Frequently Asked Questions (FAQs)

What is flow cytometry?

Basic information on the theory of flow cytometry, fluorochromes, panel design and analysis is available from a variety of sources. Many useful sources are provided from vendors. While the Flow Cytometry Core Facility does not endorse any specific vendors as a reagent supplier or educational resource, a few useful websites are listed here to help get you started.

Bio-Rad: Introduction to Flow Cytometry - Basics Guide

De Novo: Flow Cytometry – A Basic Introduction

Purdue University: Flow Cytometry Discussion List

Thermo Fisher Scientific: Flow Cytometry Basics

How do I plan a flow cytometry experiment?

Before you get started with planning your flow cytometry experiment, we recommend you first review our instrument configurations, by downloading the configurations file [PDF-66 KB], which includes all the detector filter information for all our instruments. This filter information along with the suggested tools and websites listed below will help you properly design a flow cytometry experiment. When designing panels, we suggest you speak with flow cytometry facility staff, as well as vendors’ technical advisors.

In addition to the introductory information presented in the above question, there are many tools available online to help plan a flow cytometry experiment, including spectral viewers and panel design tools. While the Flow Cytometry Core Facility does not endorse any specific vendors as a reagent supplier or educational resource, a few useful websites are listed here to help get you started.

Spectral viewers are particularly useful tools for panel design, in which you may view the excitation and emission of potential fluorochromes in the context of the specific laser lines and detector filter sets of the instrument you will use. Some common spectral viewers are available at the following vendors’ websites:

BD Bioscience: Fluorescence Spectrum Viewer

BioLegend: Spectra Analyzer

Thermo Fisher Scientific: Fluorescence SpectraViewer

You may also find useful panel design tools, which allow you to build a panel and source antibodies from multiple vendors. One such site, which contains the configurational information of our instruments may be found at the link below.

FluoroFinder: Dalhousie University - Faculty of Medicine Flow Cytometry Facility

Additionally, there are tools for finding antibody usage data, which can help you select the best antibody to use in your panel. For example, visit the website in the link below to review antibody choices.  

BenchSci - A.I. Driven Antibody Search

How should my samples be prepared?


Samples to be sorted must be prepared just prior to running on the instrument. They must be a single cell suspension and filtered through a 40 micron sieve after the last wash and resuspended in sort buffer. Samples are generally best brought on ice. See the sorting application form [PDF-314KB] for more information.  


Samples for acquisition should also be a single cells suspension, usually suspended in 300-350 microliters. These samples should be filtered through a 35-40 micron strainer as well, with particular attention paid to tissue digests. Most samples are fixed in 1% PFA. If samples will not be read immediately and tandem dyes are used it is recommended to fix for 1 hour, wash away fixative and resuspend in PBS.

How do I schedule an appointment?

On instruments booked by trained users, bookings may be made independently via the online instrument schedulers. Planning well in advance will render a much better chance of getting an available time slot when needed. Instruments are often heavily used and all users rely on schedulers to plan their experiments. As a result, you can be charged for a deleted booking cancelled within 24 hours of the intended use.

For flow staff operated instruments, booking will depend on both staff and instrument availability. We do our best to accommodate users’ needs, however we require at least 72 hours’ notice and will do our best to find a time that suits the user and the operator. Cancellation with less than 24 hours’ notice can result in invoicing for the booked slot.

We ask that all users of our facility do their best to book only the time they need to acquire or sort their samples, thus freeing up instrument time for other users. As always, please communicate with the flow cytometry staff as soon as possible if there is a problem regarding your booking.

Do I need to be present during the sorting/acquisition of my samples?

We prefer sorting customers to join us for the beginning of their sorts, while gating strategy, etc. is applied. In most cases, you may leave after this step as the sort may proceed for some time.

Acquisition customers may arrange to leave their samples and information with the flow cytometry staff and do not need to be present during acquisition.

Where can I bring/leave my samples?

Samples can be left with flow cytometry staff in the LSRI, room N-107, between 9am-5pm most days. Call ahead to be sure we will be present to receive your samples. In some cases, you may leave samples finished in the evening in the Tupper sub-basement SB-C1 lab refrigerator for an early acquisition the following day. Always communicate with the flow cytometry staff about when you will drop off samples and where you will drop them off.

How much will it cost?



There is a standard instrument setup fee plus an hourly charge. The required length of time for a sort varies greatly depending on many factors, including the abundance of the population to be sorted, the quality of sample preparation and instrument setup tailored for the sample type and intended downstream application. The average sort of 10 million or less starting cells may take about 1-2 hours. More complex sorts, or those with significantly larger numbers of starting cells will take accordingly longer, roughly 3-6 hrs per 300 million cells.


Samples acquired on the Celesta or Cytoflex may take about 1-4 hr for 30-50 tubes, depending on cell concentration, target population abundance and required events to be recorded. Acquisition on the Fortessa or Symphony due to the nature of the complexity of setup and necessary controls may be about double that of the Celesta/Cytoflex. Rates for the Celesta, Cytoflex, Fortessa and Symphony vary depending on independent (unassisted) vs operator assisted use. More information can be found on our Share point page. Please contact us for accurate costing of your project.

How are results reported?

All data is provided as FCS (flow cytometry standard) files compatible with post acquisition analysis software. Although limited help with data analysis may be provided in an advisory capacity, users are responsible for their own data analysis as the facility is not equipped with resources to accommodate this part of the process. Data is currently provided on DVD to limit viral and software problems due to internet connectivity or USB flash drives.