Joachim Goedhart @joachimgoedhart Twitter profile

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Joachim Goedhart

3 years

I released a first version of a book on data visualization with R & ggplot2. Target audience = wet lab scientists. It's work in progress, so any feedback/suggestions/comments are appreciated!! #DataViz #Rstats

DataViz protocols

This is an introduction to data visualization protocols for wet lab scientists

joachimgoedhart.github.io

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Joachim Goedhart

@joachimgoedhart

4 years

β-Mercaptoethanol

Varinder Sinngh

@varindersingh24

4 years

If 2020 was a Alcohol, what would it be???

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Joachim Goedhart

@joachimgoedhart

3 years

3.7% formaldehyde

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Joachim Goedhart

@joachimgoedhart

2 years

This online resource that introduces data visualization using #rstats & ggplot2 has 12 complete protocols available for a variety of plots.

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Joachim Goedhart

@joachimgoedhart

2 years

Finally out: mScarlet3 A brilliant and fast-maturing red fluorescent protein. Congrats to the teams of Dorus Gadella and Antoine Royant!

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Joachim Goedhart

@joachimgoedhart

7 years

Agar plate with bacterial colonies producing different fluorescent proteins

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Joachim Goedhart

@joachimgoedhart

6 years

Did you recently calculate a p-value? Please consider calculating effect sizes as well - here's why (and how):

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Joachim Goedhart

@joachimgoedhart

3 years

Prepping a lecture on fluorescent proteins - no time to dye

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Joachim Goedhart

@joachimgoedhart

1 year

Dramatic change in the shape of mitochondria after addition of digitonin

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Joachim Goedhart

@joachimgoedhart

6 years

Very happy that our manuscript on the #PlotsOfData web tool is out in @PLOSBiology . Here's a link to the paper: And the app: Some examples of #dataViz made with PlotsOfData:

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Joachim Goedhart

@joachimgoedhart

5 years

I've made the material for teaching a basic course on Image analysis for fluorescence microscopy available online. Feel free to use or modify as you like:

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Joachim Goedhart

@joachimgoedhart

5 years

Tweet me a name of a Fluorescent Protein and I will (try to) respond with an advantage and a shortcoming. I'll go first: #mTurquoise2 @joachimgoedhart

Eric Griffis

@DrGriff34

6 years

Working with someone who came from the FP development field, I'm learning all about the dirty secrets that never made it to the publications announcing several well known fluorescent proteins.

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Joachim Goedhart

@joachimgoedhart

2 years

I like timelines a lot. Here's a timeline of 60 years of GFP discovery and engineering, made for @focalplane_jcs :

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Joachim Goedhart

@joachimgoedhart

5 years

I made an app that shows ggplot2 code & plot. Hopefully useful for learning/teaching/understanding ggplot2. The app lives here: #dataViz #ggplot2 #shiny

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Joachim Goedhart

@joachimgoedhart

7 years

w00t! Pattern brushes can be used in @Illustrator to rapidly draw repetitive structures - example for phospholipids and cells

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Joachim Goedhart

@joachimgoedhart

3 years

A new biosensor for quantitative live cell imaging of ATP

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Joachim Goedhart

@joachimgoedhart

2 years

Nice overview of Mitochondrial targeting sequences from:

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Joachim Goedhart

@joachimgoedhart

8 years

Animation - from barplot to box&dotplot: step-by-step changes that improve transparency and interpretation

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Joachim Goedhart

@joachimgoedhart

7 years

Animation - detonating a dynamite plunger plot to reveal the data #rstats code (to recreate it with your own data):

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Joachim Goedhart

@joachimgoedhart

4 years

I wrote a tutorial for the @the_Node that explains how to combine animated plots with movies:

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Joachim Goedhart

@joachimgoedhart

3 years

mCherry-XL: a bright mCherry variant with a long lifetime

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Joachim Goedhart

@joachimgoedhart

4 years

FRAME-tags: genetically encoded fluorescent markers for multiplexed barcoding and time-resolved tracking of live cells

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Joachim Goedhart

@joachimgoedhart

3 years

Fluorescent proteins are often used as bright and stable lightbulbs. By moving the termini close to the chromophore, FPs can be turned into sensors.

