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 |
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 |
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 Exception.txt (2K) Download Attachment |
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 |
Any updates on my situation?
On Tue, Aug 7, 2018 at 12:19 PM Curtis Rueden < [hidden email]> wrote: > 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 > -- *Andres Barragan* College of Science Computer Science Major ECE, Physics, Mathematics Minors Undergraduate Research Student, Medical Imaging Vice President - 3D4E CV Arizona Autonomous *e: [hidden email] <[hidden email]> | p: 520-272-3640* -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
In reply to this post by Curtis Rueden
Hi Andres,
> Any updates on my situation? Did you read the comment thread of the issue? https://github.com/ClearVolume/imglib2-clearvolume/issues/14 There, I suggested an idea you could try. Best would be to follow up on that issue thread. Regards, Curtis -- 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? https://forum.image.sc/ On Fri, Oct 5, 2018 at 6:10 PM Andres Barragan < [hidden email]> wrote: > Any updates on my situation? > > On Tue, Aug 7, 2018 at 12:19 PM Curtis Rueden < > [hidden email]> wrote: > > > 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 > > > > > -- > *Andres Barragan* > College of Science > Computer Science Major > ECE, Physics, Mathematics Minors > Undergraduate Research Student, Medical Imaging > Vice President - 3D4E > CV Arizona Autonomous > > *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 |
Didn't know that existed. I'll test the idea first thing Monday.
On Fri, Oct 5, 2018, 9:46 PM Curtis Rueden < [hidden email]> wrote: > Hi Andres, > > > Any updates on my situation? > > Did you read the comment thread of the issue? > https://github.com/ClearVolume/imglib2-clearvolume/issues/14 > > There, I suggested an idea you could try. Best would be to follow up on > that issue thread. > > Regards, > Curtis > > -- > 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? https://forum.image.sc/ > > > > On Fri, Oct 5, 2018 at 6:10 PM Andres Barragan < > [hidden email]> wrote: > > > Any updates on my situation? > > > > On Tue, Aug 7, 2018 at 12:19 PM Curtis Rueden < > > [hidden email]> wrote: > > > > > 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 > > > > > > > > > -- > > *Andres Barragan* > > College of Science > > Computer Science Major > > ECE, Physics, Mathematics Minors > > Undergraduate Research Student, Medical Imaging > > Vice President - 3D4E > > CV Arizona Autonomous > > > > *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 > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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