diff --git a/README.md b/README.md
index c3c6b2e..5002ebf 100644
--- 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
index 1bbebc2..b3cddb0 100644
Binary files a/docs/doctrees/environment.pickle and b/docs/doctrees/environment.pickle differ
diff --git a/docs/doctrees/index.doctree b/docs/doctrees/index.doctree
index c8a2500..db76c5b 100644
Binary files a/docs/doctrees/index.doctree and b/docs/doctrees/index.doctree differ
diff --git a/docs/html/_sources/index.rst.txt b/docs/html/_sources/index.rst.txt
index cd9272c..32e48e1 100644
--- 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
index 90dadcc..7259056 100644
--- 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
index 125f4b2..86fd5eb 100644
--- a/docs/html/searchindex.js
+++ b/docs/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({docnames:["index","pages/modules","pages/notebooks/example_stitching_notebook","pages/tutorials"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":5,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,nbsphinx:4,sphinx:56},filenames:["index.rst","pages/modules.rst","pages/notebooks/example_stitching_notebook.ipynb","pages/tutorials.rst"],objects:{"sparcstools.image_processing":[[1,1,1,"","downsample_folder"],[1,1,1,"","downsample_img"]],"sparcstools.parse":[[1,1,1,"","parse_phenix"],[1,1,1,"","sort_timepoints"],[1,1,1,"","sort_wells"]],"sparcstools.stitch":[[1,1,1,"","generate_stitched"],[1,1,1,"","generate_thumbnail"]],sparcstools:[[1,0,0,"-","image_processing"],[1,0,0,"-","parse"],[1,0,0,"-","stitch"]]},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"]},objtypes:{"0":"py:module","1":"py:function"},terms:{"0":[1,2,3],"00":2,"01":2,"02":2,"03":[1,2,3],"04":2,"05":2,"1":[1,2,3],"10":[0,2],"100":2,"1000":2,"12":2,"14":2,"15":1,"2":[1,2,3],"20":1,"2415327986081441":2,"2x2":1,"3":[0,2,3],"30":[1,2],"3037":2,"3039":2,"33":2,"37":2,"4":2,"48":3,"5":2,"52":3,"58":3,"6":2,"67":2,"7":2,"72":3,"77":2,"8":0,"83":2,"9":2,"93":2,"97":2,"9true":2,"boolean":1,"case":[1,2,3],"default":[1,3],"do":1,"export":[1,3],"final":1,"float":1,"function":[0,1,2],"import":[1,2,3],"int":1,"new":[1,2],"true":[1,2,3],"while":1,For:[1,2],If:[0,1],In:[0,1],The:[0,3],Then:3,These:1,_:[1,2,3],_c:[1,2,3],_custom_ashlar_func:2,_r:[1,2,3],_row:[1,2,3],_well:1,_zstack3_r:1,_zstack:1,abov:[2,3],access:[0,1,3],accord:1,acquir:1,activ:0,ad:1,adapt:2,addit:[0,1],addition:1,adjust:[1,2,3],against:3,alexa488:[1,2],alexa647:3,align:[2,3],all:[0,1,2,3],allow:1,also:[0,3],altern:1,an:[1,2,3],analysi:0,ani:[1,3],anoth:[2,3],api:0,appli:1,applic:0,aquir:[0,2,3],ar:[1,3],area:1,ashlar:[0,1],assign_random_id:1,autom:3,automat:1,ax:2,axi:2,background:1,base:1,been:0,befor:1,below:3,better:3,between:1,bia:[1,3],bin:1,bool:1,bottom:[1,2,3],c:0,calcul:1,call:1,can:[0,1,2,3],caus:1,cd:0,cell:3,channel:[1,2,3],channel_nam:3,citat:0,clone:0,code:[0,2,3],col:[1,2,3],collect:1,com:[0,2],complet:2,conda:0,connect:3,contain:[0,1,3],