Diametrize cells
Project description
This code is a work in progress and will aimed at generating synthetic diameters for neurons, with parameters learned from a set of biological neurons.
Installation
The usual
pip install -e .Main usage
Step 1: Building models
In folder example, you first have to modify create_jsons.py to suit your needs.
You have the following important parameters for the dict extract_models_params:
morph_path: path to morphology files
mtypes_sort: how to learn distributions: all to use all together, mtypes to use by mtypes , super_mtypes to use home made cells types (see diameter_types below)
models: to create several models (for now they are all the same, just differen realisation of random numbers)
neurite_types: types of neurite to learn parameters for
extra_params: dict of additional model parameters
Step 2: Building diameters
Then simply run ./run_models.sh to create the models (saved in a json file).
In create_jsons.py, the dict generate_diameters_params needs to be updated, too, with entries matching the previous dict. The path in new_morph_path will be where the new morphologies will be saved.
Then run ./run_diamters.sh to generate diameters.
Additional scripts
Several additional scripts in folder scripts:
diameter-checks: run the diameter-check code (bluepymm) on the biological and sampled cells
diameter_types: cluster mtypes using distributions of surface areas (uses two privates repositories a the moment)
extract_morphometrics: from bio and sample cells, extracts and plot distribution of surface aread and diameter as a function of branch order and path lengths
extract_morphologies: from a cell release, find the ones that can be run through diameter-check
plot_morphologies: plot all morphologies in mtype folders
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