morphome is a set of Python and Amira Tcl scripts designed to easily and automatically import IMOD 3D model files into FEI Amira and perform organelle-specific morphological quantification routines. morphome uses the PyIMOD set of Python classes to read an input IMOD model file and convert its objects into individual 3D files in the Virtual Reality Modeling Language (VRML) format. Once conversion is complete, each individual VRML file is read into Amira and individual quantification routines are launced depending on the object name specified in the IMOD model file.
Currently, morphome supports quantification workflows for the following organelles:
- Mitochondrion
- Nucleus
- Nucleolus
To run using the default settings:
morphome/scripts/run_morphome.py input_file.mod /home/user/output_path
To run using custom settings stored to a JSON file:
morphome/scripts/run_morphome.py --json custom_settings.json input_file.mod /home/user/output_path
For detailed usage instructions, please visit the morphome wiki: https://github.com/CRBS/morphome/wiki