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Joachim Goedhart

@joachimgoedhart.bsky.social

4.6K followers 1.2K following 560 posts

joachimgoedhart.github.io

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Joachim Goedhart @joachimgoedhart.bsky.social · Dec 16

There are now 24 step-by-step guides, explaining how to create these ⬇️ data visualizations with R/ggplot2 - I hope this is a useful resource. Find them all here: joachimgoedhart.github.io/DataViz-prot...

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Reposted by Joachim Goedhart

Robert Haase @haesleinhuepf.bsky.social · 7d

For academic purposes, I generated 100 UMAPs from the same tabular raw data, I sorted them and the result looks too funny to not share it with you 😃
haesleinhuepf.github.io/BioImageAnal...

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Joachim Goedhart @joachimgoedhart.bsky.social · 2d

Brilliant talk by Petra Schwille at #NWOBiophysics2025 on her work on synthetic cells - which she summarized as “a lot of playing around and a bit of progress“

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Reposted by Joachim Goedhart

Phil Kyriakakis @breakliquid.bsky.social · 3d

WAChRs are excitatory opsins sensitive to indoor lighting

www.biorxiv.org/content/10.1...

WAChRs are excitatory opsins sensitive to indoor lighting

Hundreds of novel opsins have been characterized since the advent of optogenetics, but low experimental throughput has limited the scale of opsin engineering campaigns. We modified an automated patch-...

www.biorxiv.org

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Reposted by Joachim Goedhart

Kevin Terretaz @kwolbachia.bsky.social · 4d

I’m happy to share some plugins I’ve been developping this summer: "Channels and Contrast" and LUTs Manager!
I can’t find new bugs and ideas by now so I need your help to please test them in your machines and report bugs, feedbacks and ideas! forum.image.sc/t/looking-fo...

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Reposted by Joachim Goedhart

Marcel Haas 🟥 @harcel.bsky.social · 3d

Anyone here with experience with sli.dev for making slides using Markdown. I saw one example (by @fonnesbeck.bsky.social) that looked absolutely fantastic, so I'm quite interested in giving it a try. Any experience among my followers?

Slidev

Presentation slides for developers

sli.dev

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Reposted by Joachim Goedhart

Kevin J. CREATURE @kevinjkircher.com · 4d

Sometimes I think about how from 1935-1975ish, Bell Labs produced an insane amount of revolutionary science and technology, including 11 Nobel Prizes, the transistor, UNIX, C, the laser, the solar cell, information theory, etc. The secret? Provide scientists with ample, steady, no-strings funding.

sites.stat.columbia.edu

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Reposted by Joachim Goedhart

Victor Tatarskiy @greenrat.bsky.social · 5d

as this unexpectedly went semi-viral - NB: I only tried this protocol, all credit goes to www.med.upenn.edu/markslab/ and probably someone even before :)

Welcome to the Marks Lab! | Marks Lab | Perelman School of Medicine at the University of Pennsylvania

www.med.upenn.edu

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Reposted by Joachim Goedhart

Victor Tatarskiy @greenrat.bsky.social · 6d

Neat trick if you polycolonal ab's suck. Incubate them with fixed cells with a KO of your protein of interest, then spin. Protocol here: www.med.upenn.edu/markslab/ass...
I was amazed how well it worked on first try (I'm sure that I can completely eliminate unspecific bands)
#WesternBlot #cellsky

On the left - western blot of B16F10 cells wt and KO for CDK8. Our in house produced antibodies give a lot of unspecific bands. On the right same probes with antibodies preincubated with fixed CDK8 KO cells - there is a specific band and faint unspecific bands, which can be probably eliminated with increase of amount of KO cells.

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Reposted by Joachim Goedhart

Christophe 🔬 L @christlet.bsky.social · 5d

Want to hear a mid-career PI pontificate about science, career and cooking? Today's your lucky day thanks to The Microscopists podcast! Thanks Peter @yorkbioimaging.bsky.social for having me 🎙️🎧
themicroscopists.bitesizebio.com/episodes/chr...

The Microscopists | Christophe Leterrier (CNRS & Aix-Marseille Université)

This time on The Microscopists, we're joined by Christophe Leterrier, team leader at NeuroCyto in Marseille and director of a Nikon Center of Excellence for super-resolution microscopy.Christophe r...

themicroscopists.bitesizebio.com

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Reposted by Joachim Goedhart

Andreas Prokop @poppi62.bsky.social · 6d

Does anybody know whether Alexa Fluo 405 works well in the DAPI channel?
www.thermofisher.com/uk/en/home/l...

www.thermofisher.com

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Reposted by Joachim Goedhart

Garrick Aden-Buie @grrrck.xyz · 6d

You arrive at a text input and start typing. Would you rather

1️⃣ Press Enter to submit your text
2️⃣ Press Enter to add a new line

A text input interface with a submit button. In the text area: "I'm writing some text and want a new line..."

