Clear Volume with MIJ(Tool that helps connect ImageJ to MATLAB)

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Clear Volume with MIJ(Tool that helps connect ImageJ to MATLAB)

Andres Barragan
For some reason Clear Volume does not appear when running Fiji through
MATLAB, most of the other plugins, that appear when running the
Application(.exe), are present but not all. I seem to be missing 63
commands from the 788. When looking at the list of commands that do not
appear their class seems to start with "command:"

For Example "Open in ClearVolume" Commands Class is:
    "command:de.mpicbg.jug.plugins.ClearVolumePlugin"

Ones that appear in both command finders do not start with the command:

Examples:

"Split Channels" commands Class is "ij.plugin.ChannelSplitter"
"Coloc 2" commands Class is "sc.fiji.coloc.Coloc_2"

And ideas to why I cannot run Clear Volume from Fiji when it is started
from MATLAB but I can run it when started from the Application(.exe).

Any help on this subject would be much appreciated.
--
*Andres Barragan*
College of Science
Computer Science Major
Sergeant-at-Arms - University of Arizona Rotaract
Campus Map Director - 3D4E
*e: [hidden email] <[hidden email]>
| p: 520-272-3640*

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Re: Clear Volume with MIJ(Tool that helps connect ImageJ to MATLAB)

Curtis Rueden
Hi Andres,

The commands starting with "command:" are ImageJ2 commands, rather than
ImageJ1 commands.

Are you using ImageJ-MATLAB [1]? Or Miji [2]?

If you haven't tried ImageJ-MATLAB, please give that a try.

Regards,
Curtis

[1] https://imagej.net/MATLAB_Scripting#Running_ImageJ_within_MATLAB
[2] https://imagej.net/Miji

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Wed, Jul 25, 2018 at 7:31 PM, Andres Barragan <
[hidden email]> wrote:

> For some reason Clear Volume does not appear when running Fiji through
> MATLAB, most of the other plugins, that appear when running the
> Application(.exe), are present but not all. I seem to be missing 63
> commands from the 788. When looking at the list of commands that do not
> appear their class seems to start with "command:"
>
> For Example "Open in ClearVolume" Commands Class is:
>     "command:de.mpicbg.jug.plugins.ClearVolumePlugin"
>
> Ones that appear in both command finders do not start with the command:
>
> Examples:
>
> "Split Channels" commands Class is "ij.plugin.ChannelSplitter"
> "Coloc 2" commands Class is "sc.fiji.coloc.Coloc_2"
>
> And ideas to why I cannot run Clear Volume from Fiji when it is started
> from MATLAB but I can run it when started from the Application(.exe).
>
> Any help on this subject would be much appreciated.
> --
> *Andres Barragan*
> College of Science
> Computer Science Major
> Sergeant-at-Arms - University of Arizona Rotaract
> Campus Map Director - 3D4E
> *e: [hidden email] <[hidden email]>
> | p: 520-272-3640*
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: Clear Volume with MIJ(Tool that helps connect ImageJ to MATLAB)

Andres Barragan
ClearVolume appears now in the plugins but I am getting an exception. Any
ideas? For some reason I do not get this exception when simply running the
executable of ImageJ.

On Wed, Aug 1, 2018 at 1:40 PM, Curtis Rueden <
[hidden email]> wrote:

> Hi Andres,
>
> The commands starting with "command:" are ImageJ2 commands, rather than
> ImageJ1 commands.
>
> Are you using ImageJ-MATLAB [1]? Or Miji [2]?
>
> If you haven't tried ImageJ-MATLAB, please give that a try.
>
> Regards,
> Curtis
>
> [1] https://imagej.net/MATLAB_Scripting#Running_ImageJ_within_MATLAB
> [2] https://imagej.net/Miji
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Wed, Jul 25, 2018 at 7:31 PM, Andres Barragan <
> [hidden email]> wrote:
>
> > For some reason Clear Volume does not appear when running Fiji through
> > MATLAB, most of the other plugins, that appear when running the
> > Application(.exe), are present but not all. I seem to be missing 63
> > commands from the 788. When looking at the list of commands that do not
> > appear their class seems to start with "command:"
> >
> > For Example "Open in ClearVolume" Commands Class is:
> >     "command:de.mpicbg.jug.plugins.ClearVolumePlugin"
> >
> > Ones that appear in both command finders do not start with the command:
> >
> > Examples:
> >
> > "Split Channels" commands Class is "ij.plugin.ChannelSplitter"
> > "Coloc 2" commands Class is "sc.fiji.coloc.Coloc_2"
> >
> > And ideas to why I cannot run Clear Volume from Fiji when it is started
> > from MATLAB but I can run it when started from the Application(.exe).
> >
> > Any help on this subject would be much appreciated.
> > --
> > *Andres Barragan*
> > College of Science
> > Computer Science Major
> > Sergeant-at-Arms - University of Arizona Rotaract
> > Campus Map Director - 3D4E
> > *e: [hidden email] <[hidden email]>
> > | p: 520-272-3640*
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>


