From b42ec182ee0abcdf6706faa23c8d9370d9e0fb5f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sophia=20M=C3=A4dler?= <15019107+sophiamaedler@users.noreply.github.com> Date: Fri, 2 Jun 2023 09:47:24 +0200 Subject: [PATCH] add citation and link to manuscript --- README.md | 17 ++++++++++++++++- docs/doctrees/environment.pickle | Bin 27086 -> 27086 bytes docs/doctrees/index.doctree | Bin 9767 -> 11179 bytes docs/html/_sources/index.rst.txt | 7 +++++-- docs/html/index.html | 6 ++++-- docs/html/searchindex.js | 2 +- docs_source/index.rst | 7 +++++-- 7 files changed, 31 insertions(+), 8 deletions(-) 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 1bbebc21b32e393618591e58cae788b229e37711..b3cddb0d4a2db2d225b971be2d190cae94ee21df 100644 GIT binary patch delta 229 zcmX?inep6Z#tlzZCo8E5P5$Sn!`H)GkeHrYte=~oQks*x*--5OGn-uc+z*;6lfP>^ zPhOxCI5|MiX>ys4*5rk{;fz6(7wVW!(vfG31u~o`&(V@$3n8$FT9A9aEm z1Hs}pdYqG0w7n=FSw{2C(Y|JkjJA`beRF^geaq;w`Hg>(IAiqW_;lCFap|^`AEs9cY+`3%$l3}b Nc7TZWo3k^L83BezQ}h4; delta 256 zcmX?inep6Z#tlzZ`FRTx(^HG}bMsS5b5e_^O#bVqE6~Fa5iBV!$uG)G%-L+Hc7T~p z_DQvKYTD%Qn$DA@^yDTl)=ro_Pgj02o9+z8h{^uirjrY__$JrriB0y^4x7xZ6EXRm zmL{VgR7QI8W}RThD7ZRCJxRt8IL}&J7^uT#@_Zc;MhB26M@nKzYDs2p>f}DXWgI4Y z1$pUHdVD9()pKPriZ?Xg+^T<7meFK$w67T>qt)bS-<-++{N6G;ZhqrmB+eK!IX>NW ea$LIYX*x_q}=h?bY4a zhN@3iU%ayJMl}ig#+>WHR^LHqGFaE2>7YWC%${g;baXV5RT&>sM! zmD+hCJIWk5>+wkgWVVQyKTDD_SY@CmiE6a<{#A3{+Gr4Ni8c~IJZdlfA6@tMY8{U z$IUI0{avr7I!=C_6AMdFcyS#G-~TToLNk(Cxgk$pZb^A*smROiS@I$wT3O;8t#5Pg zgvNc(oWqT$g0H{t&>l(x?X-i22fBgJ1LsR)mv7QxEe-YBeeg{yDjWj>tvzxMG_9|B z0uJq|bFQh`ehyPuuU%4Ag|(Mp4EVKI@G1xPT7q$q8?(pN-oVOP?X5Sy^TziuCSUlq z51#cAM#%CBURnTBfi%uWwgr%V1)r70v_bw2LK&AfLBQvFSjDsj%vJEL&bTu2H{p*r zcTdA#H4pxZ?PIuD0wql`L9&buFP6rd`82ixjTLfvhK2<0@%SN)3D#2U_hlwV(PMv2 zHw0>(&Y{-Erl_1MGEsS{fs4dbaQT)Ibi$k}v_LT}(=+roy{Qeu OVf3D+Ox$ff==%najfKYm delta 658 zcmZ1-zTAhkfpw~k+D6t?2}aAwZzWVFPmmDdvYL{?9y=vNum>(AVl}08O5>E;DH<89 zS(6wU7&64NCQMEgHJ!XsO2Vy2#M3X>H7G>E*)zm3#M9qT!NWDk6=n!_NrZ6=AjZuD z8|NxNhjIVpNAislM}fkn8LC+uLDK3O8X212CO}))O|DijV_Y-&prVAxTA-9B)KwX5 zAU9`intV?|mu(MFB5UttK}DJRgFq%w{1K2!%sLDty_vI)0I43XkkXR;qRhmcVyh`x z$ABW8S;xWT2{3sQNcui!&N>C=od%LXQ_cdZtfxQ%&0$tRhg}5;CnaWxg91qs7<|$| z4Hrd$qKO%@K(0IxE5=R%=_Jne3QFdpP}lzgnF4qHSA0D z7T?UJ{DFzlV)Jj+`^;=YOu&%fpZq{mij51zWS^uZVgnNN%gE};=Installation

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:

-

INSERT CITATION HERE

+

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

Modules:

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to SPARCStools documentation!","Modules","1. Example Stitching Notebook","1. 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