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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 This is not peer-reviewed science, but is evidence-based as much as possible.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, send in a correction to colibri.cytometry at gmail. 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.
Commenting has been deactivated. Sorry.
The comments were getting spammed.
Also, GDPR is a headache.
Honeychrome: supported cytometers
First off, if you've used Honeychrome, we'd appreciate feedback. I've tried to create this feedback form, which hopefully works as intended. If you've tried it with your data, or the example data, did it work? Did you run into issues? What did you like or dislike about the experience of working with the software? Users have reported that testing on FCS files from different instruments have revealed issues due to lack of conformity, but never fear... we are immediately rolling
Jun 13 min read
Predicting unmixing errors
One key problem in spectral cytometry is what to do when the unmixing isn’t correct. An important step towards fixing this is being able to determine when we have errors and where they are coming from.
May 205 min read
AutoSpectral: ID7000 40C examples
Today, let's look at some 40-colour data from a 5-laser Sony ID7000, using AutoSpectral for the unmixing.
Oct 30, 20252 min read
AutoSpectral: OMIP-102 examples
What happens if we run AutoSpectral on a good dataset, with cell-based controls?
Oct 29, 20252 min read
Introducing AutoSpectral: an optimized unmixing workflow
With AutoSpectral, we provide an optimized, complete pipeline in R to make the best use of the information in the single-stained controls and reproducibly generate better unmixing.
Oct 28, 20253 min read
AutoSpectral: Per Cell Fluorophore Optimization
The aim of this article is to explain a bit more about how we go about optimizing the fluorophore signatures used for unmixing on a per-cell basis in AutoSpectral. Let me know if the explanation doesn't make sense.
Oct 27, 20259 min read
AutoSpectral: Single Cell Autofluorescence
The aim of this article is to show you how to use AutoSpectral’s per-cell autofluorescence (AF) extraction. This method selects the best AF signature to use for each cell (or point of debris, noise, whatever) in the data.
Oct 27, 20256 min read
AutoSpectral: cleaning
In this article, we’ll try to cover the functions that AutoSpectral offers for cleaning your single-stained control data.
Oct 27, 20257 min read
AutoSpectral: basic workflow
In this article, I'll cover the basic workflow for using AutoSpectral for unmixing spectral flow cytometry data.
Oct 27, 20252 min read
Spectral mixing matrix normalization
Should we normalize the fluorophore signatures to the peak or to the sum of all the signals?
Sep 22, 20253 min read
What's an unmixing matrix?
In the last post, we looked at what the spectral mixing (sometimes called spillover) matrix looked like. Today, let's go through a bit about the unmixing matrix.
Aug 26, 20255 min read
What's in a spectral matrix?
Today the plan is to try to explain what a spillover or spectral matrix is
Aug 11, 20257 min read
AutoSpill 2: Spectral Boogaloo
AutoSpectral is a new way of getting better unmixing.
Jun 30, 20251 min read
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 12, 20252 min read
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 28, 20255 min read
Unmixing: the tortoise beats the hare
Today's tip: when running your single-color controls, take it slow.
Mar 31, 20254 min read
Creating and using settings on the Aurora
Create settings to ensure reproducible results across experiments.
Mar 17, 20259 min read
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
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
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
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