Python tools for interacting with CATMAID projects
This is a slowly increasing toolbox for extracting CATMAID (http://www.catmaid.org) annotations, typically EM reconstructions of neurons and eventually visualizing and doing various kinds of analysis of neuronal morphology, connectivity, and connections between the two. See Quantitative neuroanatomy for connectomics in Drosophila for more details of what sort of things will eventually be possible.
Currently it needs the following python packages through your favorite package manager:
- json - for parsing and handling the JSON files that CATMAID trades in.
- requests - for happily interacting with a CATMAID server.
Additionally, if you want to do analysis in Python, you'll need at least
- scipy - For quickly handling graphs using sparse matrices.
If you'd rather use Matlab, you will need to install
- matlab-json — To quickly parse JSON files. Download here.
A similar tool, nat, has been developed by Greg Jefferis for R.