liom-toolkit 0.7.8

Package to support the research of LIOM.

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
• tqdm
• scikit-image
• ome-zarr
• nibabel
• zarr
• h5py
• pynrrd
• PyWavelets
• SimpleITK
• allensdk
• dask
• opencv-python
• torch
• torchvision
• wandb
• patchify
• natsort
• albumentations

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.