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BodenmillerGroup · Oct 19, 2023 · d9730f8 · d9730f8
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diff --git a/README.md b/README.md
@@ -80,14 +80,13 @@ To add new libraries to the container please add them to the [Dockerfile](Docker
 
 ## Citation
 
-The workflow is currently under development for final publication.
-In the meantime please refer to the 
-[preprint](https://www.biorxiv.org/content/10.1101/2021.11.12.468357v1) 
+The workflow has been published in  
+[Nature Protocols](https://www.nature.com/articles/s41596-023-00881-0) 
 which you can site as follows:
 
 ```
-Jonas Windhager, Bernd Bodenmiller, Nils Eling (2020). An end-to-end workflow for multiplexed image processing and analysis. 
-    bioRxiv, doi: 10.1101/2021.11.12.468357
+Windhager, J., Zanotelli, V.R.T., Schulz, D. et al. An end-to-end workflow for multiplexed image processing and analysis.
+    Nat Protoc (2023). 
 ```
 
 ## Funding

diff --git a/index.Rmd b/index.Rmd
@@ -59,14 +59,13 @@ issues. Have a look at the source code at:
 
 ## Citation
 
-The workflow is currently under development for final publication.
-In the meantime please refer to the 
-[preprint](https://www.biorxiv.org/content/10.1101/2021.11.12.468357v1) 
+The workflow has been published in  
+[Nature Protocols](https://www.nature.com/articles/s41596-023-00881-0) 
 which you can site as follows:
 
 ```
-Jonas Windhager, Bernd Bodenmiller, Nils Eling (2020). An end-to-end workflow for multiplexed image processing and analysis. 
-    bioRxiv, doi: 10.1101/2021.11.12.468357
+Windhager, J., Zanotelli, V.R.T., Schulz, D. et al. An end-to-end workflow for multiplexed image processing and analysis.
+    Nat Protoc (2023). 
 ```
 
 ## Changelog

diff --git a/publication/README.md b/publication/README.md
@@ -3,9 +3,12 @@
 This folder of the repository contains the code to reproduce the analysis presented in the following paper:
 
 ```
-TODO upon acceptance
+Windhager, J., Zanotelli, V.R.T., Schulz, D. et al. An end-to-end workflow for multiplexed image processing and analysis.
+    Nat Protoc (2023). 
 ```
 
+It is accessible at [https://www.nature.com/articles/s41596-023-00881-0](https://www.nature.com/articles/s41596-023-00881-0)
+
 ### System requirements
 
 To run the workflow, a computer with a recent version of a Windows, Mac, or Linux operating system (OS) is required.