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Nicolas Denans

@nicolasdenans.bsky.social
113 followers 112 following 27 posts

Scientist- Jack of all trades - Interest in #microscopy #immunology #devbio

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Reposted by Nicolas Denans
Chad Hobson @cmhobson.bsky.social · 27/08/2026
A couple years in the making, but the preprint is finally out! We developed a pipeline for timelapse, volumetric FLIM (vFLIM) that incorporates multi-channel light sheet excitation, a SPAD array detector for widefield FLIM, and machine learning lifetime processing. www.biorxiv.org/content/10.6...
biorxiv.org
vFLIM: Machine Learning-enabled Light Sheet Fluorescence Lifetime Imaging
The lifetime of fluorescent molecules provides an orthogonal readout to fluorescence intensity, opening experimental possibilities of measuring changes in local molecular environments, mechanical tens...
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Nicolas Denans @nicolasdenans.bsky.social · 20/08/2026
Why can't journals store plasmid maps (in .gb) as supplementary material? It doesn't take any space. @natureportfolio.nature.com @cellpress.bsky.social
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Nicolas Denans @nicolasdenans.bsky.social · 02/08/2026
any recommendation for a high throughput imaging system to sort zebrafish larvae based on fluorescence? Thinking about the VAST or AcquiferIM or..... Any input welcome!! #zebrafish
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Nicolas Denans @nicolasdenans.bsky.social · 31/07/2026
It was a pleasure to be part of this fantastic microscopy bootcamp one last time. The group of students was phenomenal, so was the teaching team, the conference team and @hhmijanelia.bsky.social food services!
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Reposted by Nicolas Denans
Luke Lavis @rhodamine110.bsky.social · 17/07/2026
Excited to see this collaboration now in print. Dye chemistry meets AI-designed proteins. Three small, orthogonal tags; lifetime modulation; split versions. Request the free dyes at dyes.janelia.org www.science.org/doi/10.1126/...
science.org
De novo design of orthogonal far-red, orange, and green fluorophore-binding proteins for multiplexed imaging
Fluorescent proteins and small-molecule dyes offer complementary advantages for biological imaging: proteins are amenable to genetic tagging, whereas dyes provide superior brightness and photostabilit...
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Valentin Dunsing-Eichenauer @dunsingvalentin.bsky.social · 06/07/2026
Already out for a while as the final version: Our @elife.bsky.social paper presenting an experimental and computational pipeline for whole mount deep imaging and multi-scale analysis of organoid systems: elifesciences.org/articles/107... A great collaboration during my postdoc in Marseille.
elifesciences.org
A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales
The Tapenade pipeline enables single-cell, whole-mount 3D quantification in dense multilayer organoids, linking spatial gene co-expression and nuclear deformation to emerging tissue-scale organization...
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Reposted by Nicolas Denans
James Gagnon @james-gagnon.bsky.social · 28/05/2026
Excited to share the published version of MIC-Drop-seq @natcomms.nature.com! Shoutout to co-lead authors @claycarey.bsky.social @sparvez.bsky.social for driving this work. Excited to see where this new scale of single-cell perturbation screening goes next. www.nature.com/articles/s41...
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Reposted by Nicolas Denans
Carsen Stringer @computingnature.bsky.social · 22/05/2026
🚨🧠 Our paper is out! We introduce a simple computational model that generates macroscopic, long-timescale dynamics as seen in large-scale neural recordings. #neuroscience #dynamics @marius10p.bsky.social @zhong-lin.bsky.social @hhmijanelia.bsky.social Link: go.nature.com/4tRNjIu
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Nicolas Denans @nicolasdenans.bsky.social · 18/05/2026
Looking forward to this conference www.janelia.org/you-janelia/... . Just realized @jeromegros.bsky.social will be giving a talk, that should be fun!
janelia.org
Intersection of Mechanics and Metabolism Across Biological Scales
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Nicolas Denans @nicolasdenans.bsky.social · 28/04/2026
Great work! This will have a huge impact for zebrafish transgenesis strategies. We knew it but didn't have the data to back it up!
