Re: ImageJ under Ubuntu 10.04 64-bit

Posted by Daniel James White on Mar 23, 2011; 10:41am
URL: http://imagej.273.s1.nabble.com/ImageJ-under-Ubuntu-10-04-64-bit-tp3685262p3685268.html

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 )