BrainLes-Preprocessing
BrainLes preprocessing is a comprehensive tool for preprocessing tasks in biomedical imaging, with a focus on (but not limited to) multi-modal brain MRI. It can be used to build to build modular preprocessing pipelines:
This includes normalization, co-registration, atlas registration and skulstripping / brain extraction.
BrainLes is written backend-agnostic meaning it allows to swap the registration and brain extration tools.
Installation
With a Python 3.10+ environment you can install directly from pypi.org:
pip install brainles-preprocessing
Usage
A minimal example can be found following these badges:
For further information please have a look at our Jupyter Notebook tutorials illustrating the usage of BrainLes preprocessing.
Documentation
We provide a (WIP) documentation. Have a look here
FAQ
Please credit the authors by citing their work.
Atlas Reference
We provide the SRI-24 atlas from this publication. However, custom atlases can be supplied.
Brain extraction
We currently provide support for HD-BET.
Registration
We currently provide support for ANTs (default), Niftyreg (Linux), eReg (experimental)
1 maintainer
Release files for brainles-preprocessing 0.1.6
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Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| brainles_preprocessing-0.1.6-py3-none-any.whl | Python 3 | none | any | Details |
Release files / brainles_preprocessing-0.1.6-py3-none-any.whl
| Download URL | brainles_preprocessing-0.1.6-py3-none-any.whl |
|---|---|
| Size | 19.7 MB |
| Tags | Python 3 |
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