https://github.com/bluebrain/me-features-to-mo-id-mapping
https://github.com/bluebrain/me-features-to-mo-id-mapping
Last synced: about 1 year ago
JSON representation
- Host: GitHub
- URL: https://github.com/bluebrain/me-features-to-mo-id-mapping
- Owner: BlueBrain
- License: apache-2.0
- Created: 2022-01-05T15:11:42.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2022-05-04T07:21:28.000Z (about 4 years ago)
- Last Synced: 2025-04-02T13:22:31.813Z (about 1 year ago)
- Language: Python
- Size: 1.72 MB
- Stars: 4
- Watchers: 5
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
# BBP-me-type-to-mol-ID
## Description:
This is a repository containing configuration code that use me-types-mapper to reproduce results from *Roussel et al.,
2021* (https://www.biorxiv.org/content/10.1101/2021.11.24.469815v1)
## Installation:
To install this tool, run the following steps in your shell:
```
git clone https://bbpgitlab.epfl.ch/molsys/bbp_me_type_to_mol_id.git
pip install -r bbp_me_type_to_mol_id/requirements.txt
pip install git+https://bbpgitlab.epfl.ch/molsys/me_types_mapper.git
pip install git+https://github.com/BlueBrain/BluePyEfe@da783256a4212b14d4f152687238754a99d1a78b
```
## How to use:
Step 1 and 2 are optional as we made the extracted features available in the `feature_extraction folder`.
### Step 1: Download the data (optional)
Go into `downloader` directory
#### Morphologies and electrophysiological recording from Gouwens et al., 2019:
Due to open source license issues, the python script for downloading AIBS data from Gouwens et al. (2019) could not be
included.
Please refer to `allensdk` from Allen Institute for Brain Science to download data from the Gouwens et al paper.
Clear instructions on how to download morphological and electrophysiological data are provided in the `allensdk`
documentation:
Electrophysiology: https://allensdk.readthedocs.io/en/latest/_static/examples/nb/cell_types.html#Cell-Types-Database
Morphologies: https://allensdk.readthedocs.io/en/latest/_static/examples/nb/cell_types.html#Cell-Morphology-Reconstructions
The cell ids used in the manuscript are provided in the `downloader/41593_2019_417_MOESM5_ESM.xlsx` file.
Data should be stored in the `downloader` directory in a new folder named after the dataset name (i.e. `Gouwens_2019`)
and organized into two sub-directories: one named as `ephys_traces` containing the raw traces in nwb format and another
named `morphologies` containing the morphology reconstruction in swc format.
Downloading of AIBS data should be done in a dedicated virtual environment.
#### Morphologies and electrophysiological recording from Blue Brain Project:
Create a dedicated virtual environment for downloading BBP data. Install dependencies using
`pip install -r requirements_BBP_dl.txt`. Finally, run `python BBP_downloader.py`.
### Step 2: Extract features (optional)
Go into the `feature_extraction` directory and run first `python efeatures_extractor.py`
and then `python mfeatures_extractor.py`.
### Step 3: Select common features
Go into the `feature_selection` directory and run first `python feature_selector.py`. It should create two directories named
`figures` and `filtered_datasets`. Then run `python compute_dataset_labels.py`.
### Step 4: Mapping
Go into the `mapping` directory and run `python clustering.py` to reproduce the main results of the paper
(https://www.biorxiv.org/content/10.1101/2021.11.24.469815v1). To reproduce
the other figures run `python dataset_overlap_validation.py` for figure 2, `python alpha_optimization_validation.py` for
figure 3 and `python pipeline_validation.py` for Table 1.
## 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.
Copyright (c) 2022-2022 Blue Brain Project/EPFL