Problem with reading Leica .lei files

[Joel Sheffield]

Greetings,

After many years of being able to read the Leica .lei files with LOCI, I
have suddenly been unable to open the files correctly.  I am running the
latest version of ImageJ, 32 bit, running on Java 1.6.0_25 and the latest
version of Loci tools.  When I drag or click on the .lei file, I see the
normal set of operations --ie. "reading base data, populating metadata
etc.", but then, instead of the usual LOCI menu, I get a single, two
channel image of a single plane.  The occurs even if I have multiple data
sets within the Leica directory.  Oddly, this happens on two of my
computers, one running XP and the other running Win7.  It does not happen
on a third computer, which is a tablet running XP.  MIght it be in the Java
installation?

Thanks for all of your help, as usual.

--


Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs

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

[Aurélien Dauphin]

Hello,

If this help : the latest version of Loci is still working with .lei
files on an ImageJ 64 bits running openjdk-7-jre 7u15-2.3.7 on
Ubuntu1~12.04.1

Cheers
Aurélien

On 04/07/2013 07:15 PM, JOEL B. SHEFFIELD wrote:

> Greetings,
>
> After many years of being able to read the Leica .lei files with LOCI, I
> have suddenly been unable to open the files correctly.  I am running the
> latest version of ImageJ, 32 bit, running on Java 1.6.0_25 and the latest
> version of Loci tools.  When I drag or click on the .lei file, I see the
> normal set of operations --ie. "reading base data, populating metadata
> etc.", but then, instead of the usual LOCI menu, I get a single, two
> channel image of a single plane.  The occurs even if I have multiple data
> sets within the Leica directory.  Oddly, this happens on two of my
> computers, one running XP and the other running Win7.  It does not happen
> on a third computer, which is a tablet running XP.  MIght it be in the Java
> installation?
>
> Thanks for all of your help, as usual.
>

--
Dr. Aurélien Dauphin
Directeur adjoint
Plateforme d'Imagerie Cellulaire de la Pitié-Salpêtrière
Bât. ICM
Hôpital de la Pitié Salpêtrière
47 Bd de l'Hôpital,
75013 Paris
Tel : ++33 (1) 57 27 45 10
http://picps.upmc.fr/
http://icm-institute.org/menu/fondation/se-rendre-a-licm

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

[Melissa Linkert-2]

Hi Joel,

> After many years of being able to read the Leica .lei files with LOCI, I
> have suddenly been unable to open the files correctly.  I am running the
> latest version of ImageJ, 32 bit, running on Java 1.6.0_25 and the latest
> version of Loci tools.  When I drag or click on the .lei file, I see the
> normal set of operations --ie. "reading base data, populating metadata
> etc.", but then, instead of the usual LOCI menu, I get a single, two
> channel image of a single plane.  The occurs even if I have multiple data
> sets within the Leica directory.  Oddly, this happens on two of my
> computers, one running XP and the other running Win7.  It does not happen
> on a third computer, which is a tablet running XP.  MIght it be in the Java
> installation?

I would guess that either the two non-working computers have a different
version of Bio-Formats installed, or there is some other plugin
installed that reads .lei files.

What is the version number and build date shown in "Help > About Plugins > LOCI
Plugins"?  Is it the same for all three computers?

Do you see the same behavior if you open the dataset by clicking "Plugin >
LOCI > Bio-Formats Importer" and then choosing the .lei file?

Regards,
-Melissa

On Sun, Apr 07, 2013 at 01:15:36PM -0400, JOEL B. SHEFFIELD wrote:

> Greetings,
>
> After many years of being able to read the Leica .lei files with LOCI, I
> have suddenly been unable to open the files correctly.  I am running the
> latest version of ImageJ, 32 bit, running on Java 1.6.0_25 and the latest
> version of Loci tools.  When I drag or click on the .lei file, I see the
> normal set of operations --ie. "reading base data, populating metadata
> etc.", but then, instead of the usual LOCI menu, I get a single, two
> channel image of a single plane.  The occurs even if I have multiple data
> sets within the Leica directory.  Oddly, this happens on two of my
> computers, one running XP and the other running Win7.  It does not happen
> on a third computer, which is a tablet running XP.  MIght it be in the Java
> installation?
>
> Thanks for all of your help, as usual.
>
> --
>
>
> Joel B. Sheffield, Ph.D
> Department of Biology
> Temple University
> Philadelphia, PA 19122
> Voice: 215 204 8839
> e-mail: [hidden email]
> URL:  http://astro.temple.edu/~jbs
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[Melissa Linkert-2]

Hi Joel,

> > The Loci tools Jar on the working computer is old, revision 6126, April
> > 2010 build, trunk release, installed 4/14/2010
> >
> > The version on the computer that does not work is f796122 built 2, Jan
> > 2012, Release 4.4 Dev, installed 4/4/2013

Note that the latest stable version is 4.4.6, from January 2013.

> > BUT.  I just copied the old version to my newer computer, first renaming
> > the existing jar file, and I get the same behavior.
> >
> > AND when I copy the newest build to the functioning computer, it works
> > fine.
> >
> > On both machines, the Java is 1.6.0., but on the computer that is
> > misbehaving, it is version _25 , according to the ImageJ header.
>
> Whoops, I forgot to add that if I go from the LOCI menu and select
> "importer", it seems to work fine.

