I love a good recipe 💚✨️

It is not often that a new flow cytometry protocol makes the newspaper! I also got a kick out of seeing our science tagged as "quirky"! www.cambridgeindependent.co.uk/news/fairy-l...

Foreign Scholars Skip US Conferences “I don’t agree with the politicization of scientific funding, the destruction of data collection and openness... and I feel like traveling to America at this point is a partial endorsement of what’s going on,” Liston said. www.insidehighered.com/news/faculty...

Foreign Scholars Skip US Conferences “I don’t agree with the politicization of scientific funding, the destruction of data collection and openness... and I feel like traveling to America at this point is a partial endorsement of what’s going on,” Liston said. www.insidehighered.com/news/faculty...

Fascinating talk tonight from Malala Yousafzai

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As the editor of CSH Protocols, I wholeheartedly agree. And if you have an idea for a topic to do a protocols collection on, or know of a field that would benefit from such a collection, let's talk!

Haven't read this one yet, but looks like a fantastic resource for everyone working with complex #spectral #flowcytometry panels!

A small 🧵 encouraging people to publish protocols. Our #AutoSpectral release has made me reflect on how much the community tends to appreciate protocol papers. People rarely present protocols as their main achievements, but they are often the most impactful work. www.biorxiv.org/content/10.1...

A small 🧵 encouraging people to publish protocols. Our #AutoSpectral release has made me reflect on how much the community tends to appreciate protocol papers. People rarely present protocols as their main achievements, but they are often the most impactful work. www.biorxiv.org/content/10.1...

Pre-print alert! And this one really is a must read for anyone that does spectral #flowcytometry. It is a complete, fully-automated spectral unmixing pipeline that reduces error up to 9000-fold. Want to get a tough sample, like lung, looking like this? Read more! www.biorxiv.org/content/10.1...

Today I accidentally discovered the ySG podcast "Climbing the Immunological Ladder". Highlight: an absolutely incredible episode with Adrian Liston @labliston.bsky.social: "Caring about people and caring about their growth ends up being the most impactful thing you can do in science"

The problem is that spectral unmixing is complex. The basis is a linear regression of positive versus negative signals, a highly error-prone process. This issue is largely solved by the use of robust linear regression with iterative rounds of improvement (AutoSpill): www.nature.com/articles/s41...

Three addition problems: 1)This unmixing solution still requires ideal positive-negative matching to find the right linear regression. 2) Cells have variation in background fluorescence 3) Fluorophores actually stuck on cells have variation in emissions #AutoSpectral solves these!

Huge credit to @colibricytometry.bsky.social, who has spent years working on every aspect of the spectral flow cytometry pipeline. Follow the Colibri blog to get tips in real-time, pre-pre-print! www.colibri-cytometry.com

First, pos-neg gating. Ideal controls are your actual antibodies on the actual cells. However different antibodies bind different cells (see: CD4 vs XCR1 below), meaning they have different backgrounds to control. AutoSpectral matches the FSC-SSC of each pos to a suitable neg: with results!

The whole pipeline is available right now on GitHub. It includes comprehensive notes on every step from installation to utilisation. github.com/DrCytometer/... Hopefully soon (like with AutoSpill) it becomes standard on commercial platforms too. But don't wait - fix your data issues today!

Not often discussed, but fluorophores also emit differently on different cells. Just as with autofluorescence we can test the different fits on a per cell basis, and use the fit that leaves the least residual. It means more signal is attributed to the correct fluorophore!

The cumulative effect of these improvements (and others not mentioned!) is enormous. For tough samples, like lung, incorrectly assigned signals are reduced by up to 9000-fold, and a 10- to 3000-fold improvement is common. Look at this ground truth experiment, showing wildtype vs GFP lung:

We fix this by identifying all autofluorescence patterns in the unstained sample, then applying each pattern to each individual cell in the real sample. We select the autofluorescence index that leaves the least residual, subtract that signal and unmix the rest. The results are gorgeous!

Second, autofluorescence variation. An unmixing matrix that doesn't account for autofluorescence will force all signal into one of the flurophore channels, giving misassigned signal. Past approaches only use autofuorescence index, which means heterogenous mixtures have cells with misassigned signal

I remember, 20 years ago, cancelling my news subscriptions. The poor quality of journalism and support for the Iraq war was the cause. Science journalism had already died, and why pay to read right-wing propaganda? Newspapers died *after* they became rubbish. Suicide, not murder.