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Reposted by Nicolas Denans
Emily Kolenbrander Ho @emkolen.bsky.social · 22/04/2026
New review on optogenetics in development is out in @genesdev.bsky.social with @toettch.bsky.social and Yang Gao! 💙💡🔦 genesdev.cshlp.org/content/earl... We aim to capture why opto is such a powerful tool for devbio and how future advances can make it even better. Some highlights:
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Reposted by Nicolas Denans
Luke Lavis @rhodamine110.bsky.social · 15/04/2026
Out in @natmethods.nature.com: More dyes. They work. Quite well. And blink. Pick the one that fits your target, your technique, and your labeling density. With too many collaborators and institutes to list, but anchored at @hhmijanelia.bsky.social www.nature.com/articles/s41...
nature.com
A series of spontaneously blinking dyes for super-resolution microscopy - Nature Methods
A series of spontaneously blinking dyes in the far-red range facilitate single-molecule localization microscopy. These dyes vary in their blinking properties and can be matched to the applications and...
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Reposted by Nicolas Denans
Stephan Saalfeld @herrsaalfeld.bsky.social · 20/02/2026
If your imaging system has poorly characterized constant distortions leading to chromatic aberration, shoddy stitching, or false measurements (the answer is likely yes), you may want to give this tool a try. Native installers for Linux, Mac, Win under Releases github.com/saalfeldlab/...
github.com
GitHub - saalfeldlab/lens-correct: Correcting lens-distortion in confocal stacks
Correcting lens-distortion in confocal stacks. Contribute to saalfeldlab/lens-correct development by creating an account on GitHub.
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Nicolas Denans @nicolasdenans.bsky.social · 18/02/2026
So many great conferences @hhmijanelia.bsky.social . Don't miss the opportunity to participate in one of these unique experiences! www.janelia.org/you-janelia/...
janelia.org
Conferences
Application deadlines vary by meeting. See descriptions for more details.
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Reposted by Nicolas Denans
Carsen Stringer @computingnature.bsky.social · 18/02/2026
Are you working at the interface of #neuroscience and ML/AI? Share your research at Janelia in Nov! 🧠 🤖 janelia.news/NAI26
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Alison Tebo @agtebo.bsky.social · 17/02/2026
We’re excited to announce the next Fluorescent Proteins & Biological Sensors conference! Abstract submissions are now open—hope to see you there. www.janelia.org/you-janelia/...
janelia.org
Fluorescent Proteins and Biological Sensors VIII
Organizers Eric Schreiter, HHMI/Janelia Research Campus Alison Tebo, HHMI/Janelia Research Campus Invited Participants Xiaolu Cambronne, University of Texas at Austin Katharine Diehl, University of
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Reposted by Nicolas Denans
Teng-Leong Chew @scopeshifu.bsky.social · 28/01/2026
🧪 We are excited to share this novel open access paper on Phasor Mixing Coefficient to analyze colocalization, developed by folks @i2janelia.bsky.social and @aicjanelia.bsky.social. This is also the first technical paper jointly published with our sister imaging center @malacridalab.bsky.social!
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Nicolas Denans @nicolasdenans.bsky.social · 18/12/2025
Wow, @erturklab.bsky.social team did it again! Bringing science fiction to the real world 👋👋
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Nicolas Denans @nicolasdenans.bsky.social · 16/12/2025
really cool, congrats! #microscopy
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Reposted by Nicolas Denans
AIC at Janelia @aicjanelia.bsky.social · 15/12/2025
Getting started with analysis can be daunting, especially given the many tools available. In our latest @focalplane.bsky.social post, @scientistrachel.bsky.social & Owen Puls discuss framing analysis questions to extract informative biological information. focalplane.biologists.com/2025/12/15/h...
focalplane.biologists.com
How do I get started with image analysis? - FocalPlane
How do I get started with image analysis? - AIC at HHMI Janelia
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Nicolas Denans @nicolasdenans.bsky.social · 08/12/2025
Pretty cool tool! Would have been extremely useful during my academic career. #Microscopy
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Reposted by Nicolas Denans
FocalPlane @focalplane.bsky.social · 24/11/2025
📢Did you know that researchers from around the world can apply for access to the latest microscopy technology & expert advice @aicjanelia.bsky.social? In this blog series, the AIC team will give us an insight into how the Center works & their global impact. focalplane.biologists.com/2025/11/20/a...
