Metadata-Version: 2.1
Name: py-lmd
Version: 1.0.0
Summary: Read, Modify and Create new shape files for the Leica LMD6 & LMD7
Home-page: https://github.com/MannLabs/py-lmd
Author: Georg Wallmann, Sophia Maedler, Niklas Schmacke
Author-email: wallmann@biochem.mpg.de
Project-URL: Documentation, https://mannlabs.github.io/py-lmd/html/index.html
Project-URL: Bug Tracker, https://github.com/MannLabs/py-lmd/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: matplotlib
Requires-Dist: lxml
Requires-Dist: networkx>=3.1
Requires-Dist: scikit-image>=0.19
Requires-Dist: svgelements
Requires-Dist: setuptools
Requires-Dist: numba
Requires-Dist: tqdm
Requires-Dist: hilbertcurve


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![logo](https://github.com/MannLabs/py-lmd/assets/15019107/e7c619a2-69c9-4cb6-8723-fab94c8d3558)

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](https://www.biorxiv.org/content/10.1101/2023.06.01.542416v1):

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


