index.Rmd

--- 
title: "Analysis workflow for IMC data"
author: "**Authors:** Nils Eling [<sup>1</sup>](#DQBM)<sup>,</sup>[<sup>2</sup>](#IMHS)<sup>,</sup>[<sup>*</sup>](#email), Vito Zanotelli [<sup>1</sup>](#DQBM)<sup>,</sup>[<sup>2</sup>](#IMHS), Michelle Daniel [<sup>1</sup>](#DQBM)<sup>,</sup>[<sup>2</sup>](#IMHS), Daniel Schulz [<sup>1</sup>](#DQBM)<sup>,</sup>[<sup>2</sup>](#IMHS), Jonas Windhager [<sup>1</sup>](#DQBM)<sup>,</sup>[<sup>2</sup>](#IMHS), Lasse Meyer [<sup>1</sup>](#DQBM)<sup>,</sup>[<sup>2</sup>](#IMHS)"
date: "**Compiled:** `r Sys.Date()`"
site: bookdown::bookdown_site
github-repo: "BodenmillerGroup/IMCDataAnalysis"
documentclass: book
bibliography: [book.bib, packages.bib]
biblio-style: apalike
link-citations: yes
description: "This bookdown project highlights possible down-stream analyses performed on imaging mass cytometry data."
---

# IMC Data Analysis Workflow {#preamble}

This workflow highlights the use of common R/Bioconductor packages
to analyze single-cell data obtained from segmented imaging mass cytometry (IMC)
images. We will not perform multi-channel image processing and segmentation in R
but rather link to available approaches in Section \@ref(processing). While we
use IMC data as an example, the concepts presented here can be applied to images
obtained by other highly-multiplexed imaging technologies (e.g. CODEX, MIBI,
mIF, etc.).

We will give an introduction to IMC in Section \@ref(intro) and highlight
strategies to extract single-cell data from IMC images in Section
\@ref(processing).

Reproducible code written in R is available from Section \@ref(prerequisites)
onwards and the workflow can be largely divided into the following parts:

1. Preprocessing (reading in the data, spillover correction)
2. Image- and cell-level quality control, low-dimensional visualization
3. Sample/batch effect correction
4. Cell phenotyping via clustering or classification
5. Image visualization
6. Spatial analyses

## Feedback and contributing

If you notice an issue or missing information, please report an issue
[here](https://github.com/BodenmillerGroup/IMCDataAnalysis/issues). We also
welcome contributions in form of pull requests or feature requests in form of
issues. Have a look at the source code at:

[https://github.com/BodenmillerGroup/IMCDataAnalysis](https://github.com/BodenmillerGroup/IMCDataAnalysis)

## 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) 
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
```

---

<a name="email"><sup>*</sup></a> nils.eling@uzh.ch  
<a name="DQBM">1:</a> Department for Quantitative Biomedicine, University of Zurich  
<a name="IMHS">2:</a> Institute for Molecular Health Sciences, ETH Zurich