py-lmd#
The py-lmd package provides an opensource python interface to generate cutting directions for the Leica LMD6 & LMD7 laser microdissection microscopes. These cutting directions can be used to perform laser microdissection on arbitrary sample types.
py-lmd interfaces directly with your existing python workflows to make your samples accessible via LMD. For example you could use the output of your ML-based region detection on clinical tissue samples to export cutting shapes to excise these same regions on the LMD.
In addition, you can build reproducible workflows to calibrate slides, import SVG files and convert them to cutting masks, and can convert existing segmentation masks to cutting XMLs.
Installation#
py-lmd has been tested with Python 3.9, 3.10 and 3.11. It is recommended to use the library with a conda environment. You can install py-lmd from PyPI using pip.
conda create -n "py-lmd-env"
conda activate py-lmd-env
conda install python=3.9 -c conda-forge
pip install py-lmd
If you are installing on an M1 apple silicon Mac you will need to install numba via conda instead of pip before proceeding with the installation of the py-lmd library.
conda install numba
Citing our Work#
py-lmd was developed by Georg Wallmann, Sophia Mädler and Niklas Schmacke in the labs of Veit Hornung and Matthias Mann. If you use our code please cite the following manuscript:
SPARCS, a platform for genome-scale CRISPR screening for spatial cellular phenotypes Niklas Arndt Schmacke, Sophia Clara Maedler, Georg Wallmann, Andreas Metousis, Marleen Berouti, Hartmann Harz, Heinrich Leonhardt, Matthias Mann, Veit Hornung bioRxiv 2023.06.01.542416; doi: https://doi.org/10.1101/2023.06.01.542416
Documentation