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Joachim Goedhart @joachimgoedhart.bsky.social · 6d

2️⃣

Reposted by Joachim Goedhart

Matthijs Dorst @mattneuro.bsky.social · 7d

Whelp, I did not make the cut. Luckily, I have been given an amazing opportunity elsewhere; and who knows, maybe in a few years things there will be a similar position.

But maybe this is a good opportunity to talk about what it's like to apply for academic positions as a postdoc:

Matthijs Dorst @mattneuro.bsky.social · Aug 16

Whelp, fingers crossed: application submitted for my dream job!

A total of 42 pages for the application, an additional 106 pages for my most relevant papers; it's a doozy!

a cartoon character holding a stack of papers with the word intuitive in blue

Alt: a cartoon character holding a stack of papers, and dropping them on someone else's desk

media.tenor.com

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Reposted by Joachim Goedhart

Lucien Hinderling @lhinderling.bsky.social · 7d

Want to get started with smart microscopy? 🧠🔬
Check out our online repository with implementations from labs and industry -- lots of practical tips and links to sample code! smartmicroscopy.github.io/implementati...

More details in the ✨updated preprint!✨
www.biorxiv.org/content/10.1...

screenshots of some of the sample implementations

Screenshot of smartmicroscopy.github.io/implementations.html, showing an overview of collected implementation examples

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Reposted by Joachim Goedhart

Magnus Bauer @kinasekid.bsky.social · 8d

Phosphorylation on tyrosines control key pathways in immunity, cancer, and metabolism. For the first time, we can now design proteins that specifically recognize individual phosphotyrosines, even in disordered regions. (1/8)

Preprint: www.biorxiv.org/content/10.1...

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Reposted by Joachim Goedhart

Darren Dahly @statsepi.bsky.social · 8d

Carefully reading the papers you cite is like a superpower. You might be surprised what you actually find! 😜

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Joachim Goedhart @joachimgoedhart.bsky.social · 8d

Identification of optimal fluorophores for use in the Drosophila embryo by Timothy E Saunders and team: www.biorxiv.org/content/10.1...

Figure 1: Fluorophore intensity in the Drosophila blastoderm (n.c. 14). Comparison of (A) green and (B) red fluorescence intensity using the same intensity scaling in n.c. 14. The fluorescence signal did
not saturate. Shown are single imaging planes. Normalised histograms of fluorescence intensity for green (C) and red (D) fluorophores averaged across at least n=3 embryos per line. Scale bars = 20 μm

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Reposted by Joachim Goedhart

INNOQ @innoq.bsky.social · 9d

Excited to kick off the INNOQ Technology Day with @felienne.bsky.social. Her keynote explores how coding skills shift (or don’t) in the age of AI with tools like ChatGPT and Cursor.

📅 Nov 20, 9 AM CET, online
👉 technologyday.innoq.com/programm/increasing-your-skill-in-programming-in-the-age-of-ai

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Joachim Goedhart @joachimgoedhart.bsky.social · 8d

Anyone else attending #NWOBiophysics2025 ?

Joachim Goedhart @joachimgoedhart.bsky.social · 8d

Are you attending #NWOBiophysics2025 ?

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Joachim Goedhart @joachimgoedhart.bsky.social · 8d

Cool, hope to get a chance to catch up!

Joachim Goedhart @joachimgoedhart.bsky.social · 8d

I do agree!
I'm not sure that people realize that unmixing spatially separated probes is much easier than unmixing species that occupy the same pixel/voxel. I see potential for FLIM for the first application, not convinced that FLIM is ideal for the second application....

Joachim Goedhart @joachimgoedhart.bsky.social · 8d

Are you attending #NWOBiophysics2025 ?

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Joachim Goedhart @joachimgoedhart.bsky.social · 8d

Unmixing tau-STED, is that also unmixing two species in the same spectral channel?

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Joachim Goedhart @joachimgoedhart.bsky.social · 8d

I think it would be cool to generate synthetic data and see how far one can theoretically get...

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Joachim Goedhart @joachimgoedhart.bsky.social · 8d

From my experience (which is anecdotal and qualitative, I realize that), one needs really high S/N for proper unmixing.
Even under these conditions the structures do not look crisp and free from crosstalk ⬇️ (cropped from figure 4)

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