Ah - right I was envisaging a continuous cylinder being sliced into sections.
Individual seedlings, yeah that's a serious handling problem.

What you want is a robotics forum.
Cheap robotic arms could probably be taught to do this task.
And there are some really useful and relatively cheap arms around.

You'd need to design a special gripper/hand/holder for the seedlings and a feeding system - which is where the 3d printing comes into play.
But for the actual job itself - you need a robotic arm or two :-)

My knowlefe on such things is pretty sketchy. But I do remember seeing a kickstarter recently about one with easy to change 'tools' and a simple learning curve.
this kind of thing: https://www.kickstarter.com/projects...rial-robot-arm
quick glance shows a lot of them around.

So you need a bunch of roboticists to tell you which one can do what you want and to actually write the software and artificial intelligence routines to make it work :-)