Probabilistic Mapping Extension

The Probabilistic Mapping Extension is a Python package designed to facilitate the creation and analysis of probabilistic maps for voxel-based datasets. It provides tools to download experimental data, compute probabilistic maps, and perform optional density transcriptions and visualizations.

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Features

• Download experimental data for mapping workflows.
• Compute probabilistic maps in a structured sequence of steps.
• Optional transcription and visualization of voxel densities.
• Override specific regions for custom analyses.

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Installation

To install and use this package, follow these steps:

1. Clone the Repository
   Clone the repository to your local machine:

   git clone https://github.com/YannRoussel/probabilistic_mapping_extention.git
   cd probabilistic_mapping_extention

2. Install Dependencies
   Install the required dependencies with pip:

   pip install -r requirements.txt

3. Set Up the Package
   Install the package locally using:

   pip install .

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Usage Guide

Step 1: Download Experimental Data

Navigate to the experimental_data directory and run the scripts provided to download the necessary experimental data:

cd experimental_data
# Run the appropriate script(s)

Step 2: Compute the Probabilistic Map

Sequentially execute the scripts in the probability_map directory:

1. Align T-types:

   python t_type_alignement.py

2. Compute the probabilistic ME-T map:

   python compute_p_me_t.py

3. Extend the ME-T map:

   python extend_p_me_t.py

Step 3 (Optional): Transcribe and Visualize Densities

1. Transcribe T-types to ME-types
   Use the dens_app/transcribe_t_types_to_me_types.ipynb Jupyter notebook to convert T-type densities (from another package) into ME-type densities.

2. Visualize Results
   Visualize the results using the following notebooks:

   • dens_app/Validation_compute_m_type_gene_expressions.ipynb
   • dens_app/visualisation_multiproc.ipynb

Step 4 (Optional): Override Specific Regions

Override certain ME-type densities using the special_region_override/densities_override.py script:

python special_region_override/densities_override.py

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Contributing

Contributions are welcome! If you'd like to contribute:

1. Fork the repository.
2. Create a new branch for your feature or bugfix:

   git checkout -b my-feature-branch

3. Make your changes and commit them:

   git commit -m "Add my feature"

4. Push to your branch:

   git push origin my-feature-branch

5. Open a pull request on GitHub.

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License

This project is licensed under the MIT License. See the LICENSE file for more details.

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Acknowledgments

Special thanks to all contributors and collaborators who helped bring this project to life!