CATMAID-to-Blender

Plugin for Blender to interface with CATMAID servers, request and analyze data. Tested with Blender 2.92 and CATMAID 2020.02.15

Important notice

As of version 7.0.0 this plugin is compatible with Blender 2.9x (2.8x and 3.x should also work but I haven't tested it). This unfortunately also makes it incompatible with older Blender <=2.7x.

I took this opportunity to do a full refactor of the code to make things faster and easier to maintain. This includes dropping a bunch of functionality and to focus on the visualization aspects.

Notably, I removed:

• coloring neurons by user
• importing pairs of neurons
• importing synaptic partners
• neuron statistics (cable length, # of branch points, etc)
• exporting neurons/connectors as SVGs
• similarity metrics
• animation of history

If, for some reason, you really really need a function that got dropped, please open an issue here on Github. I also highly recommend you check out pymaid and navis which - in combination - let you do all the stuff that was dropped from this plugin (see the tutorials).

Installation:

First download CATMAIDImport.py, then:

Option A:

1. Start Blender -> Edit -> Preferences -> Addons -> Install from File and select CATMAIDImport.py
2. Activate by ticking check box and click Save User Setting

Option B:

1. Directly place CATMAIDImport.py in \Blender\...\scripts\addons
2. Start Blender -> Edit -> Preferences -> Addons -> Search for the CATMAID addon
3. Activate the script by ticking the check box and click Save User Settings (see here for more detailed description)

Dependencies:

None! Blender for Windows and MacOS brings its own Python distribution and the plugin is written such that it works without any external libraries.

Setting a default connection:

Open Edit -> Preferences, navigate to Add-ons -> CATMAID Import and change CATMAID Server URL in preferences to your server. I also recommend saving your credentials for convenience:

Public CATMAID instances (like the one hosted by VirtualFlyBrain) do not require an API token or HTTP users/passwords. If you want to connect to a private instance however, chances are you will need to add credentials. For Information on how to retrieve your Token look here.

Quickstart Guide:

The CATMAID panel will show up in the Sidebar of the 3D View. This sidebar might be hidden by default in which case you can either press "N" while hovering over the 3D view or click the little left-pointing arrow in the upper right corner to open it.

A couple notes:

• functions that need you to be logged into your CATMAID server will be disabled (greyed out) until you did so by using 'Connect to CATMAID'
• in order to identify cell bodies, the plugin searches for nodes with a soma tag
• try hovering over a button/field or click on the "?" next to it to get a helpful tooltip

Tutorials:

Please check out the Github Wiki for additional information and tutorials.

Note: these tutorials are still based on pre 7.0.0 version.

License:

This code is under GNU GPL V3.

Acknowledgments and how to cite:

General:

Please cite Schlegel et al., 2016 (eLife) if you use the plugin in your publication.