I am in the process of migrating a rather large tracing project from Amira to CATMAID and I figured I'd reach out to see if anyone has advice for importing a large number of neuron files into CATMAID. I am currently able to export neurons from Amira as .swc files and then import them into CATMAID using the import/export widget. My workflow looks like this:
1.) Select neuron in Amira and define a tree node (Amira will not allow a file to be saved as .swc without a tree node defined)
2.) Save neuron as .swc
3.) Import neuron into CATMAID using import widget
4.) Name and annotate neuron, also using a widget
This works fine, however I have 1000+ neurons, so this method will take me quite some time...
Does anyone have advice as to how I might be able to do this more efficiently? Perhaps a way to import a batch of neurons or a way to add annotation/neuron name metadata to the .SWC file?
As a side note, Amira is able to save neuron skeletons in the following formats:
SkeletonGraph ascii (.am)
SkeletonGraph binary (.am)
neuron format (.hoc)
swc neuron geometry file (.swc)
Thanks for any suggestions!