content:3,control:1,convent:1,coordin:3,copi:1,correct:[1,2,3],creat:[0,2,3],crop:[1,2,3],cultur:3,current:0,dapi:1,data:[0,1,2],de44147ed2974457ad6372750bbe5751:2,defin:[1,2,3],degre:1,depend:0,deprec:2,destin:1,develop:0,dictionari:1,differ:1,differentoper:1,dimens:1,directli:[],directori:[0,1,2,3],displot:2,distplot:2,do_intensity_rescal:1,document:2,doe:[1,2,3],down:1,downsampl:1,downsample_fold:1,downsample_img:1,downstream:[0,1],duplic:3,e:1,each:[1,3],edg:2,either:[1,2],element:1,elimin:3,els:1,enabl:3,end:1,enter:1,entir:3,environ:0,equival:1,error:2,etc:1,exact:1,exampl:1,example1:2,exist:[2,3],experi:[1,2,3],export_as_symlink:[1,3],export_exampl:1,export_meta:1,export_xml:1,f:2,fals:[1,3],faster:1,fig:2,figsiz:2,figur:2,fiji:1,file:1,file_end:1,filenam:3,filepath:1,filesystem:1,filetyp:[1,2,3],filter:1,find:[1,2,3],first:3,flatfield:1,flatfield_export:[1,3],flexibl:2,folder:[1,2,3],folder_path:1,follow:[0,1,3],forg:0,form:1,format:1,framework:0,from:[0,1,2],g:1,gener:[0,1,2],generate_stitch:[1,2,3],generate_thumbnail:1,get:1,gist:2,git:0,github:[0,2],give:1,given:3,good:3,guid:2,ha:0,hardcopi:3,harmoni:[1,3],here:[0,2],high:1,histogram:2,histplot:2,hornung:0,how:1,hpc:3,http:[0,2],i:1,id:[1,2],identifi:1,illumin:1,imag:[0,3],image_process:1,img_path:1,implement:2,improv:1,imread:2,imshow:2,indic:1,individu:1,inform:3,input:3,input_dir:[1,2,3],insert:0,issu:1,java:0,job:3,join:[2,3],lab:0,larg:2,lead:1,leav:1,left:[1,2,3],level:2,librari:3,linux:0,list:1,locat:3,loop:3,low:1,lt:2,machin:0,maco:0,maedler:0,main:0,make:0,makedir:[2,3],mani:1,mann:0,mannlab:0,manuscript:0,match:1,matplotlib:2,matthia:0,max_shift:1,maximum:1,mean:1,meant:1,measur:1,merg:2,metadata:1,microscop:[0,1],minut:2,more:1,much:1,multi:1,multipl:[1,3],multithread:1,mwaskom:2,n:[0,1],name:[1,3],navig:0,need:[1,2,3],nikla:0,no_rescale_channel:1,none:1,num_thread:1,number:[1,2],nxn:1,off:2,om:[1,2,3],one:[1,2,3],openjdk:0,opera:0,origin:1,os:[1,2,3],other:[0,1,3],out:1,outdir:[1,2,3],output:[0,1],output_filetyp:[2,3],overhead:1,overlap:[1,2,3],overview:1,overwrit:1,packag:0,paramet:[1,2,3],pars:[0,2],parse_phenix:[1,2,3],parsed_dir:1,parsed_imag:3,partial:1,pass:[1,2,3],path:[1,2,3],pattern:[1,2,3],pdf:3,perform:[0,1,2],perkinelm:0,phenix:[0,1],phenix_dir:1,pip:0,pipelin:[1,2],pixel:1,plan:3,pleas:[0,2],plot:[1,3],plot_qc:1,plt:2,posit:[1,3],potenti:1,pp:3,prepend:1,present:1,process:0,produc:1,project:3,protocol:3,provid:1,put:3,py:2,pyplot:2,python:0,qc:1,qc_edge_qu:3,qc_edge_scatt:3,qualiti:3,quantifi:2,quick:1,random:1,raw_image_til:2,read:3,recogn:[2,3],record:1,regex:1,region:1,regular:1,relev:3,rememb:[2,3],remot:1,remov:2,renam:[1,3],repositori:0,requir:3,rescal:1,rescale_p1_p99:1,resolut:1,result:[0,1,2],right:[1,2,3],row1_well2_:1,row:[1,2,3],run:[0,1,3],s:2,same:1,sampl:3,save:1,scale:1,scan:1,schmack:0,script:[1,3],seaborn:2,second:1,see:[1,2],segment:1,select:1,seper:3,set:[1,3],sever:[2,3],shift:1,should:[0,1,2,3],show:3,signficiantli:1,similar:2,simpl:1,singl:1,slide1:3,slide:[2,3],slidenam:[1,2,3],sn:2,sophia:[0,2],sort:1,sort_timepoint:1,sort_wel:1,space:3,sparcspi:[0,3],sparcstool:[1,2,3],speciifc:[2,3],speed:3,src:2,stain:1,standard:1,step:1,stich:1,sticht:2,stitch:0,stitching_channel:[1,2,3],stitching_test:[2,3],stitching_test_alexa488:[2,3],stitching_test_dapi:[2,3],stitching_test_mcherri:[2,3],stitching_test_tile_posit:3,str:[1,2,3],string:1,subplot:2,subset:3,symlink:[1,3],system:1,test:0,test_data:2,than:1,thi:[0,1,2,3],those:1,thread:1,threshold:1,thumbnail:1,tif:[1,2,3],tiff:1,tifffil:2,tile:[1,2,3],time:1,timecours:1,timecourse_sort:1,timepoint:[1,2,3],todo:2,togeth:1,top:[1,2,3],tsv:3,tupl:1,type:1,uint16:1,uniqu:1,unqiu:1,updat:2,us:[0,1,2],usabl:1,use_symlink:1,use_symlonk:1,user:2,userwarn:2,util:0,v0:2,valu:[1,2,3],veit:0,via:0,virtual:0,visual:0,wa:[0,1,2,3],want:[2,3],well:[0,1,2,3],wga:1,wgabackground:1,wgachannel:1,when:[1,3],where:[1,3],which:[1,2,3],window:0,without:[1,3],work:3,workflow:0,wrapper:0,write:[1,2],written:1,xml:[1,3],you:[0,2,3],your:[2,3],zarr:[1,2,3],zfill:[2,3],zstack:[1,2,3],zstack_valu:[2,3]},titles:["Welcome to SPARCStools documentation!","Modules","<span class=\"section-number\">1. </span>Example Stitching Notebook","<span class=\"section-number\">1. </span>Tutorials"],titleterms:{cite:0,data:3,document:0,exampl:[0,2,3],file:3,from:3,gener:3,imag:1,instal:0,modul:[0,1],notebook:[0,2],opera:3,our:0,output:[2,3],pars:[1,3],phenix:3,process:1,result:3,sparcstool:0,stitch:[1,2,3],tutori:[0,3],visual:2,welcom:0,work:0}})
\ No newline at end of file
+Search.setIndex({docnames:["index","pages/modules","pages/notebooks/example_stitching_notebook","pages/tutorials"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":5,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":3,"sphinx.domains.rst":2,"sphinx.domains.std":2,nbsphinx:4,sphinx:56},filenames:["index.rst","pages/modules.rst","pages/notebooks/example_stitching_notebook.ipynb","pages/tutorials.rst"],objects:{"sparcstools.image_processing":[[1,1,1,"","downsample_folder"],[1,1,1,"","downsample_img"]],"sparcstools.parse":[[1,1,1,"","parse_phenix"],[1,1,1,"","sort_timepoints"],[1,1,1,"","sort_wells"]],"sparcstools.stitch":[[1,1,1,"","generate_stitched"],[1,1,1,"","generate_thumbnail"]],sparcstools:[[1,0,0,"-","image_processing"],[1,0,0,"-","parse"],[1,0,0,"-","stitch"]]},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"]},objtypes:{"0":"py:module","1":"py:function"},terms:{"0":[1,2,3],"00":2,"01":[0,2],"02":2,"03":[1,2,3],"04":2,"05":2,"06":0,"1":[1,2,3],"10":[0,2],"100":2,"1000":2,"1101":0,"12":2,"14":2,"15":1,"2":[1,2,3],"20":1,"2023":0,"2415327986081441":2,"2x2":1,"3":[0,2,3],"30":[1,2],"3037":2,"3039":2,"33":2,"37":2,"4":2,"48":3,"5":2,"52":3,"542416":0,"542416v1":0,"58":3,"6":2,"67":2,"7":2,"72":3,"77":2,"8":0,"83":2,"9":2,"93":2,"97":2,"9true":2,"boolean":1,"case":[1,