Installing BioVoxxel toolbox using ImageJ update site fails

I tried to install the BioVoxxel toolbox today, as its Erode and Dilate functions are far superior to those standard in FIJI. However using the update site I copied from FIJI it throws an error: "No repository found at http://sites.imagej.net/BioVoxxel/ ." First I thought it was because there was a point in the end of the url, but that is just from the error message, the site url ends with a "/". Any thoughts on this?

Hi Luuklag,

I'm a bit confused. Are you trying to install the BioVoxxel Toolbox into KNIME? The BioVoxxel Toolbox is a set of plugins for ImageJ1 / FIJI. KNIME hat it's own system of update-sites, not yet integrated with ImageJ. We are planning, that in the future KNIME will support ImageJ2 update-sites but this is not possible yet.

May I ask what you are trying to do? Maybe we have something similar like the BioVoxxel Toolbox in KNIME.


Cheers,

Chrsitian

I want to use their Erode and Dilate. As it produces far better results in terms of using them after each other. The end result resembles the original better.

 

Edit:

I found the .jar file of the biovoxxel toolbox, and moved that into the KNIME folders, under ImageJ2, however not showing up in KNIME after a restart. What would be the appropriate place?

 

Edit2:

I also saw the Tubeness plugin is installed as a demo, but I can't find that as a Node. Perhaps for the same reasons I can't install the BioVoxxel toolbox?

Hi Luuklag,

BioVoxxel Toolbox is ImageJ1 based. We can only auto-generate nodes from ImageJ2 plugins. However, you can try the KNIME node called "Morphological Image Operations" to perform arbitrary combinations of erode/dilate. On our example server there are several tutorials how to use the nodes.

Cheers,

Christian

I figured this out, so I thought I'd share if maybe someone else wants to know.

I used winzip to get the .class files out of the .jar file, and put these files in the imageJ1 plugin folder in the KNIME folder. Then using the Macro Node I was able to execute them. Downside of this is that settings would need to be found out in ImageJ or FIJI, and then copied into KNIME through the record macro options.

Hi all,

 

a bit late but I just stumbled over this conversation.

Since I want to stepwise also migrate my plugins into IJ2 compatible mode, I could start with e.g. the EDM Binary Operations since this is still a moderate amount of modifications.

Before I start on that...

What are the minimal requirements for the plugin to be recognized by KNIME later on?

Is it already sufficient to start the class with the standard IJ2 parameter annotation and create a dialog using the parameterized dialog or is there other things in addition?

Do I have to exchange every usage of any IJ1 object and method to get it running in KNIME?

Regards,

Jan

Hi Jan,

 

the minimum requirement is that you have an IJ2 plugin which has KNIME compatible Input/Output parameters, a menu path and the headless flag in the Plugin annotation is set to true.  You can of course still use IJ1 functionality. However, when it comes to deployment (i.e. distributing your plugin via a KNIME update-site) I suggest that we have a quick chat how we can easily facilitate this.

Please find some examples here: https://github.com/knime-ip/knip-imagej2/tree/master/org.knime.knip.imagej2.fragmentdemo/src.

I'm happy to discuss all options how to integrate the BioVoxxel Toolbox into KNIME via IJ2 here or via Skype / telephone.  I think at the moment my favourite solution would be that you implement your stuff as IJ2 plugins and I would help you settings everything up to work with KNIME (i.e. a plugin which can be distributed via the KNIME update-site etc). What do you think?

Cheers,


Christian

 

 

Hi Christian,

I'd also be interested in getting help how to set up a KNIME update site for own IJ2 plugins. Maybe we could add a guide/tutorial to the wiki at http://imagej.net/KNIME ? I'd be willing to contribute and test :)

Jan

 

Hi Jan,

at the moment you'd have to create a KNIME Plugins which includes the plugins (see e.g. https://github.com/knime-ip/knip-imagej2/tree/master/org.knime.knip.imagej2.fragmentdemo/src). Afterwards you have to export/expose the plugin on an eclipse-update site which can then be accessed by others.

However, the best solution for IJ2 plugins would be that we somehow enhance the IJ2/FIJI update-sites such that KNIME can consume them.... I'll check with the IJ2 guys about how realistic this is and how fast we could achieve this.

Best,

Christian