https://github.com/bluebrain/diameter-synthesis

Synthesize diameters of neuronal morphologies
https://github.com/bluebrain/diameter-synthesis

morphology neuroscience

Last synced: about 1 year ago
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Synthesize diameters of neuronal morphologies

• Host: GitHub
• URL: https://github.com/bluebrain/diameter-synthesis
• Owner: BlueBrain
• License: apache-2.0
• Created: 2021-06-21T09:27:22.000Z (almost 5 years ago)
• Default Branch: main
• Last Pushed: 2024-11-06T13:27:08.000Z (over 1 year ago)
• Last Synced: 2024-11-13T01:02:58.695Z (over 1 year ago)
• Topics: morphology, neuroscience
• Language: Python
• Homepage:
• Size: 5.51 MB
• Stars: 3
• Watchers: 8
• Forks: 2
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE.txt
  • Citation: CITATION.cff
  • Authors: AUTHORS.md

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README

          
> [!WARNING]

> The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization.

> Future development will take place at: https://github.com/openbraininstitute/diameter-synthesis

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# Diameter synthesis

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

## Installation

Use pip:

```bash

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](http://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:

```bash

./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