2,3],"default":[1,3],"do":1,"export":[1,3],"final":1,"float":1,"function":[0,1,2],"import":[1,2,3],"int":1,"new":[1,2],"true":[1,2,3],"while":1,For:[1,2],If:[0,1],In:[0,1],The:[0,3],Then:3,These:1,_:[1,2,3],_c:[1,2,3],_custom_ashlar_func:2,_r:[1,2,3],_row:[1,2,3],_well:1,_zstack3_r:1,_zstack:1,abov:[2,3],access:[0,1,3],accord:1,acquir:1,activ:0,ad:1,adapt:2,addit:[0,1],addition:1,adjust:[1,2,3],against:3,alexa488:[1,2],alexa647:3,align:[2,3],all:[0,1,2,3],allow:1,also:[0,3],altern:1,an:[1,2,3],analysi:0,andrea:0,ani:[1,3],anoth:[2,3],api:0,appli:1,applic:0,aquir:[0,2,3],ar:[1,3],area:1,arndt:0,ashlar:[0,1],assign_random_id:1,autom:3,automat:1,ax:2,axi:2,background:1,base:1,been:0,befor:1,below:3,berouti:0,better:3,between:1,bia:[1,3],bin:1,biorxiv:0,bool:1,bottom:[1,2,3],c:0,calcul:1,call:1,can:[0,1,2,3],caus:1,cd:0,cell:3,cellular:0,channel:[1,2,3],channel_nam:3,citat:[],clara:0,clone:0,code:[0,2,3],col:[1,2,3],collect:1,com:[0,2],complet:2,conda:0,connect:3,contain:[0,1,3],content:[0,3],control:1,convent:1,coordin:3,copi:1,correct:[1,2,3],creat:[0,2,3],crispr:0,crop:[1,2,3],cultur:3,current:0,dapi:1,data:[0,1,2],de44147ed2974457ad6372750bbe5751:2,defin:[1,2,3],degre:1,depend:0,deprec:2,destin:1,develop:0,dictionari:1,differ:1,differentoper:1,dimens:1,directli:[],directori:[0,1,2,3],displot:2,distplot:2,do_intensity_rescal:1,document:2,doe:[1,2,3],doi:0,down:1,downsampl:1,downsample_fold:1,downsample_img:1,downstream:[0,1],duplic:3,e:1,each:[1,3],edg:2,either:[1,2],element:1,elimin:3,els:1,enabl:3,end:1,enter:1,entir:3,environ:0,equival:1,error:2,etc:1,exact:1,exampl:1,example1:2,exist:[2,3],experi:[1,2,3],export_as_symlink:[1,3],export_exampl:1,export_meta:1,export_xml:1,f:2,fals:[1,3],faster:1,fig:2,figsiz:2,figur:2,fiji:1,file:1,file_end:1,filenam:3,filepath:1,filesystem:1,filetyp:[1,2,3],filter:1,find:[1,2,3],first:3,flatfield:1,flatfield_export:[1,3],flexibl:2,folder:[1,2,3],folder_path:1,follow:[0,1,3],forg:0,form:1,format:1,framework:0,from:[0,1,2],g:1,gener:[0,1,2],generate_stitch:[1,2,3],generate_thumbnail:1,genom:0,georg:0,get:1,gist:2,git:0,github:[0,2],give:1,given:3,good:3,guid:2,ha:0,hardcopi:3,harmoni:[1,3],hartmann:0,harz:0,heinrich:0,here:2,high:1,histogram:2,histplot:2,hornung:0,how:1,hpc:3,http:[0,2],i:1,id:[1,2],identifi:1,illumin:1,imag:[0,3],image_process:1,img_path:1,implement:2,improv:1,imread:2,imshow:2,indic:1,individu:1,inform:3,input:3,input_dir:[1,2,3],insert:[],issu:1,java:0,job:3,join:[2,3],lab:0,larg:2,lead:1,leav:1,left:[1,2,3],leonhardt:0,level:2,librari:3,linux:0,list:1,locat:3,loop:3,low:1,lt:2,machin:0,maco:0,maedler:0,main:0,make:0,makedir:[2,3],mani:1,mann:0,mannlab:0,manuscript:0,marleen:0,match:1,matplotlib:2,matthia:0,max_shift:1,maximum:1,mean:1,meant:1,measur:1,merg:2,metadata:1,metousi:0,microscop:[0,1],minut:2,more:1,much:1,multi:1,multipl:[1,3],multithread:1,mwaskom:2,n:[0,1],name:[1,3],navig:0,need:[1,2,3],nikla:0,no_rescale_channel