focalplane.biologists.com
AIC at HHMI Janelia
Introduction to the AIC at HHMI Janelia blog on FocalPlane
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Reposted by Nicolas Denans
Luke Lavis @rhodamine110.bsky.social · 11/11/2025
ahem, ONE of THE chemical biology conferences of 2026:) www.janelia.org/you-janelia/...
janelia.org
Chemical Tools for Complex Biological Systems IV
Organizers Luke Lavis, HHMI/Janelia Research Campus Matthew Bogyo, Stanford University Zev Gartner, University of California, San Francisco Jennifer Prescher, University of California, Irvine
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Nicolas Denans @nicolasdenans.bsky.social · 31/10/2025
Another #FluorescenceFriday contribution for #Halloween a dive inside zebrafish vasculature
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Nicolas Denans @nicolasdenans.bsky.social · 31/10/2025
For #SpookyMicroscopyFriday I present the mugshot of the head of the zebrafish mafia
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AIC at Janelia @aicjanelia.bsky.social · 27/10/2025
Our team is hard at work preparing for #InsightFromImaging 2025! We can't wait to welcome HHMI #HannaGrayFellows to @hhmijanelia.bsky.social next week for lectures, hands-on labs, and activities focused on designing informative and quantitative bioimaging experiments 🔬
A microscopy image of a cell stained for actin (magneta color) and focal adhesions (green color).
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Nicolas Denans @nicolasdenans.bsky.social · 20/10/2025
For #MicroscopyMonday a cleared mouse embryos labeled with an antibody targeting neurofilaments (2H3, DSHB) @hhmijanelia.bsky.social @aicjanelia.bsky.social
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Nicolas Denans @nicolasdenans.bsky.social · 17/10/2025
for #FluorescenceFriday : is your ExM sample too large to be imaged with high NA objectives? VIPS it! Very clever way to tackle one of the biggest challenge in large volumetric ExM www.science.org/doi/10.1126/...
science.org
Mesoscale volumetric fluorescence imaging at nanoscale resolution by photochemical sectioning
Optical nanoscopy of intact biological specimens has been transformed by recent advancements in hydrogel-based tissue clearing and expansion, enabling the imaging of cellular and subcellular structure...
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Nicolas Denans @nicolasdenans.bsky.social · 19/09/2025
The WB-ExM protocol described here works with.... every sample we tested! Here a 3do quail embryo (white= pan-protein; red=MF20) www.biorxiv.org/content/10.1...
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Reposted by Nicolas Denans
Melanie D. White @melaniedwhite.bsky.social · 22/07/2025
Today was a super fun first day of imaging @aicjanelia.bsky.social with @vanderspuy.bsky.social and @samarar.bsky.social. All hail the quail!🧪🔬#DevBio
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mojtabart.bsky.social @mojtabart.bsky.social · 17/07/2025
🧠 Excited by synapse-level brain mapping? Join us at a world-class institute to build molecular tools based on our new #LICONN work — and push the frontier of #MolecularConnectomics. Let’s decode the brain, one synapse at a time. hhmi.wd1.myworkdayjobs.com/en-US/Extern...
hhmi.wd1.myworkdayjobs.com
Research Specialist - Tavakoli Lab
Primary Work Address: 19700 Helix Drive, Ashburn, VA, 20147 Current HHMI Employees, click here to apply via your Workday account. The Howard Hughes Medical Institute’s Janelia Research Campus is a pio...
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Reposted by Nicolas Denans
AIC at Janelia @aicjanelia.bsky.social · 06/06/2025
Just over a week left to apply for this round of the AIC Call for Proposals! Submit at www.aicjanelia.org/apply by Monday, June 16 (5 pm US ET).
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Nicolas Denans @nicolasdenans.bsky.social · 13/05/2025
Is this amazing ExM conference still happening? www.rizzoli-lab.de/gef25/
rizzoli-lab.de
GEF25-Homepage - rizzoli-lab
Program Location & Travel About Home GEF25, organized in the 10th anniversary year of ExM, focuses on cutting-edge advancements in expansion microscopy, as a part of global initiatives to democratize ...
