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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 This is not peer-reviewed science, but is evidence-based as much as possible.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.
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AutoSpectral: Automated Workflow
This post is intended to provide detailed instructions on how to use AutoSpectral's full workflow for extraction of fluorochrome profiles from single-stained controls, proceeding through unmixing of the spectral flow data.
Jul 812 min read
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 14 min read
AutoSpectral in Honeychrome
I'm happy to announce that the AutoSpectral workflow for unmixing is being incorporated into the Honeychrome application.
May 2611 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: Gating by landmarks and tuning gates
AutoSpectral 1.5.0 introduces a “Landmarks” gating system and a suite of tuning tools.
Mar 253 min read
AutoSpectral: Gating troubleshooting
In this article, we'll go into more depth on how the automated density-based gating in AutoSpectral works, covering the parameters that modify it.
Mar 239 min read
AutoSpectral: Full workflow example
A full workflow example for using AutoSpectral to perform spectral unmixing
Nov 24, 202518 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: plotting
In this article, let’s look at a couple of the functions that AutoSpectral offers for plotting your spectra and data. AutoSpectral isn't intended to replace flow analysis software like FlowJo or FCS Express, but it's essential to have some options for visualizing the outputs.
Oct 27, 20254 min read
AutoSpectral: reopening and rerunning
In this article, we'll cover some shortcuts to allow you to return to AutoSpectral once you've already run an experiment.
Oct 27, 20254 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: gating
In this article, we’ll try to cover some of the features and tuning for the automated gating in AutoSpectral.
Oct 27, 20257 min read
AutoSpectral: creating the control file
In this article, we’re going to cover how to create a control file, which is an essential first step in running AutoSpectral. The control file is a specifically formatted spreadsheet describing your single-stained control files.
Oct 27, 20255 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
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