Course · Cardinal
Analysis of mass spectrometry images with Cardinal
Days 1–2 · November 5–6, 2026 · 10:00 a.m.–12:30 p.m. EST. Led by Kylie Bemis, Sai Srikanth Lakkimsetty, Ethan Rogers, and Yinyue Zhu.
Background
This course covers the basics of data manipulation, visualization, and statistical analysis of mass spectrometry imaging (MSI) experiments using Cardinal and R. We begin by introducing the fundamental ways of interacting with MSI datasets and experimental metadata in Cardinal, followed by preprocessing and visualization of mass spectra and ion images. We then demonstrate the application and interpretation of statistical and machine learning methods for segmentation, classification, and hypothesis testing. Sessions mix lectures with code demonstrations using datasets from public repositories such as PRIDE and MassIVE.
Who it’s for
Biologists, chemists, bioinformaticians, computer scientists, data scientists, statisticians, and engineers who are comfortable with the basics of R and interested in working with MSI data in Cardinal.
Schedule
Two online sessions, each 10:00 a.m.–12:30 p.m. EST (7:00–9:30 a.m. PST · 4:00–6:30 p.m. CET). Every day follows the same format: two one-hour lectures with a short break, followed by general discussion. Lecture titles will be added as the program is finalized.
- 10:00–11:00 Lecture 1 — to be announced
- 11:00–11:15 Break and questions
- 11:15–12:15 Lecture 2 — to be announced
- 12:15–12:30 General discussion
- 10:00–11:00 Lecture 1 — to be announced
- 11:00–11:15 Break and questions
- 11:15–12:15 Lecture 2 — to be announced
- 12:15–12:30 General discussion
Software and installation
If you would like to follow along with the code demonstrations, please install the software below ahead of time. We will use recent versions of R and Bioconductor:
- R (≥ 4.6)
- Bioconductor (current release)
- Cardinal
- CardinalWorkflows (example datasets and workflows)
Please install or update to these versions if you wish to follow along with the examples.
- Install R (≥ 4.6) from CRAN, and (recommended) RStudio Desktop. On Windows, also install Rtools.
- Open R or RStudio and run the installation code below in the console.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(c("Cardinal", "CardinalWorkflows"))Materials
Presentation slides, code, and datasets are shared with registered participants ahead of each session, and recordings are published afterward.