diameter-synthesis 0.7.0

Diametrize cells.

Diameter synthesis

This code aims at generating synthetic diameters for neurons, with parameters learned from a set of biological neurons.

Installation

Use pip:

pip install diameter-synthesis

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 different 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 area 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

Examples

The examples folder contains a simple example that will fetch morphologies from neuromorpho.org, learn a diameter model, rediametrize these morphologies, and perform some analysis of the results to compare original and diametrized morphologies. This example can simply be run using the following command:

./run.sh

Funding & Acknowledgment

The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.

For license and authors, see LICENSE.txt and AUTHORS.md respectively.

Copyright © 2021-2022 Blue Brain Project/EPFL