How to publish a plugin

[Daniel Lélis Baggio]

Hi, all.
I have checked the old files and found that the way of publishing a plugin
to ImageJ official plugins page was sending an e-mail to Wayne... but as
I've searched for him, and saw that his last message was in 2004, do you
know if there's a different way to publish a plugin?
I would like to publish a LiveWire Segmentation plugin, whose info is at:
http://ivussnakes.sourceforge.net/
Thanks in advance, and congratulations for the great software!

[Vincenzo Della Mea]

Il giorno 26/set/06, alle ore 08:41, Daniel Lelis Baggio ha scritto:
> Hi, all.
> I have checked the old files and found that the way of publishing a  
> plugin
> to ImageJ official plugins page was sending an e-mail to Wayne...  
> but as
> I've searched for him, and saw that his last message was in 2004,  
> do you
> know if there's a different way to publish a plugin?


The last message  by Wayne was yesterday:
        Da:  [hidden email]
        Oggetto: Re: Circularity = -1 ??
        Data: 25 settembre 2006 16:20:28 GMT+02:00
        A:  [hidden email]
        Rispondi a:  [hidden email]


> I am measuring the circularity of cells. I noticed there are  
> circularity values equal to -1. What does -1 in circularity mean?
>

It means that the calculated circularity value was greater than 1.0,  
which can happen with very small particles. In ImageJ 1.37,  
circularity values greater than 1.0 are set to 1.

-wayne


* Vincenzo Della Mea
* Medical Informatics, Telemedicine and Ehealth Lab
* University of Udine, Italy
* http://mitel.dimi.uniud.it/  -  http://www.eslide.net

[dscho]

Hi Daniel,

On Tue, 26 Sep 2006, Daniel Lelis Baggio wrote:

> I would like to publish a LiveWire Segmentation plugin, whose info is at:
> http://ivussnakes.sourceforge.net/

What a great plugin!

The best way to publish a plugin is to look at example pages at
http://rsb.info.nih.gov/ij/plugins/. Take one, and edit the HTML to suit
your needs. Then, send it as an attachment to Wayne.

A few notes about the plugin:

You could bundle it as a jar with a '_' in the name; such a jar can be
dropped into the plugins/ folder directly (without unpacking).

The showAbout() method shows a wrong description.

In source/compiling as well as source/install, you reference Snakes_.java,
which is not there.

For plain users, the three generated images are only distracting; the
plugin does not really need them. Maybe show a dialog asking if the images
should be shown, or alternatively do away with them altogether?

Ciao,
Dscho

[Gabriel Landini]

On Tuesday 26 September 2006 07:41, Daniel Lelis Baggio wrote:
> I would like to publish a LiveWire Segmentation plugin, whose info is at:
> http://ivussnakes.sourceforge.net/

Hi,

You can also use the new documentation site (or use both sites):
http://imagejdocu.tudor.lu/

The plugin is really good, but I get stuck in some situations.

I have some suggestions:

1. It would be better to pack it as a jar file, and keep the LiveWire_ or
Live_Wire name (there are other Snakes plugins, so this would not interfere
for those who have those also installed and also would make it easy to move
to other folders. For instance I like keeping all the segmentation plugins in
a Segmentation folder, because otherswise I never find them! :-) so the jar
format allows you to do this.

2. I agree with Dscho that there is no need to keep the other files open.

3. You may want to have a look at the new function to disable the popup menu
(when one right clicks the image) and use the right click to end the
segmentation and link the starting point to the last current point (this will
close the ROI.
In a plugin, to disable the popup menu you can do:

IJ.runMacro("setOption('DisablePopupMenu', true)");

and "false" at the end to enable it back.

Even better I would use only one click to lock the points and right-click to
end.

4. For some reason (maybe it is me, not knowing how to use it) there is a new
button on the toolbar. Not sure why this is necessary. If I run the plugin
twice I get 2 buttons and so on.

5. I cannot find a way to end the detection. How does one stop it?

I hope that you can implement some of these. I really like it and it seems
very useful.

Cheers,

Gabriel

[Daniel Lélis Baggio]

Hi, Gabriel!
Thanks for your feedback.

Hi,
>
> You can also use the new documentation site (or use both sites):
> http://imagejdocu.tudor.lu/


That's a great site. I'll put up a link there and send it to Wayne.

The plugin is really good, but I get stuck in some situations.

>
> I have some suggestions:
>
> 1. It would be better to pack it as a jar file, and keep the LiveWire_ or
> Live_Wire name (there are other Snakes plugins, so this would not
> interfere
> for those who have those also installed and also would make it easy to
> move
> to other folders. For instance I like keeping all the segmentation plugins
> in
> a Segmentation folder, because otherswise I never find them! :-) so the
> jar
> format allows you to do this.

I'll pack it up in a .jar file and put it in the next release. I really
didn't know ImageJ would open .jar files, sorry... newbie, hehhe.

2. I agree with Dscho that there is no need to keep the other files open.


Oh, those were only debug files that could  help me see how good would the
segmentation be and if I was not making mistakes in the code... really not
useful now, I'll cut them out.

3. You may want to have a look at the new function to disable the popup menu

>
> (when one right clicks the image) and use the right click to end the
> segmentation and link the starting point to the last current point (this
> will
> close the ROI.
> In a plugin, to disable the popup menu you can do:
>
> IJ.runMacro("setOption('DisablePopupMenu', true)");
>
> and "false" at the end to enable it back.
>
> Even better I would use only one click to lock the points and right-click
> to
> end.

That sounds... way better!

4. For some reason (maybe it is me, not knowing how to use it) there is a
> new
> button on the toolbar. Not sure why this is necessary. If I run the plugin
> twice I get 2 buttons and so on.
>
> 5. I cannot find a way to end the detection. How does one stop it?


Actually, one can end the detection selecting another tool. I mean, if you
are in the midle of the segmentation, you can just choose some other tool,
and the livewire will stop working.
If you  wanna go back to the livewire segmentation, it's just a matter of
selecting the Lw (livewire) button again. In the case you have multiple
segmentations working, there will be one button for each image, so that one
will be able to restore any of those segmentations. But maybe this is not
necessary. As you said, one could only right-click the image and the
selection would be over.

I am having some problem using ImageJ clipboard area. I'm not able to use
the "Copy to System" function. Everytime I make a selection, use the
function and try to paste it, I get nothing. It surely works inside the
program (the "Copy" function) but does not seem to work outside.
Here my configurations are, for Java:
java version "1.5.0_08"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_08-b03)
Java HotSpot(TM) Client VM (build 1.5.0_08-b03, mixed mode, sharing)
for Operating System:
Ubuntu Dapper Drake.
Oh, and imageJ version is: 1.37g



I hope that you can implement some of these. I really like it and it seems
> very useful.
>
> Cheers,
>
> Gabriel


Thanks, Gabriel. As soon as I put them working, I e-mail the list the new
version.
Your support at ImageJ list has been really useful for me. Thank you all!
[]'s

[Gabriel Landini]

Hi,
> I am having some problem using ImageJ clipboard area. I'm not able to use
> the "Copy to System" function. Everytime I make a selection, use the
> function and try to paste it, I get nothing. It surely works inside the
> program (the "Copy" function) but does not seem to work outside.

I think this is a common problem with linux (suse 10.1 here).

> Oh, and imageJ version is: 1.37g

For disabling the right click you'll need a newer version.
Here are some useful links about how to upgrade.

http://imagejdocu.tudor.lu/imagej-documenation-wiki/faq/how-do-i-update-imagej

(you only need to download the latest ij.jar to the ImageJ folder).

Cheers,

Gabriel