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Joachim Goedhart

@joachimgoedhart

6 years

In a new blog I discuss a straightforward method for calculating p-values

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Joachim Goedhart

@joachimgoedhart

5 years

In a new blog @the_Node I highlight several qualitative color schemes for data visualization that are color blind friendly:

Color blind friendly palettes for data visualizations with categories

A discussion of color blind friendly palettes for labeling unique catergories in data visualization.

thenode.biologists.com

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Joachim Goedhart

@joachimgoedhart

6 years

Once it runs, creating graphs with PlotsOfData is a breeze. Let me know if you need help to get the app () running. #DataViz

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Joachim Goedhart

@joachimgoedhart

4 years

Let me celebrate this, right here, right now. #subtweet

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Joachim Goedhart

@joachimgoedhart

1 year

Proudly presenting our first Shiny app that runs in python made by Xinwei Song: ezReverse - simple background inversion of full color images and plots Try it here:

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Joachim Goedhart

@joachimgoedhart

4 years

What???

Genetic manipulation of the optical refractive index in living cells

The optical refractive index of cellular components is generally not a property considered amenable to manipulation in microscopy as this is an intrinsic physical property of materials. Here we show...

www.biorxiv.org

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Joachim Goedhart

@joachimgoedhart

2 years

Protocol #14 is a step-by-step guide to make a Volcano plot with R/ggplot2. Useful if you want more control over the #dataViz than is offered by the VolcaNoseR web app.

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Joachim Goedhart

@joachimgoedhart

2 years

Mechanosensitive channel-based optical membrane tension biosensor

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Joachim Goedhart

@joachimgoedhart

3 years

Bright, fluorogenic and photostable avidity probes for RNA imaging

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Joachim Goedhart

@joachimgoedhart

1 year

qMaLioffG: A single yellow fluorescent protein FLIM indicator enabling quantitative imaging of endogenous ATP

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Joachim Goedhart

@joachimgoedhart

1 year

Red fluorescent proteins engineered from green fluorescent proteins

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Joachim Goedhart

@joachimgoedhart

6 years

Our server is up! It is now possible to run PlotsOfData as a web tool (no need to run R/Rstudio):

Joachim Goedhart

@joachimgoedhart

6 years

Once it runs, creating graphs with PlotsOfData is a breeze. Let me know if you need help to get the app () running. #DataViz

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Joachim Goedhart

@joachimgoedhart

5 years

This is how our lab gets into the mood of Xmas #AgarArt by @TannevanderWal @EikeMahlandt @AnoeskaMoosdijk @Saskia_deMan et al. #DeckTheLab @Addgene

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Joachim Goedhart

@joachimgoedhart

4 years

SuperPlot meets PlotsOfData = SuperPlotsOfData

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Joachim Goedhart

@joachimgoedhart

2 years

I added three more protocols to my book on data visualization in R/ggplot2 for wet lab scientists. Protocol 13 explains how to plot multiple plots side-by-side. Find all protocols here:

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Joachim Goedhart

@joachimgoedhart

5 years

"I screwed up" - a student explaining in this mornings lab meeting that he mixed up some plasmids. (The honesty is much appreciated)

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Joachim Goedhart

@joachimgoedhart

6 years

Movie made by master students (with help of Janine Arts) showing white blood cells passing through a monolayer of endothelial cells - three cells pass at the same point, coincidence?

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Joachim Goedhart

@joachimgoedhart

3 years

This white blood cell (magenta) is trapped under an endothelical cell by focal adhesions (grey) and makes a 180 degrees turn to escape. TIRF timelapse imaging by @EikeMahlandt & Janine Arts. Details:

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Joachim Goedhart

@joachimgoedhart

2 years

Excited to announce a new preprint from our lab in which we optimized an optogenetic toolbox to control endothelial cell function - fantastic work by @EikeMahlandt !

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Joachim Goedhart

@joachimgoedhart

4 years

An update of SuperPlotsOfData: -uses dashed lines to display paired data -can display the distribution of replicates to create raincloud plots.

