FIJI Plugin

[LMAnovitz]

I am trying to load 3D X-ray CT images obtained at the APS into FIJI.
According to the APS website, this requires two files, labeled

GSETomo.txt and NetCDF_-3.jar

The description of both how the data are processed, and how to visualize it with ImageJ is at

http://cars9.uchicago.edu/software/idl/tomography.html

Unfortunately, when I try to use FIJI’s Install Plugin feature it SAYS that GSETomo.txt has been installed, but
it does not show up under plugins, either immediately or after a restart.

Here is all that is in GSETomo.txt

run("Load NetCDF File");
run("XOR...", "value=1000000000000000 stack");
run("Calibrate...", "function=[Straight Line] unit=[Gray Value] text1=[0 65535] text2=[-32768 32767 ]");
run("Enhance Contrast", "saturated=0.5");


I am told this works on ImageJ, but not on FIJI, although I have not tried the former.
NetCDF does show up, and can be run, although it just yields a binary image.
Can anyone tell us how to fix this? Thank you.

—Larry Anovitz






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

[MRivers]

I think the current convention is files like the GSETomo one should have the .ijm (ImageJ Macro) extension rather than .txt.  I have tried that and the results are the same.  It does not show up in the plugins menu either before or after doing Install Plugin.

Note that the netCDF is not actually yielding a binary image.  It is interpreting your data as unsigned 16-bit integers, while it is actually signed 16-bit integers.  What the GSETomo macro does is some operations to get the netCDF data to display correctly as signed 16-bit integers.

Mark


From: Anovitz, Lawrence {Larry} M. [mailto:[hidden email]]
Sent: Tuesday, September 08, 2015 10:23 AM
To: [hidden email]
Subject: FIJI Plugin

I am trying to load 3D X-ray CT images obtained at the APS into FIJI.
According to the APS website, this requires two files, labeled

GSETomo.txt and NetCDF_-3.jar

The description of both how the data are processed, and how to visualize it with ImageJ is at

http://cars9.uchicago.edu/software/idl/tomography.html

Unfortunately, when I try to use FIJI’s Install Plugin feature it SAYS that GSETomo.txt has been installed, but
it does not show up under plugins, either immediately or after a restart.

Here is all that is in GSETomo.txt

run("Load NetCDF File");
run("XOR...", "value=1000000000000000 stack");
run("Calibrate...", "function=[Straight Line] unit=[Gray Value] text1=[0 65535] text2=[-32768 32767 ]");
run("Enhance Contrast", "saturated=0.5");


I am told this works on ImageJ, but not on FIJI, although I have not tried the former.
NetCDF does show up, and can be run, although it just yields a binary image.
Can anyone tell us how to fix this? Thank you.

—Larry Anovitz






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

[MRivers]

I just renamed GSETomo_.txt to GSETomo.ijm.

I updated to the latest version of ImageJ (1.50b) in a normal ImageJ (not Fiji) installation.  I put GSETomo.ijm in the ImageJ/plugins folder.  When ImageJ starts up it shows GSETomo in the plugins menu.  So it works fine.

I then did exactly the same thing with Fiji.  GSETomo does not show up in the plugins menu.  I also tried Plugins/Install Plugin and selected GSETomo.ijm.  It reported that it was installed and told me to restart Fiji, but GSETomo still does not appear in the plugins menu.  It appears that Fiji is not just ImageJ ☺

There must be some other trick required to get a macro to show up in the plugins menu in Fiji that is not required with regular ImageJ.

Mark



From: Anovitz, Lawrence {Larry} M. [mailto:[hidden email]]
Sent: Tuesday, September 08, 2015 10:23 AM
To: [hidden email]
Subject: FIJI Plugin

I am trying to load 3D X-ray CT images obtained at the APS into FIJI.
According to the APS website, this requires two files, labeled

GSETomo.txt and NetCDF_-3.jar

The description of both how the data are processed, and how to visualize it with ImageJ is at

http://cars9.uchicago.edu/software/idl/tomography.html

Unfortunately, when I try to use FIJI’s Install Plugin feature it SAYS that GSETomo.txt has been installed, but
it does not show up under plugins, either immediately or after a restart.

Here is all that is in GSETomo.txt

run("Load NetCDF File");
run("XOR...", "value=1000000000000000 stack");
run("Calibrate...", "function=[Straight Line] unit=[Gray Value] text1=[0 65535] text2=[-32768 32767 ]");
run("Enhance Contrast", "saturated=0.5");


I am told this works on ImageJ, but not on FIJI, although I have not tried the former.
NetCDF does show up, and can be run, although it just yields a binary image.
Can anyone tell us how to fix this? Thank you.

