iiinova — where your digital self keeps evolving

Reposted by AIC at Janelia

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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Reposted by AIC at Janelia

Jesse Aaron @jesseaic.bsky.social · 31/07/2026

Always great fun doing the #IALSJanelia boot camp. Absolutely phenomenal group of participants!

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Reposted by AIC at Janelia

Rachel Lee, PhD @scientistrachel.bsky.social · 30/07/2026

As #IALSJanelia 2026 draws to a close, I want to express my gratitude as a co-organizer! The @aicjanelia.bsky.social team prepared & taught while @janeliaconf.bsky.social provided awesome support. We had an amazing group of participants and I cannot wait to see what they do next with microscopy! 🔬

A photo of a coffee mug. The foam in the mug has the words "IALS Janelia 2026" printed in coffee.

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AIC at Janelia @aicjanelia.bsky.social · 30/07/2026

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!

A photo of a group of people. Two rows stand, while a front row kneels. Below the photo there is a caption listing the workshop name and dates.

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AIC at Janelia @aicjanelia.bsky.social · 30/07/2026

During the final group project at #IALSJanelia, participants are combining their knowledge of light sheet microscopy, large data handling, and tracking to measure macrophage motion in a zebrafish tail. The data shown here was taken on our SiMView microscope by @anjanja1024.bsky.social.

Color visualization of microscopy data. Each color corresponds to a point in time, ranging from 0 hours (purple) to 12 hours (yellow). The structures in the image correspond to macrophages in a zebrafish tail.

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AIC at Janelia @aicjanelia.bsky.social · 29/07/2026

We're discussing the pros and cons of approaches for increasing imaging depth at #IALSJanelia. One benefit of two-photon microscopy (2P) is label-free second harmonic generation (SHG). Here SHG (purple) reveals structures surrounding macrophages (teal) in a zebrafish tail.

A microscopy image with macrophages (teal cells) and second harmonic generation (purple fibers).

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Reposted by AIC at Janelia

Teng-Leong Chew @scopeshifu.bsky.social · 28/07/2026

🧪 Want to image specimens that require air-liquid interface on a microscope with water-dipping lenses such as the lattice light sheet system? @aicjanelia.bsky.social, @cmhobson.bsky.social and TokaiHIT have just made that a reality. Check out our new paper: www.nature.com/articles/s44...

nature.com

Adapting upright light sheet fluorescence microscopy for imaging at air-liquid interface - npj Imaging

npj Imaging - Adapting upright light sheet fluorescence microscopy for imaging at air-liquid interface

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AIC at Janelia @aicjanelia.bsky.social · 28/07/2026

Continuing our discussion of super-resolution techniques, our morning lecture at #IALSJanelia focused on analysis of localization microscopy data. Tessellation of this iPALM dataset reveals not only the boundary of the focal adhesion, but also internal structure within.

Visualization of a tessellation of point coordinates. White lines indicate the boundaries of the tessellation, while color indicates the area of the tessellation region (blue = large region, yellow = small region).

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Reposted by AIC at Janelia

Stephan Huveneers @huveneerslab.bsky.social · 28/07/2026

How do endothelial cells interact while migrating? Together with @jesseaic.bsky.social @scopeshifu.bsky.social @aicjanelia.bsky.social, we used #Cryo-SIM and #FIB-SEM to reveal a surprising diversity of nanoscale plasma membrane curvatures at asymmetric junctions. rupress.org/jcb/article/...

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Reposted by AIC at Janelia

Rachel Lee, PhD @scientistrachel.bsky.social · 27/07/2026

Today at #IALSJanelia, we're exploring super-resolution. This includes spending time at @aicjanelia.bsky.social's iPALM system, where participant are exploring tubulin networks (purples) and focal adhesions (light blue) at the ~20 nm scale! iPALM data by @anjanja1024.bsky.social

A 3D rendering of iPALM microscopy data. A network of tubulin (purple fibers) lays on top of focal adhesions (blue blobs).

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AIC at Janelia @aicjanelia.bsky.social · 27/07/2026

Today is super-resolution day at #IALSJanelia! We're spending the afternoon at the microscope exploring these beautiful tubulin networks🔬 Images by @harikrushnan.bsky.social

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Reposted by AIC at Janelia

Rachel Lee, PhD @scientistrachel.bsky.social · 25/07/2026

Lattice light sheet data taken by the participants of #IALSJanelia 2026, with guidance from @cmhobson.bsky.social. I rendered the actin dynamics using #AGAVE 🔬

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AIC at Janelia @aicjanelia.bsky.social · 24/07/2026

How does resolution impact colocalization? This afternoon at #IALSJanelia participants are exploring the impact of imaging modality on measurements of co-occurrence and correlation.