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Joachim Goedhart

@joachimgoedhart

3 years

An ImageQuiz I made for students to evaluate how well they recognize cellular structures - it can be easily extended to other types of images:

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Joachim Goedhart

@joachimgoedhart

6 years

I was contacted for advice on setting up expts with a #FRET biosensor. Me: “Can you think of a simpler experiment to address your question?” Him: “Yes” Me: “That’s my advice”

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Joachim Goedhart

@joachimgoedhart

2 years

Used this FIJI plugin by @Daetwyler_St for annotating movies with custom arrows and I love it! HT @guijacquemet - link to paper:

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Joachim Goedhart

@joachimgoedhart

3 years

Genetically Encoded Multimeric Nanoparticles

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Joachim Goedhart

@joachimgoedhart

6 years

For fluorescent proteins, there may be a large mismatch between in vitro (theoretical) brightness and brightness in cells. This is explained in my blog:

A Practical Approach to Choosing the B(right)est Fluorescent Protein

Learn how to determine the practical brightness of your fluorescent protein in your specific experimental setup.

blog.addgene.org

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Joachim Goedhart

@joachimgoedhart

3 years

The quantification of intracellular calcium concentrations is difficult. That's why we engineered a biosensor that uses lifetime contrast to simplify quantitative calcium imaging:

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Joachim Goedhart

@joachimgoedhart

3 years

Multicolor strategies for investigating clonal expansion and tissue plasticity

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Joachim Goedhart

@joachimgoedhart

4 years

What's your favorite movie that stars a fluorescent protein? One of my favorites is from a cell cycle indicator made by Atsushi Miyawaki and colleagues:

Joachim Goedhart

@joachimgoedhart

4 years

@christlet @kabirhbiswas @TimESaunders @guijacquemet @NathanShaner When it's online only I recommend: movies, movies, movies. There are so many fantastic movies of FPs in action, demonstrating the full potential of FPs

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Joachim Goedhart

@joachimgoedhart

7 years

Petri dish with bacteria expressing three of our brightest fluorescent proteins #mTurquoise2 / #SYFP2 / #mScarlet -I #sciart #agarart

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Joachim Goedhart

@joachimgoedhart

10 months

Actually, I have a student that can see fluorescence emitted by miRFP670. Two other people cannot see it. It needs a larger cohort, but it's quite intriguing....

zara weinberg 🧪🧙🏻‍♀️

@weinberz

10 months

nobody needs a near-IR fluor, you can't even see that shit by eye!!!

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Joachim Goedhart

@joachimgoedhart

5 years

Super happy that the paper reporting 'PlotTwist' is online: Thanks for the smooth process @PLOSBiology

PlotTwist: A web app for plotting and annotating continuous data

This Community Page article describes PlotTwist, an open source app created with R/shiny to simplify state-of-the-art visualization and annotation of results from experiments that generate continuous...

journals.plos.org

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Joachim Goedhart

@joachimgoedhart

6 years

I wrote a very basic step-by-step instruction for quantifying intensities from time-lapse imaging data for our students, maybe it's useful for others - it uses only freely available software (no Excel!):

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Joachim Goedhart

@joachimgoedhart

4 years

A genetically encoded, pH-sensitive mTFP1 biosensor for probing lysosomal pH

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Joachim Goedhart

@joachimgoedhart

1 year

"Here, we successfully use LIVE-PAINT to image yeast membrane proteins that do not tolerate the direct fusion of a fluorescent protein by using peptide tags as short as 5-residues"

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Joachim Goedhart

@joachimgoedhart

4 years

Proudly announcing our efforts to improve a Rho GTPase biosensor for detecting endogenous RhoA activity. Congrats to first author @EikeMahlandt , the driving force behind the project! A thread explaining the main findings follows ⬇️

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Joachim Goedhart

@joachimgoedhart

5 years

Wouldn't it be great to have journals with a take-it-or-leave-it option: Authors submit a full(!) paper, with the condition that no extra experiments can be requested, only textual changes (or re-analysis of data). Editor/reviewers decide to take it or leave it.

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Joachim Goedhart

@joachimgoedhart

1 year

Functional principles of genetically encoded fluorescent biosensors for metabolism and their quantitative use

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Joachim Goedhart

@joachimgoedhart

3 years

Have a nice Xmas and I hope you can enjoy a well-deserved break!!

