Package to support the research of LIOM.
Project description
Liom Toolkit
This package supports the research being done by the Laboratoire d’Imagerie Optique et Moléculaire at Polytechnique Montréal. It hosts a collection of scripts used to process and analyze data collected by the lab.
Installation
The package can be installed using pip:
pip install liom-toolkit
Requirements
The package requires the following packages to be installed and will attempt to install them using installation:
- antspyx
- allensdk
- scikit-image
- ome-zarr
- nibabel
- zarr
- h5py
- pynrrd
- SimpleITK
To create an anaconda environment with all the required packages, run the following commands:
conda create -n <name>
conda activate <name>
conda install python=3.10
# The line below is for Apple Silicon specifically.
# Hdf5 needs to be installed using homebrew.
HDF5_DIR=/opt/homebrew/Cellar/hdf5/1.14.3 pip install tables
pip install allensdk
pip install antspyx
pip install liom-toolkit
Package Structure
The package contains the following modules:
Registration
The registration module is concerned with performing registration on brain imagery. It hosts a collection of scripts for registering mouse brains to the Allen Atlas as well as functions for creating brain templates to use in registration.
Segmentation
The segmentation module is concerned with segmenting brain imagery. It contains scripts to segment vessels in 2d slices.
Utils
Various utility functions used by the other modules. These include function for converting between the different data files used within the lab.
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