diameter-synthesis 0.2.5

Diametrize cells

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