—Larry Anovitz






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

[Mark Hiner]

Hi Mark,

> There must be some other trick required to get a macro to show up in the
plugins menu in Fiji that is not required with regular ImageJ.

It needs an underscore. There is an underscore in the version shipped with
your idl_tomography.tar so simply renaming it to .ijm should be sufficient
(I just tested and GSETomo_.ijm in my Fiji.app/plugins/ directory worked).

I started an issue[1] for making this functionality a bit less confusing in
Fiji.

This would potentially be a good fit for an update site[2].

Best,
Mark Hiner
ImageJ2 developer
LOCI, UW-Madison

[1] https://github.com/imagej/imagej-legacy/issues/124
[2] http://imagej.net/How_to_set_up_and_populate_an_update_site

On Tue, Sep 8, 2015 at 11:45 AM, Mark Rivers <[hidden email]>
wrote:

> I just renamed GSETomo_.txt to GSETomo.ijm.
>
> I updated to the latest version of ImageJ (1.50b) in a normal ImageJ (not
> Fiji) installation.  I put GSETomo.ijm in the ImageJ/plugins folder.  When
> ImageJ starts up it shows GSETomo in the plugins menu.  So it works fine.
>
> I then did exactly the same thing with Fiji.  GSETomo does not show up in
> the plugins menu.  I also tried Plugins/Install Plugin and selected
> GSETomo.ijm.  It reported that it was installed and told me to restart
> Fiji, but GSETomo still does not appear in the plugins menu.  It appears
> that Fiji is not just ImageJ ☺
>
> There must be some other trick required to get a macro to show up in the
> plugins menu in Fiji that is not required with regular ImageJ.
>
> Mark
>
>
>
> From: Anovitz, Lawrence {Larry} M. [mailto:[hidden email]]
> Sent: Tuesday, September 08, 2015 10:23 AM
> To: [hidden email]
> Subject: FIJI Plugin
>
> I am trying to load 3D X-ray CT images obtained at the APS into FIJI.
> According to the APS website, this requires two files, labeled
>
> GSETomo.txt and NetCDF_-3.jar
>
> The description of both how the data are processed, and how to visualize
> it with ImageJ is at
>
> http://cars9.uchicago.edu/software/idl/tomography.html
>
> Unfortunately, when I try to use FIJI’s Install Plugin feature it SAYS
> that GSETomo.txt has been installed, but
> it does not show up under plugins, either immediately or after a restart.
>
> Here is all that is in GSETomo.txt
>
> run("Load NetCDF File");
> run("XOR...", "value=1000000000000000 stack");
> run("Calibrate...", "function=[Straight Line] unit=[Gray Value] text1=[0
> 65535] text2=[-32768 32767 ]");
> run("Enhance Contrast", "saturated=0.5");
>
>
> I am told this works on ImageJ, but not on FIJI, although I have not tried
> the former.
> NetCDF does show up, and can be run, although it just yields a binary
> image.
> Can anyone tell us how to fix this? Thank you.
>
> —Larry Anovitz
>
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[LMAnovitz]

I checked that the underscore was there, and changed .txt to .ijm
and still get the same results. Here is the current file name

GSETomo_.ijm

I also went into the advanced section of update FIJI and removed the .txt version
I get a warning that there are locally modified files but I don’t see any  un the advanced
section but I do see

plugins/GSETomo_ijm.txt Local-only

even thought the .txt is not in the file name

I also get an error when I do the plugin install in the log that states

ReferenceError: "importPackage" is not defined in <eval> at line number 1

even though it states that the installation was successful and asks me to restart ImageJ

—Larry

PS - I also get a window when I launch FIJI  listing Plugin configuration errors
warning that there are several duplicate commands, although none seems to be related to
GSETomo.  How do I fix these?

