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README.md

Blender2NeuroML

Conversion script to bring neuron models drawn in Blender into NeuroML format

In root folder two files are which you can run in console independent and blenderToNeuroMl you can run in eclipse

  1. CheckWrlFile.py - compare wrl file Virtual_Worm_March_2011.wrl (located in folder Data) with 302.ods and NeuronConnect.xls. It find neurons which is in 302.ods and NeuronConnect.xls but isn't in Virtual_Worm_March_2011.wrl. Output of scripts infers to console. Before you run you'll need to install some plugins for your Eclipse to work with python (http://pydev.org/). Also you need to install a plugin for your python to get it to work with an MS Excel file:
  2. WrlToNeuroML.py - create morphoMl form wrl file Virtual_Worm_March_2011.wrl for neurons listed in neurons.txt file. This script takes data form Data folder and create one morphoMl file in folder Output.
  3. blenderToNeuroMl.py - create morphoMl form blender file for all mottor neurons from Virtual_Worm_March_2011.blend (should located in folder 'path to your blender.blender'). For run you should do in eclipse this: "Run->External Tools->External Tools..." with the following settings: Main-Tab: Location: blender executable Working directory: blender executable directory Arguments:-b "path to file Virtual_Worm_March_2011.blend" -w -P ${resource_loc} Environment-Tab: Variable: PYTHONPATH Value: ${container_loc} and choose "Append environment to native environment" Also you need in your blender folder create folder with name Output there are will be save output file.
  4. blenderStraighten.py - edit blender file, straightening the worm body; see the file header for details.
  5. blenderExportSpine.py - export spine information from the Blender model (e.g. for NeuroML transformation); see the file header for details.

If you have any problem will be glad to help write s.khayrulin@gmail.com or openworm-discuss@googlegroups.com

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Conversion script to bring neuron models drawn in Blender into NeuroML format

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