Skip to content

FibreTracker

A python library to track fibre in a volume

💻 Getting Started

Create a new environment (highly recommended)

Miniconda installation and setup

Miniconda is a free lightweight installer for conda.

Here are commands to quickly setup the conda. For reference, you can also use installation link

Following commands will install the latest 64-bit version and delete the installer. To install different version change the .exe version to desired version in the curl command line.

curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe -o miniconda.exe
start /wait "" miniconda.exe /S
del miniconda.exe
After successful installation, search and open "Ananconda prompt (miniconda3)".

Following commands will install the latest 64-bit version and delete the installer. To install different version change the .sh version to desired version in the curl command line.

mkdir -p ~/miniconda3
curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh -o ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm -rf ~/miniconda3/miniconda.sh

After successful installation, initialize your miniconda (in general, it is intialized; just close the current terminal and open a new terminal). If not, following commands initialize for bash and zsh shells :

~/miniconda3/bin/conda init bash
~/miniconda3/bin/conda init zsh

Following commands will install the latest 64-bit version and delete the installer. To install different version change the .sh version to desired version in the wget command line.

mkdir -p ~/miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh
bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3
rm -rf ~/miniconda3/miniconda.sh

After installing, initialize your newly-installed Miniconda (in general, it is initialized; just close the current terminal and open a new terminal). If not, following commands initialize for bash and zsh shells:

~/miniconda3/bin/conda init bash
~/miniconda3/bin/conda init zsh

Once installed, create the environment

conda create -n fibretracker python=3.11

Activate the environment by running

conda activate fibretracker

To read .txm file, install dxchange using conda [install before fibretracker module to avoid version conflicts and related error]

conda install -c conda-forge dxchange

Install the FibreTracker tool using pip

pip install fibretracker

Open jupyter notebook and create a new notebook

jupyter notebook

Go to Example and run the notebook with fibretracker enviroment

Data

Following are the dataset for which fibre tracking is tested on 250 slices

  • Mock and UD [link] - UD-01_FoV_2_B2_recon.txm Mock-01_FoV_2_B2_recon.txm
  • GFRP [link] - GFRP_Initial.zip
  • XCT Low-Res [link] - XCT_L.zip

License

fibretracker was created by Kumari Pooja. It is licensed under the terms of the MIT license.

Credits

This work is supported by the RELIANCE doctoral network via the Marie Skłodowska-Curie Actions HORIZON-MSCA-2021-DN- 01. Project no: 101073040

Project based on the cookiecutter data science project template. #cookiecutterdatascience