ImageJ under Ubuntu 10.04 64-bit

[Divakar Ramachandran-2]

Hello,

I have just started using ImageJ under Linux (Ubuntu 10.04 LTS 64-bit)
and would like to get clarification regarding to the following points:

1. Is there a Ubuntu (deb) package for default plugins and macros? Both
paths listed in man page (under /usr/share/... and ~/.imageJ are
practically empty.
2. I have copied some of my essential plugins directly from ImageJ
website into the latter path and this seems to work fine. Will there be
any stability or other issues with this? Should I be doing 'sudo cp'
into /usr/share instead? I guess these will not be updated when I
auto-update ImageJ - which could be a blessing for plugins such as
Microscope_Scale.
3. How do I compile a modified plugin from the command line, preferably
using the system installed jdk?

Thanks,
Divakar


--
*Divakar Ramachandran* _Anupuram, TN 603127, INDIA._

[Divakar Ramachandran-2]

On Monday 21 March 2011 04:10 PM, Daniel James White wrote:

> Hi,
>
>
>
> On Mar 21, 2011, at 5:00 AM, IMAGEJ automatic digest system wrote:
>
>> Date:    Mon, 21 Mar 2011 00:23:20 +0530
>> From:    Divakar Ramachandran <[hidden email]>
>> Subject: ImageJ under Ubuntu 10.04 64-bit
>>
>> Hello,
>>
>> I have just started using ImageJ under Linux (Ubuntu 10.04 LTS 64-bit)
>> and would like to get clarification regarding to the following points:
>>
>> 1. Is there a Ubuntu (deb) package for default plugins and macros? Both
>> paths listed in man page (under /usr/share/... and ~/.imageJ are
>> practically empty.
>> 2. I have copied some of my essential plugins directly from ImageJ
>> website into the latter path and this seems to work fine. Will there be
>> any stability or other issues with this? Should I be doing 'sudo cp'
>> into /usr/share instead? I guess these will not be updated when I
>> auto-update ImageJ - which could be a blessing for plugins such as
>> Microscope_Scale.
>> 3. How do I compile a modified plugin from the command line, preferably
>> using the system installed jdk?
>
> you need to use Fiji (is just imageJ - batteries included)
>
> it s a distribution of imageJ that contains the stuff you need , as you describe below.
>
> see
>
>
> http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
>
> cheers
>
>
> Dan
>

Thanks, Dan. I have had a quick look at Fiji. It seems to be a good
package for life science work. However, the only pointer to plugin
compilation I found was to use the Compile and Run menu option. This
works only when you install ImageJ along with a JRE. A couple of years
ago there was a posting on this mail list giving a command-line syntax
for compiling ImageJ on a windows OS computer. I have unfortunately lost
the post and am also not able to find it on the archives in spite of
trying all search terms I could think of. I would like to use this type
of command on the Linux box for ImageJ / plugins. Is this possible and
if so, could someone point me to the original post / solution.

Divakar

>> Thanks,
>> Divakar
>>
>>
>> --
>> *Divakar Ramachandran* _Anupuram, TN 603127, INDIA._
> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Visualisation, Processing and Analysis
> Light Microscopy and Image Processing Facilities
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstrasse 108
> 01307 DRESDEN
> Germany
>
> [phone] (German Mobile)
> [phone] (Work phone at MPI-CBG)
> [phone] (Fax MPI-CBG LMF)
>
> http://www.bioimagexd.net  BioImageXD
> http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
> http://www.chalkie.org.uk                Dan's Homepages
> https://ifn.mpi-cbg.de  Dresden Imaging Facility Network
> dan (at) chalkie.org.uk
> ( white (at) mpi-cbg.de )

[dscho]

Hi,

On Mon, 21 Mar 2011, Divakar Ramachandran wrote:

> On Monday 21 March 2011 04:10 PM, Daniel James White wrote:
> >
> > On Mar 21, 2011, at 5:00 AM, IMAGEJ automatic digest system wrote:
> >
> >> From:    Divakar Ramachandran <[hidden email]>
> >>
> >> I have just started using ImageJ under Linux (Ubuntu 10.04 LTS
> >> 64-bit) and would like to get clarification regarding to the
> >> following points:
> >>
> >> 1. Is there a Ubuntu (deb) package for default plugins and macros?
> >>    Both paths listed in man page (under /usr/share/... and ~/.imageJ
> >>    are practically empty.
> >> 2. I have copied some of my essential plugins directly from ImageJ
> >>    website into the latter path and this seems to work fine. Will
> >>    there be any stability or other issues with this? Should I be
> >>    doing 'sudo cp' into /usr/share instead? I guess these will not be
> >>    updated when I auto-update ImageJ - which could be a blessing for
> >>    plugins such as Microscope_Scale.
> >> 3. How do I compile a modified plugin from the command line,
> >>    preferably using the system installed jdk?
> >
> > you need to use Fiji (is just imageJ - batteries included)
> >
> > it s a distribution of imageJ that contains the stuff you need , as
> > you describe below.
> >
> > see
> >
> >
> > http://pacific.mpi-cbg.de Fiji - is just ImageJ (Batteries Included)
>
> Thanks, Dan. I have had a quick look at Fiji. It seems to be a good
> package for life science work.