--
*Andres Barragan*
College of Science
Computer Science Major
Sergeant-at-Arms - University of Arizona Rotaract
Campus Map Director - 3D4E
*e: [hidden email] <[hidden email]>
| p: 520-272-3640*

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

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Re: Clear Volume with MIJ(Tool that helps connect ImageJ to MATLAB)

Curtis Rueden
In reply to this post by Curtis Rueden
Hi Andres,

Thanks, I filed an issue in the relevant GitHub repository:

    https://github.com/ClearVolume/imglib2-clearvolume/issues/14

Just to set expectations: I would not expect a quick response, since the
people behind that plugin have moved on and/or are very busy with many
other things.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden


On Tue, Aug 7, 2018 at 1:27 PM, Andres Barragan <
[hidden email]> wrote:

> ClearVolume appears now in the plugins but I am getting an exception. Any
> ideas? For some reason I do not get this exception when simply running the
> executable of ImageJ.
>
> On Wed, Aug 1, 2018 at 1:40 PM, Curtis Rueden <
> [hidden email]> wrote:
>
> > Hi Andres,
> >
> > The commands starting with "command:" are ImageJ2 commands, rather than
> > ImageJ1 commands.
> >
> > Are you using ImageJ-MATLAB [1]? Or Miji [2]?
> >
> > If you haven't tried ImageJ-MATLAB, please give that a try.
> >
> > Regards,
> > Curtis
> >
> > [1] https://imagej.net/MATLAB_Scripting#Running_ImageJ_within_MATLAB
> > [2] https://imagej.net/Miji
> >
> > --
> > Curtis Rueden
> > LOCI software architect - https://loci.wisc.edu/software
> > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> > Did you know ImageJ has a forum? http://forum.imagej.net/
> >
> >
> > On Wed, Jul 25, 2018 at 7:31 PM, Andres Barragan <
> > [hidden email]> wrote:
> >
> > > For some reason Clear Volume does not appear when running Fiji through
> > > MATLAB, most of the other plugins, that appear when running the
> > > Application(.exe), are present but not all. I seem to be missing 63
> > > commands from the 788. When looking at the list of commands that do not
> > > appear their class seems to start with "command:"
> > >
> > > For Example "Open in ClearVolume" Commands Class is:
> > >     "command:de.mpicbg.jug.plugins.ClearVolumePlugin"
> > >
> > > Ones that appear in both command finders do not start with the command:
> > >
> > > Examples:
> > >
> > > "Split Channels" commands Class is "ij.plugin.ChannelSplitter"
> > > "Coloc 2" commands Class is "sc.fiji.coloc.Coloc_2"
> > >
> > > And ideas to why I cannot run Clear Volume from Fiji when it is started
> > > from MATLAB but I can run it when started from the Application(.exe).
> > >
> > > Any help on this subject would be much appreciated.
> > > --
> > > *Andres Barragan*
> > > College of Science
> > > Computer Science Major
> > > Sergeant-at-Arms - University of Arizona Rotaract
> > > Campus Map Director - 3D4E
> > > *e: [hidden email] <[hidden email]
> >
> > > | p: 520-272-3640*
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>
> --
> *Andres Barragan*
> College of Science
> Computer Science Major
> Sergeant-at-Arms - University of Arizona Rotaract
> Campus Map Director - 3D4E
> *e: [hidden email] <[hidden email]>
> | p: 520-272-3640*
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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