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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

Krista Koeller @kristalerista.bsky.social · 13h

Dear funding agencies,

I know we all want to discover the wonder drug that will cure the horrible diseases, but to do that, we need to invest in basic, unsexy, foundational research on how the systems work. Funding can’t all be drug development.

Sincerely,
Looking for basic research grants.

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Joachim Goedhart @joachimgoedhart.bsky.social · 1h

Cell culture media have complex formulations (> 30 different compounds), and the only colored additive is phenol red. Often, it is assumed that this absorbing compound also fluoresces, but it does not. It is actually the riboflavin that is present at ~ 1 µM.

Joachim Goedhart @joachimgoedhart.bsky.social · 12h

Periodic reminder that the fluorescent compound in mammalian cell culture media, such as DMEM, is riboflavin (not phenol red)

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Reposted by Joachim Goedhart

John Ngo @johntngo.bsky.social · 15h

Pleased to share our review on “Synthetic Mechanotransduction” — now live at Nature Reviews Bioengineering.

May the force be with you!

www.nature.com/articles/s44...

Synthetic mechanotransduction - Nature Reviews Bioengineering

Cells convert mechanical forces into biochemical signals through mechanotransduction, a process which can now be synthetically engineered. In this Review, we examine engineered artificial mechanotrans...

www.nature.com

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Reposted by Joachim Goedhart

Origami Organelles @origamiorganelles.bsky.social · 21h

When you look at animal & plant cells remember what they give rise to... mind blowing stuff!
Find out more about our paper models here: buff.ly/fqKSYnW

#EduSky #plantcell #animalcell #cells #iteachbio #scienceteacher #biologyteacher

Reposted by Joachim Goedhart

INOUE lab. (ISSP, Univ. Tokyo) @labinoue.bsky.social · 1d

Our paper on the first UV-sensitive rhodopsin channel, the Apusomonad rhodopsin, has been published in PNAS! 🎉
This is a new family distinct from canonical ChRs with a novel transport mechanism🦠—paving the way for future multi-wavelength optogenetics! 🔬
www.pnas.org/doi/full/10....
#OpenAccess

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Reposted by Joachim Goedhart

Lucy Dornan @lucygdornan.bsky.social · 5d

After many years of hm-ing and haw-ing about why some of the fusion proteins I’ve cloned showed cytoplasmic background I’ve finally found the culprit

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Reposted by Joachim Goedhart

Anne Carpenter @drannecarpenter.bsky.social · 4d

15 years in the making, we confirmed that mitochondria - the powerhouse of the cell - have an unusual localization in patients who experience psychosis (including schizophrenia and bipolar disorders). You’ll never guess what kind of patient cells we used to make this discovery… 🧵

mitochondria from bipolar patients are closer to the nucleus in these images; control patients' are spread out further

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Reposted by Joachim Goedhart

Andrea Caldarola @andreacaldarola.bsky.social · 4d

For #FluorescenceFriday : 3 cells start at the same Ca2+ concentration but undergo 3 different Histamine responses. Imaged using the lifetime-based sensor Tq-Ca-FLITS.

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Joachim Goedhart @joachimgoedhart.bsky.social · 4d

Visualizing PINK1 Activity Dynamics in Single Cells with a Phase Separation-Based Kinase Activity Reporter by @schmittwitt.bsky.social and team: www.biorxiv.org/content/10.1...

Figure 1. Design, development, and characterization of PINK1-SPARK.

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Reposted by Joachim Goedhart

Oded Rechavi @odedrechavi.bsky.social · 5d

I really enjoyed recording "Big Biology"! We talked about A LOT of things, including my new passion project qedscience.com (check it out, more on this and big announcement coming soon:) 😍😍😍🔥🔥⚡️⚡️@bigbiology.bsky.social open.substack.com/pub/bigbiolo...

Biology outside the box (Ep 140)

What’s the value of risk-taking in research?

open.substack.com

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Joachim Goedhart @joachimgoedhart.bsky.social · 5d

FLIM Playground: An interactive, end-to-end graphical user interface for analyzing single-cell fluorescence lifetime data by Rupsa Datta and team: www.biorxiv.org/content/10.1...

Fig 1. System overview of FLIM Playground.

After (A) loading a saved configuration, (B) Data Extraction collects and validates channel inputs across all fields of views, (C) calibrates for IRF shifts or uses reference standards, and (D) extracts single-cell lifetime (fitting and phasor), morphology, and texture features in one step. (E) To bridge the data extraction with downstream analysis, FLIM Playground combines multiple single-cell datasets and assists users with assigning category labels to each cell. (F) The three feature classes include identifiers (red), numerical features (yellow), and categorical features (blue), are transformed into interactive widgets shared by all analysis methods. (G) Data Analysis includes univariate, bivariate, and multivariate modules. (H) FLIM Playground can either be deployed online in major operating systems or as a data analysis web application. Interactive interfaces are indicated by green backgrounds.

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Reposted by Joachim Goedhart

Nicola Rennie @nrennie.bsky.social · 5d

Wondering if you can outsource your data viz work to ChatGPT? 📊

I tested out a few different generative AI tools, giving them prompts to visualise two different data sets. If you're interested in the results, you can read them here: nrennie.rbind.io/blog/gen-ai-...

#RStats #Python #DataViz #GenAI

Generative AI for Data Visualisation – Nicola Rennie

Can generative AI create good data visualisations? This blog post compares the performance of ChatGPT, Claude, Copilot, and Gemini when presented with a generic request to visualise a dataset.

nrennie.rbind.io

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Reposted by Joachim Goedhart

Robert Haase @haesleinhuepf.bsky.social · 13d

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 · 8d

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 · 9d

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 · 10d

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 · 10d

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 · 10d

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 · 11d

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 · 12d

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 · 11d

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...