Plugin for Blender to interface with CATMAID servers, request and analyze data. Tested with Blender 2.77 and CATMAID 2015.12.21
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'
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.
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.
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.
####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.
This code is under GNU GPL V3