onurserce / py-lmd

Read, create and write cutting data for the Leica LMD6 & LMD7 microscope. Build reproducible workflows to calibrate, import SVG files and convert single-cell segmentation masks.

Installation from Github

py-lmd has been tested with Python 3.8 and 3.9. To install the py-lmd library clone the Github repository and use pip to install the library in your current environment. It is recommended to use the library with a conda environment. Please make sure that the package is installed editable like described. Otherwise static glyph files might not be available.

We recommend installing the non-python dependencies with conda before installing py-lmd:

git clone https://github.com/MannLabs/py-lmd

conda create -n "py-lmd-env"
conda activate py-lmd-env
conda install python=3.9 scipy 'scikit-image>=0.19' numpy numba -c conda-forge
pip install -e .

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

Documentation

The current documentation can be found under https://mannlabs.github.io/py-lmd/html/index.html.

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