StemCore Laboratories · Ottawa Hospital Research Institute
Free, open-access training in cytometry and genomics — built by the scientists who run the instruments. For researchers at OHRI, uOttawa, and beyond who want to design better experiments and make smarter decisions about their data.
Foundations, practical protocols, and analysis tools. Start with the core theory and work through to data analysis in FlowJo.
Core
The complete introduction — light scatter, fluorescence detection, instrument design, and how it all translates to your data. 120 slides.
A narrative walkthrough of core cytometry concepts, built for researchers coming to flow cytometry for the first time.
Practically...
What your cells need before they reach the instrument — tissue dissociation, viability, fixation, and storage.
Why untitrated antibodies undermine your data, and how to titrate correctly before committing to a panel.
Fluorochrome selection, compensation strategy, and spillover management for multicolour panels.
Planning and executing a sort — sample preparation, tube setup, post-sort viability, and yield expectations.
The most common mistakes in flow cytometry experiments and how to design around them from the start.
How to present flow cytometry data clearly in papers and talks — figure standards and what to avoid.
Analysis
Getting started with FlowJo — importing data, building gating hierarchies, and extracting statistics.
Dimensionality reduction, tSNE, and UMAP for researchers moving beyond conventional gating strategies.
The Make Smarter Sequencing Decisions seminar series — five talks designed to help researchers understand what goes into a sequencing experiment before they book one. Developed by StemCore, 2025.
Make Smarter Sequencing Decisions
Short-read and long-read sequencing compared — how each works, what each is best for, and how to choose for your experiment.
The original sequencing method — still the gold standard for validation. When to use it and what its limitations are.
Experimental design for genomics — how the choices you make before you sequence determine the quality of what you get back.
Single-cell sequencing — what it reveals that bulk sequencing can't, and what it takes to do it well.
Long-read sequencing with Oxford Nanopore — the applications it unlocks and how to get the most from it.
Foundation
A broad introduction to the technologies used to detect, measure, and sequence DNA — from PCR through to nanopore. 43 slides.
A practical course covering cytometry data analysis in R — from import and QC through to dimensionality reduction and population identification. In development.
A complete practical course for analysing flow and mass cytometry data in R, built on Bioconductor tools.
In developmentStemCore Laboratories is a multi-platform genomics and cytometry core facility at the Ottawa Hospital Research Institute, serving researchers across OHRI, uOttawa, CHEO, UOHI, and beyond.
What StemCore offers, who we work with, and how to access our services.
An overview of the shared research infrastructure available to investigators at OHRI.
Technical guides and practical resources for CyTOF and Helios users. Covers the instrument, sample preparation, panel design, and data quality. Largely established content, updated as the field develops.
Guides & Protocols
Everything you need to plan and execute a CyTOF project at OHRI — from first contact through to data delivery.
The physics of mass cytometry — metal-tagged antibody detection and what instrument design means for sample quality.
CyTOF-specific sample preparation — fixation, barcoding compatibility, and what degrades signal quality.
Metal conjugation, mass channel selection, and avoiding panel design problems unique to CyTOF.
Sample numbers, experimental controls, and timeline — what to decide before you start staining.
Step-by-step guidance — cell counts, viability, cisplatin staining, and freezing for CyTOF.
Why barcoding reduces batch effects and improves data quality — and how to implement it.
Removing doublets and dead cells — the gating strategy that applies to every CyTOF experiment.
StemCore's CyTOF service overview presented at OHRI Research Day 2021.