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Reposted by Nicolas Denans
Janelia Research Campus @hhmijanelia.bsky.social · 22/04/2025
🥼A new tissue expansion method developed by researchers in the Wang & Tillberg labs & collaborators @uwmadison.bsky.social enables scientists to use mass spectrometry imaging to simultaneously detect hundreds of molecules at the single cell level in their native locations ➡️ hhmi.news/4ixHOZZ
hhmi.news
New technique expands tissues so hundreds of biomolecules can be seen inside cells
A new tissue expansion method developed by Janelia and University of Wisconsin-Madison researchers enables scientists to use mass spectrometry imaging to simultaneously detect hundreds of molecules
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Nicolas Denans @nicolasdenans.bsky.social · 17/04/2025
I guess they renamed their protein from mYongHong to mScarlet3H www.nature.com/articles/s41...
nature.com
A highly stable monomeric red fluorescent protein for advanced microscopy - Nature Methods
The red fluorescent protein mScarlet3-H is bright, photostable and very robust to high temperature, chaotropic conditions and oxidative environments. mScarlet3-H works well in correlative light and el...
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Nicolas Denans @nicolasdenans.bsky.social · 15/04/2025
A new call for proposals just opened with @aicjanelia.bsky.social . Do not miss this unique opportunity to collaborate with microscopy experts to advance your project!
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Nicolas Denans @nicolasdenans.bsky.social · 12/02/2025
Amazing opportunity!! #microscopy #bioImaging
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Nicolas Denans @nicolasdenans.bsky.social · 11/02/2025
Looks impressive! Check it out!
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Nicolas Denans @nicolasdenans.bsky.social · 11/02/2025
Do you want to help developing new groundbreaking methodologies with US @i2janelia.bsky.social ? We need another BioImage Analyst to join our growing team! hhmi.wd1.myworkdayjobs.com/en-US/Extern...
hhmi.wd1.myworkdayjobs.com
BioImage Analyst
Primary Work Address: 19700 Helix Drive, Ashburn, VA, 20147 Current HHMI Employees, click here to apply via your Workday account. The Howard Hughes Medical Institute’s Janelia Research Campus is a pio...
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Reposted by Nicolas Denans
Nikita Vladimirov @nvladimus.bsky.social · 20/01/2025
Please welcome our official #mesoSPIM channel on this platform, @mesospim.bsky.social. Repost is appreciated!
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Nicolas Denans @nicolasdenans.bsky.social · 20/12/2024
VVDviewer developed @hhmijanelia.bsky.social is a FREE software that makes beautiful rendering, is very easy to use and can handle large datasets. Did I mentioned it is FREE? #microscopy
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Nicolas Denans @nicolasdenans.bsky.social · 04/12/2024
still amazes me that journals that you pay $10000 to publish in can't even correct typos. That's called editing? Not blaming the authors at all, it happens to all of us. Disappointed in the publisher.
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Nicolas Denans @nicolasdenans.bsky.social · 24/11/2024
sounds about right. Everything but microscopy 😂
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Reposted by Nicolas Denans
Florian Jug @florianjug.bsky.social · 27/10/2023
😱📣 BlueSky-ers: WE NEED YOUR HELP!!! 🙏 All of you who ever liked a lecture of mine... All of you who liked one of the courses I teach in... All of you I work(ed) with in one way or another... All of you who see my desperation! 😜 PLEASE re-post! 🙏 careers.humantechnopole.it/o/postdoc-in...
careers.humantechnopole.it
Postdocs in Artificial Intelligence
Human Technopole (HT) is an interdisciplinary life science research institute, created and supported by the Italian Government, with the aim of developing innovative strategies to improve human health
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Stephan Saalfeld @herrsaalfeld.bsky.social · 15/11/2024
We are looking for exceptional #AIScientist|s to join our #AI@HHMI initiative at #HHMIJanelia. We want to uncover fundamental principles underlying complex biological systems that are inaccessible without new innovations that combine #AI with experimental design. ai.hhmi.org#join-our-team 1/4
AI@HHMI teaser saying "AI@HHMI | Accelerating Innovation in Biology". The backdrop is an artistic rendering of the compute graph of a network architecture for semantic image segmentation that I think looks really cute.
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Nicolas Denans @nicolasdenans.bsky.social · 14/11/2024
I guess that's where all the cool kids hangout now. Even @aicjanelia.bsky.social joined! #microscopy
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