I think that fairly safely rules out a problem with Bio-Formats.

It's possible that there is a plugin installed on the non-working
computer that takes precedence in opening Leica datasets, so I would suggest
making sure that the exact same plugins are installed on both computers.

If that doesn't fix the problem, then the only other thing I can think
of is that somehow on the non-working computer one of the TIFF files is being
dragged and dropped (instead of the .lei file).

Regards,
-Melissa

On Mon, Apr 08, 2013 at 10:00:52AM -0400, JOEL B. SHEFFIELD wrote:

> Whoops, I forgot to add that if I go from the LOCI menu and select
> "importer", it seems to work fine.
> Joel
>
>
>
> On Mon, Apr 8, 2013 at 9:54 AM, JOEL B. SHEFFIELD <[hidden email]> wrote:
>
> > Hi Melissa,
> >
> > The Loci tools Jar on the working computer is old, revision 6126, April
> > 2010 build, trunk release, installed 4/14/2010
> >
> > The version on the computer that does not work is f796122 built 2, Jan
> > 2012, Release 4.4 Dev, installed 4/4/2013
> >
> > BUT.  I just copied the old version to my newer computer, first renaming
> > the existing jar file, and I get the same behavior.
> >
> > AND when I copy the newest build to the functioning computer, it works
> > fine.
> >
> > On both machines, the Java is 1.6.0., but on the computer that is
> > misbehaving, it is version _25 , according to the ImageJ header.
> >
> >
> >
> > Joel
> >
> >
> > On Mon, Apr 8, 2013 at 9:25 AM, Melissa Linkert <
> > [hidden email]> wrote:
> >
> >> Hi Joel,
> >>
> >> > After many years of being able to read the Leica .lei files with LOCI, I
> >> > have suddenly been unable to open the files correctly.  I am running the
> >> > latest version of ImageJ, 32 bit, running on Java 1.6.0_25 and the
> >> latest
> >> > version of Loci tools.  When I drag or click on the .lei file, I see the
> >> > normal set of operations --ie. "reading base data, populating metadata
> >> > etc.", but then, instead of the usual LOCI menu, I get a single, two
> >> > channel image of a single plane.  The occurs even if I have multiple
> >> data
> >> > sets within the Leica directory.  Oddly, this happens on two of my
> >> > computers, one running XP and the other running Win7.  It does not
> >> happen
> >> > on a third computer, which is a tablet running XP.  MIght it be in the
> >> Java
> >> > installation?
> >>
> >> I would guess that either the two non-working computers have a different
> >> version of Bio-Formats installed, or there is some other plugin
> >> installed that reads .lei files.
> >>
> >> What is the version number and build date shown in "Help > About Plugins
> >> > LOCI
> >> Plugins"?  Is it the same for all three computers?
> >>
> >> Do you see the same behavior if you open the dataset by clicking "Plugin >
> >> LOCI > Bio-Formats Importer" and then choosing the .lei file?
> >>
> >> Regards,
> >> -Melissa
> >>
> >> On Sun, Apr 07, 2013 at 01:15:36PM -0400, JOEL B. SHEFFIELD wrote:
> >> > Greetings,
> >> >
> >> > After many years of being able to read the Leica .lei files with LOCI, I
> >> > have suddenly been unable to open the files correctly.  I am running the
> >> > latest version of ImageJ, 32 bit, running on Java 1.6.0_25 and the
> >> latest
> >> > version of Loci tools.  When I drag or click on the .lei file, I see the
> >> > normal set of operations --ie. "reading base data, populating metadata
> >> > etc.", but then, instead of the usual LOCI menu, I get a single, two
> >> > channel image of a single plane.  The occurs even if I have multiple
> >> data
> >> > sets within the Leica directory.  Oddly, this happens on two of my
> >> > computers, one running XP and the other running Win7.  It does not
> >> happen
> >> > on a third computer, which is a tablet running XP.  MIght it be in the
> >> Java
> >> > installation?
> >> >
> >> > Thanks for all of your help, as usual.
> >> >
> >> > --
> >> >
> >> >
> >> > Joel B. Sheffield, Ph.D
> >> > Department of Biology
> >> > Temple University
> >> > Philadelphia, PA 19122
> >> > Voice: 215 204 8839
> >> > e-mail: [hidden email]
> >> > URL:  http://astro.temple.edu/~jbs
> >> >
> >> > --
> >> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >>
> >
> >
> >
> > --
> >
> >
> > Joel B. Sheffield, Ph.D
> > Department of Biology
> > Temple University
> > Philadelphia, PA 19122
> > Voice: 215 204 8839
> > e-mail: [hidden email]
> > URL:  http://astro.temple.edu/~jbs
> >
>
>
>
> --
>
>
> Joel B. Sheffield, Ph.D
> Department of Biology
> Temple University
> Philadelphia, PA 19122
> Voice: 215 204 8839
> e-mail: [hidden email]
> URL:  http://astro.temple.edu/~jbs

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