I will write a complete guide how you get your stuff running or how one can develop KNIME Image Processing Plugins (with or without ImageJ2) using the KNIME SDK. I try to write a complete guide( maybe I can put it into the Wiki later), so just ignore the parts you already know ;-)
1. Download and Install KNIME SDK
Under Windows and MAC you can use the installer, under linux just unpack th e file and run eclipse. The KNIME SDK is actually an Eclipse with all the required KNIME plugins.
2. Now you have two options:
a.) Clone our git repositories: http://github.com/knime-ip/knip and http://github.com/knime-ip/knip-imagej2. Afterwards import the Java-Projects into the KNIME SDK (File -> Import -> General -> Existing Project Into Workspace). Be careful, don't check the option "copy content to workspace" as you then won't be able to see the updates of Git reflected. Note: Of course you can also use your own Eclipse Git integration (e.g. EGit).
b.) Use the update-sites of the KNIME SDK to install KNIP and KNIP ImageJ2.
Whats the difference between (a) and (b)? Well, obviously using option (b) you won't see the code of KNIP or KNIP-IJ2, but maybe you don't need it. Additionally, with option (b) you don't need to bother with git (even if it is very easy to use).
3. Start KNIME SDK
I prefer to use the debug version of KNIME as you can set breakpoints to debug your nodes etc. Therefore you left-click on the arrow right to the small "Debug Bug" in the toolbar over your projects / code window. Then click on "Debug Configurations". Create a new Eclipse Launch configuration. The only thing you need to configure are the VM parameters in the tab tab arguments:
Depending on how much memory your machine has, you should set the -Xmx parameter. Additionally you have to set a parameter -XX:MaxPermSize=192m.
My vm argument line looks as follows: -Xms40m -Xmx6G -XX:MaxPermSize=192m
After you started KNIME from the KNIME SDK, you have to switch to the KNIME perspective in the newly started KNIME (this setting will be kept in the future).
What did you just do? Well, you started KNIME (which is an eclipse application) from your KNIME SDK. The loaded KNIME contains all plugins which are available in your project list + all plugins which are installed in the KNIME SDK.
4. What are these org.knime.knip.core etc projects?
They are not maven plugins, they are Eclipse Plugins. If you want to add additional dependencies you can do so by linking on another eclipse project or adding a new libary to the classpath. You always do that in the plugin.xml and never via any other mechanism (like build-path configuration of eclipse). You add new eclipse projects as dependencies in the dependency tab of the plugin.xml, new .jars in the Runtime tab under classpath.
5. How do I create my own plugin?
Honestly, just copy and paste an existing one. Thats the most convenient way to create a plugin.
Now related to your questions:
* You also should clone KNIP repository. If you cloned both above mentoined repos you shouldn't have any problems with dependencies anymore in the existing projects.
* The problem looks pretty doable. Actually, it seems to be a very nice use-case for learning how to write IJ2 plugins / KNIME nodes. You would write an ImageJ2 Plugin which requires a Labeling as an Input and maybe some parameters specifying your axis as an output. Before that, your workflow would first smooth the image a bit (Quantil Filter), then using a simple thresholding algorithm (looks suitable concerning your images), followed by a Connected Component Analysis. Then your node will follow.
A labeling is nothing else as a representation of a segmentation, but I think you can see that when you play around with the example workflows. :-)
I hope this somehow helps! If not, let me know, then I can update the Guide and help you at the same time ;-))