This repository hosts all protcols and code that was used to process image data in the Slice2Volume data repository. The Slice2Volume functionality that was used to register histological slices to 3D volumes is maintained in a separate repository.
The following aspects are covered by this repository:
- Histology: Staining protocols and scripts for bundle registration and image sorting (see subdirectory)
- MRI: Scripts for denoising with BM3D, longitudinal registration and image type conversion.
- QA: Scripts to auto-generate a LaTeX document with a compilation of all available image data and processing steps for each sample animal.
- Simulation: Scripts for Monte-Carlo setup and subsequent zeropadding of raw simulation output to match reference CBCT dimensions.
To install or use the Python-related functionality, install Anaconda as described here and create a new environment with:
conda create -n slice2volume Python=3.9
conda activate slice2volume
Then clone the repository using git clone (git clone https://github.com/jo-mueller/Slice2Volume_CodeAndDocs.git) or download the repository with any other method of your choice. Use the command line to navigate into the downloaded directory and install the necessary packages:
cd path_to_repository/Slice2Volume_CodeAndDocs
conda install - c conda-forge napari jupyterlab
pip install -r requirements.txt
To start jupyterlab, type jupyter-lab in the command line and navigate to the location of nnotebooks you wish to execute.