Linumpy is the main library supporting research and development at the Laboratoire d'Imagerie Numérique, Neurophotonique et Microscopie (LINUM).
Linumpy contains tools and utilities to quickly work with serial histology and microscopy data. Those tools implement the recommended workflows and parameters used in the lab. The library and scripts can be installed locally by using:
pip install linumpy
To install the tool for development, clone the repository and then install them with
pip install -e .
To use the Napari viewer, you will need to install the following dependencies:
pip install napari[all]
We highly recommend working in a Python Virtual Environment.
Linumpy documentation is available: https://linumpy.readthedocs.io/en/latest/
To execute the scripts, you can use the following command:
nextflow run workflow_soct_3d_slice_reconstruction.nf -resume