add citation and link to manuscript

MannLabs · Jun 2, 2023 · b42ec18 · b42ec18
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diff --git a/README.md b/README.md
@@ -1,6 +1,13 @@
+[![Python package](https://img.shields.io/badge/version-v1.0.0-blue)](https://github.com/MannLabs/py-lmd/actions/workflows/python-package.yml) 
+[![website](https://img.shields.io/website?url=https%3A%2F%2Fmannlabs.github.io/SPARCStools/html/index.html)](https://mannlabs.github.io/SPARCStools/html/index.html)
+
 # SPARCStools
 
-documentation can be found at: https://mannlabs.github.io/SPARCStools/html/index.html
+This python module contains wrapper functions to perform stitching with the [Ashlar API](https://github.com/labsyspharm/ashlar). In addition it contains data parsing functions to make imaging data aquired with the Perkinelmer Opera Phenix Microscope accessible Ashlar or also to other downstream applications.
+
+The generated stitched images can then be used for downstream applications, for example the [SPARCSpy](https://github.com/MannLabs/SPARCSpy) workflow or other analysis frameworks.
+
+The documentation can be found at: https://mannlabs.github.io/SPARCStools/html/index.html
 
 ## Installation
 
@@ -21,3 +28,11 @@ Install Java using conda
 Install package via pip. This should install all dependencies as well.
 
  pip install .
+
+## 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
diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/doctrees/index.doctree b/docs/doctrees/index.doctree
diff --git a/docs/html/_sources/index.rst.txt b/docs/html/_sources/index.rst.txt
@@ -45,9 +45,12 @@ Citing our Work
 
 This code was developed by Sophia Maedler and Niklas Schmacke in the labs of Matthias Mann and Veit Hornung. 
 
-If you use our work please cite the following manuscript:
+If you use our work 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
 
-INSERT CITATION HERE
 
 .. toctree::
  :maxdepth: 3

diff --git a/docs/html/index.html b/docs/html/index.html
@@ -122,8 +122,10 @@ <h2>Installation<a class="headerlink" href="#installation" title="Permalink to t
 <section id="citing-our-work">
 <h2>Citing our Work<a class="headerlink" href="#citing-our-work" title="Permalink to this headline"></a></h2>
 <p>This code was developed by Sophia Maedler and Niklas Schmacke in the labs of Matthias Mann and Veit Hornung.</p>
-<p>If you use our work please cite the following manuscript:</p>
-<p>INSERT CITATION HERE</p>
+<p>If you use our work please cite the [following manuscript](<a class="reference external" href="https://www.biorxiv.org/content/10.1101/2023.06.01.542416v1">https://www.biorxiv.org/content/10.1101/2023.06.01.542416v1</a>):</p>
+<p>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: <a class="reference external" href="https://doi.org/10.1101/2023.06.01.542416">https://doi.org/10.1101/2023.06.01.542416</a></p>
 <div class="toctree-wrapper compound">
 <p class="caption" role="heading"><span class="caption-text">Modules:</span></p>
 <ul>

diff --git a/docs/html/searchindex.js b/docs/html/searchindex.js
diff --git a/docs_source/index.rst b/docs_source/index.rst
@@ -45,9 +45,12 @@ Citing our Work
 
 This code was developed by Sophia Maedler and Niklas Schmacke in the labs of Matthias Mann and Veit Hornung. 
 
-If you use our work please cite the following manuscript:
+If you use our work 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
 
-INSERT CITATION HERE
 
 .. toctree::
  :maxdepth: 3