Description:

• blender_import : import catmaid skeletons into blender
• catmaid.py : access script for catmaid data (adjacency matrix, skeleton data, etc...)

Contributors

• Brett Graham
• Brendan Shanny
• Russel Torres
• Logan Thomas
• Rui Zheng

Description

A python package used for pulling and analyzing data from Catmaid

Installation

Download the source code (ZIP) and then run:

    python setup.py install

You may need to run this command with 'sudo'

Uses

####Basic skeleton and Neuron retreival/saving To import skeletons or neurons from a catmaid server simply run the following:

import catmaid

source = catmaid.get_source()

The catmaid.get_source() command with no arguments attempts to call on environment variables for a server, project, user, and password. If these variables do not exist it prompts for input for each one. These environment variables can be set by adding the following lines to your ~/.bashrc file.

    export CATMAID_SERVER = "http://catmaid.your.server"
    export CATMAID_PROJECT = "Your_Project_Name"
    export CATMAID_USER = "YourUserName"
    export CATMAID_PASSWORD = "yourpassword"

Once catmaid.get_source() is successfully run a ServerSource, a child of the Source class, is returned based on a server defined by the environment variables above. This ServerSource has built in methods to fetch and/or save skeletons and neurons from the server.

Examples

Plese see docs/notebooks for an ipython notebook on how to get started.