Not only life science.

> However, the only pointer to plugin compilation I found was to use the
> Compile and Run menu option.

There is also a Fiji Build system which allows defining dependencies
between multiple components.

> This works only when you install ImageJ along with a JRE.

You meant a JDK.

Fiji comes with a JRE, but includes javac specifically. So if you have a
plugin that consists of a single class (possibly including nested
classes), you can load it into the Script Editor and run it. Or you copy
the .java file into plugins/ and run it transparently, as if it was a
script.

> A couple of years ago there was a posting on this mail list giving a
> command-line syntax for compiling ImageJ on a windows OS computer.

It is easy:

        javac -cp /path/to/ij.jar path/to/source.java

The more relevant question, though, is probably: what exactly do you want
to do? Yes, you said you want to compile via command-line. There is a good
possibility, though, that there is a better solution for your problem, if
only that problem is clearly stated.

Hth,
Johannes

[Daniel James White]

Hi Divakar

On Mar 23, 2011, at 5:00 AM, IMAGEJ automatic digest system wrote:

> Date:    Mon, 21 Mar 2011 20:34:44 +0530
> From:    Divakar Ramachandran <[hidden email]>
> Subject: Re: ImageJ under Ubuntu 10.04 64-bit
>
> On Monday 21 March 2011 04:10 PM, Daniel James White wrote:
>> Hi,
>>
>>
>>
>> On Mar 21, 2011, at 5:00 AM, IMAGEJ automatic digest system wrote:
>>
>>> Date:    Mon, 21 Mar 2011 00:23:20 +0530
>>> From:    Divakar Ramachandran <[hidden email]>
>>> Subject: ImageJ under Ubuntu 10.04 64-bit
>>>
>>> Hello,
>>>
>>> I have just started using ImageJ under Linux (Ubuntu 10.04 LTS 64-bit)
>>> and would like to get clarification regarding to the following points:
>>>
>>> 1. Is there a Ubuntu (deb) package for default plugins and macros? Both
>>> paths listed in man page (under /usr/share/... and ~/.imageJ are
>>> practically empty.
>>> 2. I have copied some of my essential plugins directly from ImageJ
>>> website into the latter path and this seems to work fine. Will there be
>>> any stability or other issues with this? Should I be doing 'sudo cp'
>>> into /usr/share instead? I guess these will not be updated when I
>>> auto-update ImageJ - which could be a blessing for plugins such as
>>> Microscope_Scale.
>>> 3. How do I compile a modified plugin from the command line, preferably
>>> using the system installed jdk?
>>
>> you need to use Fiji (is just imageJ - batteries included)
>>
>> it s a distribution of imageJ that contains the stuff you need , as you describe below.
>>
>> see
>>
>>
>> http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
>>
>> cheers
>>
>>
>> Dan
>>
>
> Thanks, Dan. I have had a quick look at Fiji. It seems to be a good
> package for life science work. However, the only pointer to plugin
> compilation I found was to use the Compile and Run menu option. This
> works only when you install ImageJ along with a JRE.

Look at the script editor...
it gives you a IDE for imageJ plugin development with syntax editing, compiler, stout

http://pacific.mpi-cbg.de/wiki/index.php/Script_Editor
http://pacific.mpi-cbg.de/wiki/index.php/Using_the_Script_Editor

sorry for not making it clear the first time.

> A couple of years
> ago there was a posting on this mail list giving a command-line syntax
> for compiling ImageJ on a windows OS computer. I have unfortunately lost
> the post and am also not able to find it on the archives in spite of
> trying all search terms I could think of. I would like to use this type
> of command on the Linux box for ImageJ / plugins. Is this possible and
> if so, could someone point me to the original post / solution.

use the script editor... its all ready to go for what you want to do,
and built into the Fiji disreubution of imageJ (think Ubuntu linux vx the linux kernel)

cheers
Dan

>
> Divakar

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )

[Divakar Ramachandran-2]

On Tuesday 22 March 2011 08:34 PM, Johannes Schindelin wrote:

> Hi,
>
> On Mon, 21 Mar 2011, Divakar Ramachandran wrote:
>
>> On Monday 21 March 2011 04:10 PM, Daniel James White wrote:
>>> On Mar 21, 2011, at 5:00 AM, IMAGEJ automatic digest system wrote:
>>>
>>>> From:    Divakar Ramachandran <[hidden email]>
>>>>
>>>> I have just started using ImageJ under Linux (Ubuntu 10.04 LTS
>>>> 64-bit) and would like to get clarification regarding to the
>>>> following points:
>>>>
>>>> 1. Is there a Ubuntu (deb) package for default plugins and macros?
>>>>    Both paths listed in man page (under /usr/share/... and ~/.imageJ
>>>>    are practically empty.
>>>> 2. I have copied some of my essential plugins directly from ImageJ
>>>>    website into the latter path and this seems to work fine. Will
>>>>    there be any stability or other issues with this? Should I be
>>>>    doing 'sudo cp' into /usr/share instead? I guess these will not be
>>>>    updated when I auto-update ImageJ - which could be a blessing for
>>>>    plugins such as Microscope_Scale.
>>>> 3. How do I compile a modified plugin from the command line,
>>>>    preferably using the system installed jdk?
>>> you need to use Fiji (is just imageJ - batteries included)
>>>
>>> it s a distribution of imageJ that contains the stuff you need , as
>>> you describe below.
>>>
>>> see
>>>
>>>
>>> http://pacific.mpi-cbg.de Fiji - is just ImageJ (Batteries Included)
>> Thanks, Dan. I have had a quick look at Fiji. It seems to be a good
>> package for life science work.
> Not only life science.
>
>> However, the only pointer to plugin compilation I found was to use the
>> Compile and Run menu option.
> There is also a Fiji Build system which allows defining dependencies
> between multiple components.
>
>> This works only when you install ImageJ along with a JRE.
> You meant a JDK.

Yes. Sorry for the typo.

> Fiji comes with a JRE, but includes javac specifically. So if you have a
> plugin that consists of a single class (possibly including nested
> classes), you can load it into the Script Editor and run it. Or you copy
> the .java file into plugins/ and run it transparently, as if it was a
> script.
>
>> A couple of years ago there was a posting on this mail list giving a
>> command-line syntax for compiling ImageJ on a windows OS computer.
> It is easy:
>
> javac -cp /path/to/ij.jar path/to/source.java
>

This works great, Thanks! It took me some time to locate - the path to
ij.jar on Ubuntu 10.04 LTS 64-bit is /usr/share/java/ij.jar.

> The more relevant question, though, is probably: what exactly do you want
> to do? Yes, you said you want to compile via command-line. There is a good
> possibility, though, that there is a better solution for your problem, if
> only that problem is clearly stated.
>
> Hth,
> Johannes
Thanks Johannes. The immediate problem I had was to be able to compile a
given java source in plugins directory to a class file that can be run
form the plugins menu. For example, the command-line compilation works
quick and simple for things like re-compiling Microscope_Scale.java with
the regularly updated calibration numbers for our TEM.

My background is in Metallurgy and high-resolution TEM. Goal for me with
ImageJ is to be able to translate my Semper scripts into working ImageJ
macros / plugins since we no longer have computers that can run Semper
for Windows. Some stuff are amenable for ad-hoc macros or combinations
of operations from existing ImageJ functionality and plugins available.
Others would require custom plugins. At the moment we are using ImageJ
for scale markers and measurements on diffraction patterns and lattice
images. More complex quantification methods I will be trying to
implement will be filtering based on user selected regions of power
spectra of lattice images and quantification of strain. I am sure to
come up with more specific problems and successes as I work, which I can
share on the list.

Regards,
Divakar

[dscho]

Hi,

if you want to guarantee that I do not miss your answers to my mail,
please consider Reply-to-all in the future.

On Sat, 26 Mar 2011, Divakar Ramachandran wrote:

> The immediate problem I had was to be able to compile a given java
> source in plugins directory to a class file that can be run form the
> plugins menu.

If you use Fiji, you can accomplish that by simply copying your .java file
into Fiji.app/plugins/ and either (re-)starting Fiji or clicking on
Help>Refresh Menus.

Ciao,
Johannes

[Divakar Ramachandran-2]

On Saturday 26 March 2011 02:28 PM, Johannes Schindelin wrote:

> Hi,
>
> if you want to guarantee that I do not miss your answers to my mail,
> please consider Reply-to-all in the future.
>
> On Sat, 26 Mar 2011, Divakar Ramachandran wrote:
>
>> The immediate problem I had was to be able to compile a given java
>> source in plugins directory to a class file that can be run form the
>> plugins menu.
> If you use Fiji, you can accomplish that by simply copying your .java file
> into Fiji.app/plugins/ and either (re-)starting Fiji or clicking on
> Help>Refresh Menus.
>
> Ciao,
> Johannes

Thanks,

Divakar.