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Joachim Goedhart

@joachimgoedhart

4 years

pHmScarlet is a pH-sensitive red fluorescent protein to monitor exocytosis docking and fusion steps

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Joachim Goedhart

@joachimgoedhart

6 years

Ever determined a p-value without understanding how it is calculated or what it exactly means? Try this:

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Joachim Goedhart

@joachimgoedhart

4 years

High-fidelity, efficient, and reversible labeling of endogenous proteins using CRISPR-based designer exon insertion

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Joachim Goedhart

@joachimgoedhart

4 years

An update of SuperPlotsOfData offers a dark theme (a better fit with presentations that have a dark background?!)

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Joachim Goedhart

@joachimgoedhart

1 year

An ultrasensitive genetically encoded voltage indicator uncovers the electrical activity of non-excitable cells

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Joachim Goedhart

@joachimgoedhart

7 years

Wow, that tweet went bacterial

Joachim Goedhart

@joachimgoedhart

7 years

Agar plate with bacterial colonies producing different fluorescent proteins

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Joachim Goedhart

@joachimgoedhart

2 years

New #preprint from our lab 🎉 🥳 We report an iLID-nanobody fusion to enable #optogenetic recruitment to #GFP . This is potentially interesting when you already have a cell line or model organism expressing a GFP fusion protein.

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Joachim Goedhart

@joachimgoedhart

5 years

So am I

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Joachim Goedhart

@joachimgoedhart

5 years

#Preprint #Protip : When you include an image on the first page of the pdf submitted to @biorxivpreprint it's shown on the webpage right under the abstract - examples:

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Joachim Goedhart

@joachimgoedhart

4 years

Ten simple rules to colorize biological data visualization:

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Joachim Goedhart

@joachimgoedhart

4 years

It's there! Preprint reporting the SuperPlotsOfData web app:

SuperPlotsOfData – a web app for the transparent display and quantitative comparison of continuous...

Plots and charts are graphical tools that make data intelligible and digestible by humans. But the oversimplification of data by only plotting the statistical summaries conflicts with the transparent...

www.biorxiv.org

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Joachim Goedhart

@joachimgoedhart

2 years

LOL

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Joachim Goedhart

@joachimgoedhart

4 years

Looking for ways to make a volcano plot? Try our free online webtool VolcaNoseR for easy plotting and annotation: Preprint: Comments on the app and/or preprint are welcome!

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Joachim Goedhart

@joachimgoedhart

6 years

An incredible engineering effort has led to a beta-barrel (smaller than GFP) that enables "fluorescence on demand". One downside is the QY, of ~2%

De novo design of a fluorescence-activating β-barrel

Nature - The elucidation of general principles for designing β-barrels enables the de novo creation of fluorescent proteins.

www.nature.com

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Joachim Goedhart

@joachimgoedhart

3 years

Happy to see our work on a Turquoise biosensor for imaging of intracelluar calcium concentrations published today in @NatureComms

A turquoise fluorescence lifetime-based biosensor for quantitative imaging of intracellular calcium

Nature Communications - Currently, genetically encoded calcium indicators are not suitable for direct quantification. Here the authors engineer a fluorescence lifetime imaging calcium biosensor,...

www.nature.com

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Joachim Goedhart

@joachimgoedhart

7 years

Christmas lights generated with fluorescent proteins developed at the Molecular Cytology lab @UvA_Amsterdam #SciArt

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Joachim Goedhart

@joachimgoedhart

2 years

nlsNitraMeter3.0: a genetically encoded biosensor for visualization of nitrate dynamics:

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Joachim Goedhart

@joachimgoedhart

7 years

Three of our brightest fluorescent proteins in a Penrose triangle. #mTurquoise2 - #SYFP2 - #mScarlet -I #SciArt

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Joachim Goedhart

@joachimgoedhart

2 years

Neat! A pH resistant biosensor with mTurquoise2 for imaging NADPH generation by anisotropy measurements

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Joachim Goedhart

@joachimgoedhart

5 years

Wow! #PhDThesisCover

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Joachim Goedhart

@joachimgoedhart

4 years

I'm excited to announce a new preprint which reports the results of a trip by @EikeMahlandt and Janine Arts to the Advanced Imaging Center in Janelia @AICjanelia . I'll briefly highlight some of the findings below ⬇️

Endothelial junctional membrane protrusions serve as hotspots for neutrophil transmigration

