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Welcome to the blog
The content posted here is intended to help and is meant to be as accurate as possible. There will inevitably be mistakes or gaps in the knowledge. This is not peer-reviewed science, but is evidence-based as much as possible. If you see a factual inaccuracy or disagree, add a comment or send in a correction. Also, while some of this content tries to push the boundaries of what we know about how to do flow, it is not intended to claim invention credit. If you feel a reference has been overlooked, please let me know.


Stabilizing your unmixing: drift
Today's post is meant to illustrate why I do not recommend running new samples using the same unmixing matrix across multiple days.
May 122 min read
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Stabilizing your unmixing
Today's post pulls from a lot of previous posts on this blog to show how to effectively eliminate batch effects in your flow from an experimental side. Stabilizing the unmixing is a big part of this.
Apr 285 min read
477 views
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The peculiarities of Phenograph
Phenograph is one of the more popular clustering algorithms for flow cytometry.
Apr 145 min read
288 views
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Unmixing: the tortoise beats the hare
Today's tip: when running your single-color controls, take it slow.
Mar 314 min read
588 views
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Creating and using settings on the Aurora
Create settings to ensure reproducible results across experiments.
Mar 179 min read
511 views
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Stabilizing master mixes: what doesn't work
If you don't put in the legwork of testing the mixes for your panel, expect to run into problems.
Mar 32 min read
406 views
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Stabilizing master mixes
How to prepare and store antibody master mixes stably.
Feb 178 min read
1,124 views
2 comments


Simple tips for reducing errors with panel prep
Running large panels consistently is all about error prevention.
Feb 36 min read
614 views
4 comments


“Rescuing” GFP
Why do we lose GFP and other fluorescent proteins when we fix and permeabilize cells? How can we stop this?
Jan 206 min read
1,105 views
4 comments


Overnight staining: tetramers
Does overnight staining help for antigen-specific TCR detection with tetramers? Not so much.
Jan 63 min read
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Fluorophores for nuclear staining
What's the best type of fluorophore to use for targets that are in the nucleus of the cell?
Dec 16, 20243 min read
1,196 views
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Dealing with multiple autofluorescences
Our samples, more often than not, contain autofluorescence (AF) that varies not only in intensity but also in aspect.
Dec 2, 20248 min read
848 views
4 comments


How to: Run plates on the Cytek Aurora
Today I'm going to share my tips for successfully running lots of samples on the Aurora without having to babysit the machine.
Nov 25, 20245 min read
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Five ways to extract autofluorescence (and store it)
Let’s start by looking at the autofluorescence extraction methods available to us, their advantages and drawbacks.
Nov 18, 202412 min read
746 views
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Unmixing: should you use a universal negative?
When unmixing, we have the option to use either an internal negative population or a completely independent "Universal Negative".
Nov 11, 20244 min read
960 views
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Autofluorescence in conventional flow cytometry
Let's take a step back and look at how autofluorescence is handled in conventional flow.
Nov 4, 20247 min read
1,073 views
2 comments


ClusterID update
Thanks to franpcozar for highlighting an issue with ClusterID . The script was failing when the input clusters were named with...
Oct 31, 20241 min read
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Backgating: What is it and why will it help?
Backgating is a simple, useful technique in flow cytometry that can help you figure out where your cells are, and thus optimize your gating
Oct 28, 20243 min read
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Autofluorescence: what not to do
Today let’s look at something I think you shouldn’t be doing with AF extraction in spectral flow cytometry.
Oct 21, 20244 min read
1,041 views
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How does AutoSpill work and why does this produce better compensation?
There are three key ways in which AutoSpill differs from traditional compensation: Data usage, AF handling and Refinement.
Oct 14, 20246 min read
637 views
2 comments
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