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

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!

AIC at Janelia@aicjanelia.bsky.social · 6d ago

We are grateful to our teaching team and participants for a wonderful two weeks of intense microscopy and image analysis at #IALSJanelia 2026. Many thanks to the @janeliaconf.bsky.social team for the support that made this bootcamp possible!

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/...

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...

science.org

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.

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...

elifesciences.org

Biomedical Picture of the Day BPoD@bpodaily.bsky.social · 2mo ago

User-friendly pipeline Tapenade quantifies spatial patterns of gene expression & nuclear morphology in 3D cell assembly '...oids' 📹 @alicegros.bsky.social, @jules-vanaret.bsky.social, @dunsingvalentin.bsky.social et al @centuri-ls.bsky.social in @elife.bsky.social ➡️ bpod.org.uk/archive/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...

James Gagnon@james-gagnon.bsky.social · last yr.

To dissect the gene regulatory networks used to build organisms, we need Perturb-seq-like tools that work in whole animals. For this purpose, we developed MIC-Drop-seq, a tool that couples high-throughput CRISPR in zebrafish embryos with single-cell RNAseq. www.biorxiv.org/content/10.1...

🚨🧠 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

Nature@nature.com · 3mo ago

Nature research paper: A critical initialization for biological neural networks go.nature.com/4tRNjIu

Looking forward to this conference www.janelia.org/you-janelia/... . Just realized @jeromegros.bsky.social will be giving a talk, that should be fun!

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!

James Gagnon@james-gagnon.bsky.social · 3mo ago

Using light-activated CRISPR in zebrafish, we triggered synchronized DNA breaks and track the repair process. ⚡🐟⚡ 

 Well ... DNA repair is very different in embryos compared to tissue culture cells. Embryos repair DNA breaks incredibly fast - within minutes! www.biorxiv.org/content/10.6...

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:

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...

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...

nature.com

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 - 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.

github.com

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/...

Are you working at the interface of #neuroscience and ML/AI? Share your research at Janelia in Nov! 🧠 🤖 janelia.news/NAI26

Janelia Conferences@janeliaconf.bsky.social · 6mo ago

📢 Applications are open! This meeting brings together scientists using data-driven #AI to analyze + model neural circuits and uncover how the brain performs complex computations. 🧠 Apply by May 28 ➡️ janelia.news/NAI26 @computingnature.bsky.social @sinzlab.bsky.social @srinituraga.bsky.social

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/...

🧪 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!

Wow, @erturklab.bsky.social team did it again! Bringing science fiction to the real world 👋👋

Ali Maximilian Erturk@erturklab.bsky.social · 8mo ago

Most transcriptomics studies sample ~0.001% of a mouse. Which region do we choose? Often: we guess. Meet DISCO-seq 🤗 flipping the order: RNA-preserving clearing → whole-organ/whole-body 3D imaging → pick ROIs in 3D → unbiased scRNA-seq. Preprint: www.biorxiv.org/content/10.6...

really cool, congrats! #microscopy

Valentin Dunsing-Eichenauer@dunsingvalentin.bsky.social · 8mo ago

New paper out! Combining single-objective light-sheet microscopy and time-resolved SPAD array detection, we massively accelerate fluorescence lifetime imaging (FLIM) compared to confocal FLIM, making FLIM applicable to 3D specimen such as organoids and embryos. www.nature.com/articles/s42...

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...

How do I get started with image analysis? - FocalPlane

How do I get started with image analysis? - AIC at HHMI Janelia

focalplane.biologists.com

Pretty cool tool! Would have been extremely useful during my academic career. #Microscopy

Zimeng Wu@zimengwu33.bsky.social · 8mo ago

Pleased to say that Jonas Hartmann (bs-less) and I have finally released DySTrack (“diss track”) - Dynamic Sample Tracking. It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems. Preprint: www.biorxiv.org/content/10.6... [1/6]

📢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...

AIC at HHMI Janelia

Introduction to the AIC at HHMI Janelia blog on FocalPlane

focalplane.biologists.com

ahem, ONE of THE chemical biology conferences of 2026:) www.janelia.org/you-janelia/...

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

janelia.org

Another #FluorescenceFriday contribution for #Halloween a dive inside zebrafish vasculature

For #SpookyMicroscopyFriday I present the mugshot of the head of the zebrafish mafia

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 🔬

For #MicroscopyMonday a cleared mouse embryos labeled with an antibody targeting neurofilaments (2H3, DSHB) @hhmijanelia.bsky.social @aicjanelia.bsky.social

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/...

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...

science.org

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...

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

🧠 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...

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...

hhmi.wd1.myworkdayjobs.com

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).

AIC at Janelia@aicjanelia.bsky.social · last yr.

The latest AIC Call for Proposals is now open! Deadline is June 16, 2025. Come use @hhmijanelia.bsky.social imaging technology and expertise for FREE. Visit www.aicjanelia.org/apply for details. Before applying, contact us to schedule a technical consultation!