I've just started using KNIME. It was recommended to me because of its integration with ImageJ, which is my main working tool. The problem is, when I downloaded KNIME and tried to add the appropriate nodes, there weren't visible on the extension list.
I'm usingk KNIME 2.9.1 (knime_2.9.1.linux.gtk.x86_64) on ubuntu 12.04 (x64)
Any ideas why I can't see either of the ImageJ plugins on the list?
Sorry of this is obvoius, I'm a complete neophyte when it comes to KNIME.
I have to admit that the way to install the ImageJ plugin isn't obvious and hard to find for newbies. The reason is that KNIME Image Processing itself is part of the so called "trusted"-community contributions and the ImageJ integration is NOT (because ImageJ2 itself is still under development). Hence, it has to be installed by adding the according update site. To do so just follow the instructions here and activate the "Stable Community Contributions"-update site.
Now, to run ImageJ1 macros and plugins just look for the ImageJ Macro-node in the node repository. Please note that not every plugin may run properly and by default only the plugins that are shipped with ImageJ are supported. To add user defined plugins, copy them into the following directory: [your_KNIME_installation]/plugins/org.knime.imagej1_*/plugins
In case of any questions or problems don't hesitate to ask!
Thank for the lightinig-quick answer! I've just googled the problem from home (as opposed to my workplace where I installed KNIME) and found the same link you gave me (as a first match no less). I am face-palming as I write this.
Obviously I've angered some evil spirit and this is the punishment. What makes the situation even more embarassing is the fact that installing additional plugins in Fiji is done exactly the same way - by adding a source url to the update list.
Oh well, to err is human and all that.
Thank you again,
one more remark: A lot of functionality which is available in ImageJ is also have in our standard KNIME Image Processing Extension. So if you don't find what you need or it doesn't work with the ImageJ Integration (as especially ImageJ1 is really hard to fully integrate and ImageJ2 is still under development itself), don't hesitate to ask us how it can be done with KNIME Image Processing. We are happy to help.
PS: Our example workflows and tutorials on http://tech.knime.org/community/image-processing may be interesting for you.
Thank you, I will definitely take a look!