> On Sep 9, 2015, at 8:34 AM, Mark Hiner <[hidden email]> wrote:
>
> Hi Mark,
>
>> There must be some other trick required to get a macro to show up in the
> plugins menu in Fiji that is not required with regular ImageJ.
>
> It needs an underscore. There is an underscore in the version shipped with
> your idl_tomography.tar so simply renaming it to .ijm should be sufficient
> (I just tested and GSETomo_.ijm in my Fiji.app/plugins/ directory worked).
>
> I started an issue[1] for making this functionality a bit less confusing in
> Fiji.
>
> This would potentially be a good fit for an update site[2].
>
> Best,
> Mark Hiner
> ImageJ2 developer
> LOCI, UW-Madison
>
> [1] https://github.com/imagej/imagej-legacy/issues/124
> [2] http://imagej.net/How_to_set_up_and_populate_an_update_site
>
> On Tue, Sep 8, 2015 at 11:45 AM, Mark Rivers <[hidden email]>
> wrote:
>
>> I just renamed GSETomo_.txt to GSETomo.ijm.
>>
>> I updated to the latest version of ImageJ (1.50b) in a normal ImageJ (not
>> Fiji) installation.  I put GSETomo.ijm in the ImageJ/plugins folder.  When
>> ImageJ starts up it shows GSETomo in the plugins menu.  So it works fine.
>>
>> I then did exactly the same thing with Fiji.  GSETomo does not show up in
>> the plugins menu.  I also tried Plugins/Install Plugin and selected
>> GSETomo.ijm.  It reported that it was installed and told me to restart
>> Fiji, but GSETomo still does not appear in the plugins menu.  It appears
>> that Fiji is not just ImageJ ☺
>>
>> There must be some other trick required to get a macro to show up in the
>> plugins menu in Fiji that is not required with regular ImageJ.
>>
>> Mark
>>
>>
>>
>> From: Anovitz, Lawrence {Larry} M. [mailto:[hidden email]]
>> Sent: Tuesday, September 08, 2015 10:23 AM
>> To: [hidden email]
>> Subject: FIJI Plugin
>>
>> I am trying to load 3D X-ray CT images obtained at the APS into FIJI.
>> According to the APS website, this requires two files, labeled
>>
>> GSETomo.txt and NetCDF_-3.jar
>>
>> The description of both how the data are processed, and how to visualize
>> it with ImageJ is at
>>
>> http://cars9.uchicago.edu/software/idl/tomography.html
>>
>> Unfortunately, when I try to use FIJI’s Install Plugin feature it SAYS
>> that GSETomo.txt has been installed, but
>> it does not show up under plugins, either immediately or after a restart.
>>
>> Here is all that is in GSETomo.txt
>>
>> run("Load NetCDF File");
>> run("XOR...", "value=1000000000000000 stack");
>> run("Calibrate...", "function=[Straight Line] unit=[Gray Value] text1=[0
>> 65535] text2=[-32768 32767 ]");
>> run("Enhance Contrast", "saturated=0.5");
>>
>>
>> I am told this works on ImageJ, but not on FIJI, although I have not tried
>> the former.
>> NetCDF does show up, and can be run, although it just yields a binary
>> image.
>> Can anyone tell us how to fix this? Thank you.
>>
>> —Larry Anovitz
>>
>>
>>
>>
>>
>>
>> --
>> 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

[Mark Hiner]

Hi Larry,

> even thought the .txt is not in the file name

Sometimes your operating system will not allow you to change file
extensions by default. If you're using Windows, for example, make sure you
do not have hidden file extensions[1] and then rename the file to remove
the .txt.

> even though it states that the installation was successful and asks me to
restart ImageJ

"Successful installation" is just copying the file to your plugins
directory; right now there is no mechanism to ensure what was installed is
actually useful or correct.

> I also get a window when I launch FIJI  listing Plugin configuration
errors warning that there are several duplicate commands, although none
seems to be related to GSETomo.  How do I fix these?

Do you get a list of what's duplicated? It's hard to know what actions were
taken to get to that state, but what you want is to delete the duplicates.
You can do so manually and then run "Help>Update Fiji" to ensure you're up
to date. I also think if you have duplicates and run "Help>Update Fiji" it
will complain and offer to delete the duplicates for you? But maybe not.
You can also use "Help>Report a bug" which will display your full
installation details to help determine what's been duplicated.

Best,
Mark

[1]
http://windows.microsoft.com/en-us/windows/show-hide-file-name-extensions#show-hide-file-name-extensions=windows-7

On Wed, Sep 9, 2015 at 8:11 AM, Anovitz, Lawrence {Larry} M. <
[hidden email]> wrote:

> I checked that the underscore was there, and changed .txt to .ijm
> and still get the same results. Here is the current file name
>
> GSETomo_.ijm
>
> I also went into the advanced section of update FIJI and removed the .txt
> version
> I get a warning that there are locally modified files but I don’t see any
> un the advanced
> section but I do see
>
> plugins/GSETomo_ijm.txt                         Local-only
>
> even thought the .txt is not in the file name
>
> I also get an error when I do the plugin install in the log that states
>
> ReferenceError: "importPackage" is not defined in <eval> at line number 1
>
> even though it states that the installation was successful and asks me to
> restart ImageJ
>
> —Larry
>
> PS - I also get a window when I launch FIJI  listing Plugin configuration
> errors
> warning that there are several duplicate commands, although none seems to
> be related to
> GSETomo.  How do I fix these?
>
>
>
>
>
>
>
> > On Sep 9, 2015, at 8:34 AM, Mark Hiner <[hidden email]> wrote:
> >
> > Hi Mark,
> >
> >> There must be some other trick required to get a macro to show up in the
> > plugins menu in Fiji that is not required with regular ImageJ.
> >
> > It needs an underscore. There is an underscore in the version shipped
> with
> > your idl_tomography.tar so simply renaming it to .ijm should be
> sufficient
> > (I just tested and GSETomo_.ijm in my Fiji.app/plugins/ directory
> worked).
> >
> > I started an issue[1] for making this functionality a bit less confusing
> in
> > Fiji.
> >
> > This would potentially be a good fit for an update site[2].
> >
> > Best,
> > Mark Hiner
> > ImageJ2 developer
> > LOCI, UW-Madison
> >
> > [1] https://github.com/imagej/imagej-legacy/issues/124
> > [2] http://imagej.net/How_to_set_up_and_populate_an_update_site
> >
> > On Tue, Sep 8, 2015 at 11:45 AM, Mark Rivers <[hidden email]>
> > wrote:
> >
> >> I just renamed GSETomo_.txt to GSETomo.ijm.
> >>
> >> I updated to the latest version of ImageJ (1.50b) in a normal ImageJ
> (not
> >> Fiji) installation.  I put GSETomo.ijm in the ImageJ/plugins folder.
> When
> >> ImageJ starts up it shows GSETomo in the plugins menu.  So it works
> fine.
> >>
> >> I then did exactly the same thing with Fiji.  GSETomo does not show up
> in
> >> the plugins menu.  I also tried Plugins/Install Plugin and selected
> >> GSETomo.ijm.  It reported that it was installed and told me to restart
> >> Fiji, but GSETomo still does not appear in the plugins menu.  It appears
> >> that Fiji is not just ImageJ ☺
> >>
> >> There must be some other trick required to get a macro to show up in the
> >> plugins menu in Fiji that is not required with regular ImageJ.
> >>
> >> Mark
> >>
> >>
> >>
> >> From: Anovitz, Lawrence {Larry} M. [mailto:[hidden email]]
> >> Sent: Tuesday, September 08, 2015 10:23 AM
> >> To: [hidden email]
> >> Subject: FIJI Plugin
> >>
> >> I am trying to load 3D X-ray CT images obtained at the APS into FIJI.
> >> According to the APS website, this requires two files, labeled
> >>
> >> GSETomo.txt and NetCDF_-3.jar
> >>
> >> The description of both how the data are processed, and how to visualize
> >> it with ImageJ is at
> >>
> >> http://cars9.uchicago.edu/software/idl/tomography.html
> >>
> >> Unfortunately, when I try to use FIJI’s Install Plugin feature it SAYS
> >> that GSETomo.txt has been installed, but
> >> it does not show up under plugins, either immediately or after a
> restart.
> >>
> >> Here is all that is in GSETomo.txt
> >>
> >> run("Load NetCDF File");
> >> run("XOR...", "value=1000000000000000 stack");
> >> run("Calibrate...", "function=[Straight Line] unit=[Gray Value] text1=[0
> >> 65535] text2=[-32768 32767 ]");
> >> run("Enhance Contrast", "saturated=0.5");
> >>
> >>
> >> I am told this works on ImageJ, but not on FIJI, although I have not
> tried
> >> the former.
> >> NetCDF does show up, and can be run, although it just yields a binary
> >> image.
> >> Can anyone tell us how to fix this? Thank you.
> >>
> >> —Larry Anovitz
> >>
> >>
> >>
> >>
> >>
> >>
> >> --
> >> 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
>

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

[MRivers]

The suggestion to add an underscore worked for me.  As soon as I renamed the file to GSETomo_.ijm and started Fiji then GSETomo appeared as the last item in the Plugins menu.  Thanks to Mark Hiner and Wayne Rasband (who replied by e-mail directly) for suggesting this.  Larry, did you look down at the very bottom of the plugin list?  If so, then perhaps you should try a fresh install of Fiji.

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

[LMAnovitz]

the solution was interesting
I’m on a MAC, so changing extensions is usually not a problem.  In this case, however, it was hidden
you have to select the file, hit cmd + i to get info on the file, then change the name under name and extension
then it worked

—larry

> On Sep 9, 2015, at 1:46 PM, Mark Rivers <[hidden email]> wrote:
>
> The suggestion to add an underscore worked for me.  As soon as I renamed the file to GSETomo_.ijm and started Fiji then GSETomo appeared as the last item in the Plugins menu.  Thanks to Mark Hiner and Wayne Rasband (who replied by e-mail directly) for suggesting this.  Larry, did you look down at the very bottom of the plugin list?  If so, then perhaps you should try a fresh install of Fiji.
>
>


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