Upon inflammation, leukocytes rapidly transmigrate across the endothelium to enter the inflamed tissue. Evidence accumulates that leukocytes use preferred exit sites, though it is not yet clear how...

www.biorxiv.org

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Joachim Goedhart

@joachimgoedhart

3 years

Plasmids with the turquoise biosensor for imaging of absolute calcium concentrations are available from @Addgene Biosensor design and application are reported here:

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Joachim Goedhart

@joachimgoedhart

4 years

I received some colorful barplots from a student. My feedback included a link to this blog post:

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Joachim Goedhart

@joachimgoedhart

6 years

DAPI, FITC, TRITC

wisy

@kyliebae13

8 years

Name a more iconic trio... I'll wait

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Joachim Goedhart

@joachimgoedhart

3 years

Efficient and error-free fluorescent gene tagging in human organoids without double-strand DNA cleavage

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Joachim Goedhart

@joachimgoedhart

3 years

Today I installed two browser extensions: -One to automatically accept all cookies -One that throws away the cookies after leaving the page So far, it works like a charm!

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Joachim Goedhart

@joachimgoedhart

4 years

When I first heard about GFP, I muttered ‘this will never work’. Here is the story of how my love for GFP (and its family members) grew over the years....

My history with GFP (and other members of the family) - FocalPlane

My history with GFP (and other members of the family) -

focalplane.biologists.com

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Joachim Goedhart

@joachimgoedhart

1 year

Gathering data is easy, but processing & visualization less so. In todays lecture I discussed tools that we develop and use for #dataViz

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Joachim Goedhart

@joachimgoedhart

7 years

Effect of nocodazole on microtubule dynamics (visualized with EB3) - one of the first movies made by PhD candidate Eike Mahlandt

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Joachim Goedhart

@joachimgoedhart

1 year

Are you interested in developing web apps for data visualization? This beginners tutorial on web app development with R/Shiny may be of interest:

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Joachim Goedhart

@joachimgoedhart

3 years

I have updated the 'DataViz protocols' book with a 6th protocol - it now also includes an overview of the result of each protocol

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Joachim Goedhart

@joachimgoedhart

1 year

Photoswitchable binders enable temporal dissection of endogenous protein function

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Joachim Goedhart

@joachimgoedhart

1 year

SHRIMP: Genetically Encoded mScarlet-derived Red Fluorescent Hydrogen Peroxide Sensor with High Brightness and Minimal Photoactivation

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Joachim Goedhart

@joachimgoedhart

2 years

A serendipitous finding , reported by 1999 Tsien and colleages in 1999, led to the notion that fluorescent proteins can be turned into biosensors. 🧵with a bit of biosensor history ⬇️

Circular permutation and receptor insertion within green fluorescent proteins | PNAS

Many areas of biology and biotechnology have been revolutionized by the ability to label proteins genetically by fusion to the Aequorea green fluor...

www.pnas.org

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Joachim Goedhart

@joachimgoedhart

4 years

Updated SuperPlotsOfData, now showing the stats per replicate when the data are 'split' - a small improvement (suggested by @Schneider_Lab_ ) but it makes the plot much more intuitive

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Joachim Goedhart

@joachimgoedhart

2 years

If you want to get started with Python for image analysis, I can highly recommend the fantastic lectures on 'Interactive bioimage analysis with Python and Jupyter' by @guiwitz | @NEUBIAS_COST

Interactive bioimage analysis with Python and Jupyter PART I -...

PART I: "Interactive bioimage analysis with Python and Jupyter"Content: In the first session we show attendees how to run Python code interactively using Jup...

www.youtube.com

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Joachim Goedhart

@joachimgoedhart

2 years

A new blue fluorescent protein 'Surime' is reported in this paper: "Extension of the short wavelength side of fluorescent proteins using hydrated chromophores, and its application"

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Joachim Goedhart

@joachimgoedhart

4 years

I have a joke about a t-test, but it doesn’t make a difference

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Joachim Goedhart

@joachimgoedhart

1 year

We have validated and optimized a biosensor for Cdc42 activity and used it to detect highly localized activity of Cdc42 near invadopodia with TIRF microscopy. Movies by team @RhoPower - details in our most recent publication:

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