In this workshop we will demonstrate the main steps to perform computational analysis of highly multiplexed imaging data. The first day will start with a troubleshooting session to address possible issues when installing the required software. The first main session will highlight a number of interactive visualization approaches for imaging mass cytometry (MCDViewer) and other highly multiplexed imaging data (napari, QuPath, ImageJ/FIJI). Image processing and segmentation is performed using the steinbock framework (https://github.com/BodenmillerGroup/steinbock). We will first give an overview of the framework prior to hands-on training. The final session of the first day will include an introduction to the cytomapper and imcRtools R/Bioconductor packages for reading spatially resolved, single-cell and multiplexed imaging data into R for analysis.
The second day will focus on analysis approaches presented in our online book for multiplexed image analysis (https://bodenmillergroup.github.io/IMCDataAnalysis/). In the first session of the day we will present general single-cell analysis approaches including dimensionality reduction, visualization, clustering and cell type classification as well as channel-to-channel spillover correction and image visualization. The second session will demonstrate common spatial analysis approaches including spatial community detection, cellular neighborhood and spatial context analysis and cell type/cell type interaction testing. Finally, in the last session you can bring your own data and discuss open challenges with experts of the lab.
To access the code you can clone the current repository via
git clone https://github.com/BodenmillerGroup/ImagingWorkshop2023.git
or you can click the Code > Download ZIP button.
Please follow the instructions in the Setup folder on how to install the needed software.
The data_download.R script in the data folder allows you to download all needed data.
Session 3-5 will be conducted in R. The R markdown scripts can be found in the individual folder. Please always ensure that you open the ImagingWorkshop.Rproj file before starting the session.
11.01.2023
| Time (CET) | Topic |
|---|---|
| 9.00h | Troubleshooting session |
| 10.00h | Welcome and coffee |
| 10.15h | Introduction |
| 10.30h | Image visualization |
| 11.00h | Hands-on training: image visualization |
| 11.30h | Lunch |
| 12.30h | Image processing |
| 13.00h | Hands-on training: image processing |
| 14.30h | Coffee break |
| 15.00h | Reading data into R and visualization |
| 15.30h | Hands-on training: reading data into R and visualization |
12.01.2023
| Time (CET) | Topic |
|---|---|
| 09.00h | Single-cell analysis |
| 09.30h | Coffee break |
| 10.00h | Hands-on training: single-cell analysis |
| 11.30h | Spatial data analysis |
| 12.00h | Lunch |
| 13.00h | Hands-on training: spatial analysis |
| 14.30h | Coffee break |
| 15.00h | "Bring your own data" |
- IMCDataAnalysis for a comprehensive overview on multiplexed image analysis.
- steinbock for image processing, segmentation and feature extraction.
- imcRtools for spatial visualization and analysis.
- cytomapper for image visualization and compensation.
- Orchestrating single-cell analysis with Bioconductor for an overview on single-cell analyses using Bioconductor packages.