Metadata-Version: 2.1
Name: diameter-synthesis
Version: 0.4.2
Summary: Diametrize cells
Home-page: https://github.com/BlueBrain/diameter-synthesis
Author: Blue Brain Project, EPFL
License: GPLv3
Project-URL: Tracker, https://github.com/BlueBrain/diameter-synthesis/issues
Project-URL: Source, https://github.com/BlueBrain/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 Blue Brain Project/EPFL
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Provides-Extra: docs
Provides-Extra: plot
Provides-Extra: test
