Full Spectrum Cytometry: The Basics
- What is Full Spectrum Flow Cytometry?
- What can I run on the Aurora?
- What is it like to run samples on the Aurora?
- How do I get started?
In conventional flow cytometry, each detector is assigned to a fluorophore and picks up a small portion of the emission spectra (usually including the peak emission). With this setup, only a fraction of the fluorophore emission spectra is recorded.
In full spectrum flow cytometry, we are no longer limited by the one detector=one fluorophore setup. Instead, all the detectors in the cytometer capture a signature of the full emission spectra of each fluorophore. The raw data is mathematically unmixed to identify the fluorophores. This allows for the discrimination of similar fluorophores, as long as they have unique signatures. For example, Alexa Fluor 647 and APC and be spectrally unmixed.
- We have two 5-laser Auroras with the ultraviolet, violet, blue, yellow-green, and red lasers.
- The number of colors that can be run on the Aurora is currently limited by the mathematics of the spectral unmixing and the number of fluorophores available. Mathematically you can unmix the number of detectors minus 2, so for our 64-detector Aurora we can unmix 62 fluorophores. Cytek has successfully run a 40 marker panel, so right now we can definitely run their 40-marker panel. Please keep in mind that larger panels are more challenging and require additional time to set up properly. Most of our current users are running panels around 18-28 markers.
- As far as fluorophores, the Aurora can detect anything fluorescent – Brilliant Violets, Alexa Fluors, Super Brights, Qdots, viability stains, fluorescent proteins, etc.
- The aurora also has a volumetric counter for cell counts and a 96-well plate loader.
- One thing that may be challenging to run on the Aurora is a cell cycle stain (like DAPI) in addition to other fluorophores. DAPI can still be used for live/dead discrimination.
- Your samples can be prepared and stained exactly the same as you would with conventional cytometry
- You are welcome to try any panels you have made for the conventional cytometers and see how they look (it’s a great way to test out the Aurora!), however it is recommended that you pay close attention to panel design. The larger the panel, the more important panel design becomes.
- The software on the Aurora is similar to FACS DIVA, so you should be able to pick it up quickly
- Setup on the Aurora is easier because you typically don’t have to change voltages/gains like you do on the conventional flow cytometers
- Because the spectral unmixing is done mathematically and cannot be done manually, the Aurora is very particular about the single stains (called reference controls) being correct. This topic will be covered in detail during training.
- Currently, spectral unmixing can be done with the Cytek SpectroFlo software and in FlowJo, but once it is completed, you can analyze your data with any program that takes .FCS files (FlowJo, FCSExpress, etc.). SpectroFlo is much easier to use than FlowJo for unmixing, so we recommend using SpectroFlo on the analysis workstations.
For training, please contact Laura Johnston.
Training Slide Decks (Required Training – contact Laura Johnston to schedule)
Training Screencast Videos
- Full Aurora Training Course Videos – 07-2021 (Not a replacement for required training)
- Slides for Youtube Course – 07-2021
Spectra Viewers and Cytek Resources
Cytek User Guide
- User Guide: Software Overview
- User Guide: Creating a New Experiment
- User Guide: Unmixing and Compensation
- User Guide: Troubleshooting
- Aurora Quick Guide
- Importing and Exporting Experiments – 09-2020
- Using Experiment Templates – 09-2020
- How to Unmix a Titration Experiment with the Extra Tools Tab – 11-2020 (video)
Panel Design Tools
- 5L Fluorochrome Selection Guideline – 07-01-2021
- 5L 30 Color Spread Matrix with percentages
- 5L Perpetrators and Victims
- Panel design matrix
- 5L Stain Index
- Fluorophore Equivalence (Summary table of fluorochrome selection guide)
- List of Tandem and polymer dyes
- FluoroFinder antibody search tool (external link)
More in-depth information:
- Aurora Panel Design Full Tutorial – 07-2021 (Video)
- Aurora Panel Design Slides – 07-2021 (PDF)
- L Ferrer-Font, et al. “Design and Optimization Protocol for High-Dimensional Immunophenotyping Assays using Spectral Flow Cytometry” (Pre-print is also available here)
- Performing Spectral Unmixing – 07-2021(Video)
- Performing Spectral Unmixing – 07-2021(PDF)
- SpectroFlo Unmixing Tutorial: How to decide between beads vs cells controls -12-2020 (Video)
- Advanced tips for organizing unstained controls in SpectroFlo – 05-2021 (Video)
- How to Perform a Panel Quality Check 05-2021 (PDF)
- How to combine experiments – 09-2020 (Video)
- What does “failed QC” mean and how do I fix it?
Read blog posts related to spectral cytometry here