:1,none:1,num_thread:1,number:[1,2],nxn:1,off:2,om:[1,2,3],one:[1,2,3],openjdk:0,opera:0,org:0,origin:1,os:[1,2,3],other:[0,1,3],out:1,outdir:[1,2,3],output:[0,1],output_filetyp:[2,3],overhead:1,overlap:[1,2,3],overview:1,overwrit:1,packag:0,paramet:[1,2,3],pars:[0,2],parse_phenix:[1,2,3],parsed_dir:1,parsed_imag:3,partial:1,pass:[1,2,3],path:[1,2,3],pattern:[1,2,3],pdf:3,perform:[0,1,2],perkinelm:0,phenix:[0,1],phenix_dir:1,phenotyp:0,pip:0,pipelin:[1,2],pixel:1,plan:3,platform:0,pleas:[0,2],plot:[1,3],plot_qc:1,plt:2,posit:[1,3],potenti:1,pp:3,prepend:1,present:1,process:0,produc:1,project:3,protocol:3,provid:1,put:3,py:2,pyplot:2,python:0,qc:1,qc_edge_qu:3,qc_edge_scatt:3,qualiti:3,quantifi:2,quick:1,random:1,raw_image_til:2,read:3,recogn:[2,3],record:1,regex:1,region:1,regular:1,relev:3,rememb:[2,3],remot:1,remov:2,renam:[1,3],repositori:0,requir:3,rescal:1,rescale_p1_p99:1,resolut:1,result:[0,1,2],right:[1,2,3],row1_well2_:1,row:[1,2,3],run:[0,1,3],s:2,same:1,sampl:3,save:1,scale:[0,1],scan:1,schmack:0,screen:0,script:[1,3],seaborn:2,second:1,see:[1,2],segment:1,select:1,seper:3,set:[1,3],sever:[2,3],shift:1,should:[0,1,2,3],show:3,signficiantli:1,similar:2,simpl:1,singl:1,slide1:3,slide:[2,3],slidenam:[1,2,3],sn:2,sophia:[0,2],sort:1,sort_timepoint:1,sort_wel:1,space:3,sparc:0,sparcspi:[0,3],sparcstool:[1,2,3],spatial:0,speciifc:[2,3],speed:3,src:2,stain:1,standard:1,step:1,stich:1,sticht:2,stitch:0,stitching_channel:[1,2,3],stitching_test:[2,3],stitching_test_alexa488:[2,3],stitching_test_dapi:[2,3],stitching_test_mcherri:[2,3],stitching_test_tile_posit:3,str:[1,2,3],string:1,subplot:2,subset:3,symlink:[1,3],system:1,test:0,test_data:2,than:1,thi:[0,1,2,3],those:1,thread:1,threshold:1,thumbnail:1,tif:[1,2,3],tiff:1,tifffil:2,tile:[1,2,3],time:1,timecours:1,timecourse_sort:1,timepoint:[1,2,3],todo:2,togeth:1,top:[1,2,3],tsv:3,tupl:1,type:1,uint16:1,uniqu:1,unqiu:1,updat:2,us:[0,1,2],usabl:1,use_symlink:1,use_symlonk:1,user:2,userwarn:2,util:0,v0:2,valu:[1,2,3],veit:0,via:0,virtual:0,visual:0,wa:[0,1,2,3],wallmann:0,want:[2,3],well:[0,1,2,3],wga:1,wgabackground:1,wgachannel:1,when:[1,3],where:[1,3],which:[1,2,3],window:0,without:[1,3],work:3,workflow:0,wrapper:0,write:[1,2],written:1,www:0,xml:[1,3],you:[0,2,3],your:[2,3],zarr:[1,2,3],zfill:[2,3],zstack:[1,2,3],zstack_valu:[2,3]},titles:["Welcome to SPARCStools documentation!","Modules","<span class=\"section-number\">1. </span>Example Stitching Notebook","<span class=\"section-number\">1. </span>Tutorials"],titleterms:{cite:0,data:3,document:0,exampl:[0,2,3],file:3,from:3,gener:3,imag:1,instal:0,modul:[0,1],notebook:[0,2],opera:3,our:0,output:[2,3],pars:[1,3],phenix:3,process:1,result:3,sparcstool:0,stitch:[1,2,3],tutori:[0,3],visual:2,welcom:0,work:0}})
\ No newline at end of file
diff --git a/docs_source/index.rst b/docs_source/index.rst
index cd9272c..32e48e1 100644
--- 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