably a
> > > bona fide bug...
> > >
> > > JPK
> > >
> > > On Tue, Mar 31, 2015 at 9:51 PM, Rebecca Keller <[hidden email]>
> > > wrote:
> > >
> > > > Dear Imagers,
> > > >
> > > > Two things have recently happened with my LSM files:
> > > >
> > > > -I now need to import rather than just opening them
> > > >
> > > > -Split channels does not work; complains with "multichannel image
> > > > required." (But my images are multichannel, and I can see both with
> the
> > > > slider.)
> > > >
> > > > Neither of these was a problem before--any thoughts as to what's
> going
> > > on?
> > > >
> > > > JPK
> > > >
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> >
> >
> > --
> > Ignacio Arganda-Carreras, Ph.D.
> > Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech
> > Bâtiment 2
> > INRA Centre de Versailles-Grignon
> > Route de St-Cyr (RD10)
> > 78026 Versailles Cedex France
> >
> > Tel : +33 (0)1 30 83 30 00 - fax : +33 (0)1 30 83 33 19
> > Website: http://sites.google.com/site/iargandacarreras/
> > <http://biocomp.cnb.csic.es/~iarganda/index_EN.html>
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>