CATMAID-to-Blender

Plugin for Blender to interface with CATMAID servers, request and analyze data. Tested with Blender 2.77 and CATMAID 2015.12.21

Installation:

First download CATMAIDImport.py, then:

######Option A: 2. Directly place CATMAIDImport.py in \Blender...\scripts\addons 3. Start Blender -> 'File' -> 'User Preferences' -> 'Addons' -> Search for 'CATMAID' addon and activate by checking box -> 'Save User Settings' (see here for more detailed description)

######Option B: 2. Start Blender -> 'File' -> 'User Preferences' -> 'Addons' -> 'Install from File' and select CATMAIDImport.py 3. Activate by checking box and 'Save User Setting'

Before First Use:

Open User Preferences, navigate to 'Add-ons' -> 'CATMAIDImport' and change 'CATMAID Server URL' in 'preferences' to your server. You may also set credentials to be saved for convenience.

Tokens:

The CATMAID API authorizes requests using an API token tied to user account instead of a username and password. For Information on how to retrieve your Token look here.

Quickstart Guide:

Import/Export panel will show up under the 'Scene' tab in the 'Properties' windows

• Functions (e.g. Retrieving skeletons/connectors) that need you to be logged into your CATMAID server will be grayed-out until did so by hitting 'Connect 2 CATMAID'
• Skeletons can be retrieved by their skeleton ID, by annotations or based on connectivity (Retrieve Partners)
  • Important side node: in order to identify cell bodies, the script searches for nodes with a radius > 10
• Once imported, skeleton/connector data can be readily exported to vector graphics (SVG) with a broad range of options (e.g. coloring, filters, scaling). Look at lower left panel when exporting for these options.

Examples:

####1. Color neurons by similarity and export to vector graphic (SVG)

####2. Group postsynaptic sites based on what presynaptic neuron they connect to

####3. Check out Schlegel et al., 2016 for more examples.

License:

This code is under GNU GPL V3