Extremely useful for spectral flow cytometry enthusiasts- thanks @labliston.bsky.social I will share with our core too

We've all seen the problems - spreading, skewing, autofluorescence intrusion. Unmixing errors are so ubiquitous in high parameter panels they are often thought of as unavoidable, intrinsic to the way the hardware works. Surprisingly, they are largely artefacts of the unmixing software being used.

Fully-automated spectral unmixing pipeline that reduces error up to 9000-fold @biorxiv-immuno.bsky.social doi.org/10.1101/2025...

Assaying lung samples using spectral flow cytometry? Check out AutoSpectral:

Pre-print alert! And this one really is a must read for anyone that does spectral #flowcytometry. It is a complete, fully-automated spectral unmixing pipeline that reduces error up to 9000-fold. Want to get a tough sample, like lung, looking like this? Read more! www.biorxiv.org/content/10.1...

Catz experts have been invited to comment on current affairs this month: 📰 @labliston.bsky.social (2023) explained the science behind this year's @nobelprize.bsky.social in physiology or medicine: www.theguardian.com/... 1/2

#Medsky🧪 #immunosky #publichealth @science.org Tregs could make powerful therapies for people with #autoimmunedisease if scientists could make large numbers of them that persist long enough in the body to work… via @labliston.bsky.social www.science.org/content/arti...

The science community has been getting into a lather after our Fellow @labliston.bsky.social (2023) & his @campathology.bsky.social team revealed Fairy washing-up liquid is a cost-effective addition to chemicals used to treat cells in experiments: www.caths.cam.ac.uk/fairy-liquid @cam.ac.uk

I am trying to use AI to generate a picture of a scientist in the lab. (It is to illustrate what I want to an artist for a commission, so don't shoot me!). For some reason, the AI keeps on having her with no shoes. Even after pleading to include shoes! What is this, DungeonCrawler Carl?

Let's meet my friend Tanystropheus, a archosauromorph reptile from the Triassic. You may notice that Tany is looooooooong, with some specimens being 6 m (20 ft) long, while only weighing 30-70 kg (65-150 lbs). Which led me to an interesting question: How do LONG-NECKERS like Tany BREATHE?

Another chat to my students about not using AI for research!

Story from @stcatharines.bsky.social on Oliver's dishwashing soap protocol! www.caths.cam.ac.uk/fairy-liquid

Ouch! @xkcd.com hits some truth. Honestly, it is way too common to see academics pick the “path of ruin”. It is okay for us to not be superstars in our field :) imgs.xkcd.com/comics/physi...

On the occasion of the Nobel prize to Sakaguchi and colleagues, Nature has published a list of the laureates' works, as well as a list of noteworthy studies stemming from the prize-winning work. No 5 of this list (Related Research) brings me heaps of joy and gratitude. www.nature.com/collections/...

Listen here for an interview I did on "Climbing the Immune Ladder: Steps for Success in Science". We discuss immunology, kindness and mentorship, navigating scientific challenges, identifying high-impact research questions, and our evolving scientific careers open.spotify.com/episode/00rJ...

Exciting new data from the lab - check it out!🔥

Highly motivated and talented candidates are strongly encouraged to apply

Computational PhDs - this is a really special post-doc opportunity to join @hkoohy.bsky.social's lab at the @imm.ox.ac.uk in Oxford. It is part of a dream collaboration to identify the antigens recognised by Tregs - I'm so excited that we are really doing this! www.jobs.ac.uk/job/DOX009/s...

Enormous loss. Vale John Gurdon.

Yes, Tregs finally getting the spotlight they deserve! 🙌

Check out a lovely bitesize historical perspective from Adrian below.

A small primer on the #NobelPrize awarded to Mary E. Brunkow, Fred Ramsdell and Shimon Sakaguchi today. This prize was for combining two separate fields of immunology research - genetic research on IPEX and immunology research of regulatory T cells (#Tregs), with enormous impact on biology/medicine

Today's Nobel Prize announcement was a win for the field of genetics as well. Congrats to all involved!

I've had Sakaguchi papers on my desk since '99, when I was warned against studying cells (Treg) that may not exist. 26 years on, we've shown you need them to reproduce and we may bring them to Heart clinics. A joyous overdue toast to Sakaguchi's steadfast building of the foundations of our science!

Congratulations! #NobelPrize #Tregi