A two-panel microscopy image. Both panels show mitochondria labeled for COX8 (green) and TOMM20 (magenta). The left panel shows an image taken on a widefield microscope, and most pixels are white (a merge of magenta and green). The right panel shows an image taken using lattice SIM.

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AIC at Janelia @aicjanelia.bsky.social · 24/07/2026

We are grateful to Paul Tillberg for stopping by to give #IALSJanelia 2026 participants a guest lecture on expansion microscopy, including a hands-on #ExM demonstration!

A photo of a conference room where attendees are sitting at rows of tables. At the front of the room, a man sits alone at a separate table with a document camera. A view of the samples he is manipulating is projected on the screen behind him.

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AIC at Janelia @aicjanelia.bsky.social · 23/07/2026

This afternoon's imaging lab at #IALSJanelia is all about subcellular structures, highlighted here by myosin (white) and actin (orange). These membrane ruffles were captured on our lattice light-sheet microscope by @cmhobson.bsky.social

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AIC at Janelia @aicjanelia.bsky.social · 22/07/2026

During our first analysis lab at #IALSJanelia 2026, participants are exploring #TrackMate. How do tracking challenges (and advantages) change when you image different parts of the cell? Do you get the same results from different labels?

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AIC at Janelia @aicjanelia.bsky.social · 21/07/2026

For our first live cell imaging lab of #IALSJanelia 2026, we're exploring the migratory behavior of neutrophil-like HL60 cells. Confocal microscopy by @anjanja1024.bsky.social 🔬

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AIC at Janelia @aicjanelia.bsky.social · 21/07/2026

We're exploring Fourier transforms at #IALSJanelia. In addition to applying them computationally in #Fiji, we're performing them optically with the help of a @thorlabs.bsky.social optics kit run by @cmhobson.bsky.social!

A photograph of optics equipment on a table. The Fourier pattern is projected onto a white piece of paper, while the image pattern is seen in the upper right corner of the photo.

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AIC at Janelia @aicjanelia.bsky.social · 21/07/2026

This morning at #IALSJanelia, we're jumping into image analysis with #FIJI / #ImageJ! Our practical exercises on image filtering include comparisons of denoising approaches.

A man sitting at a table looks at his laptop. The laptop shows an image of a clown that has been overlaid with noisy speckles.

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AIC at Janelia @aicjanelia.bsky.social · 20/07/2026

This morning at #IALSJanelia we're getting started with some microscopy fundamentals in a lecture by @cmhobson.bsky.social 🔬

A photo of people in a conference room. A man stands at the front next to a large projector screen. The screen shows a presentation slide on image formation.

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AIC at Janelia @aicjanelia.bsky.social · 19/07/2026

We're kicking off #IALSJanelia 2026 with a keynote lecture by @scopeshifu.bsky.social. Our teaching team is excited to get to know all our participants and start two weeks of talking about microscopy! 🔬

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Reposted by AIC at Janelia

Teng-Leong Chew @scopeshifu.bsky.social · 15/07/2026

🧪 @aicjanelia.bsky.social and @scientistrachel.bsky.social have just published a new quantitative tool, OpticalFlow3D, for tracking amorphous motion in 3D. Try it out and let us know what you think! tinyurl.com/OpticalFlow3D

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AIC at Janelia @aicjanelia.bsky.social · 07/07/2026

Despite its nebula-like qualities, this image is from the microscopic rather than astrophysical scale. This adherent cell was labeled for focal adhesions (blue structures) and actin (orange fibers). It is one of the many samples the team is hard at work preparing for #IALSJanelia 2026!

An image taken on a microscope of a single adherent cell. Two images were combined in this visualization: an image taken with widefield illumination (orange colors) and an image taken using TIRF (blue colors). Together these colors highlight fibers of actin and elongated focal adhesion structures.

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AIC at Janelia @aicjanelia.bsky.social · 07/07/2026

We enjoyed having Wenting Zhao and team here to take data on our iPALM system with @anjanja1024.bsky.social and wish them happy data analyzing!

A photo of a group of women standing in front of a staircase.

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Reposted by AIC at Janelia

Yoseph Loyd @yosephl.bsky.social · 01/05/2026

The Krendel lab has been working investigating Myo1e/f’s involvement in cell eating. Here’s a fun video of our work collected with @aicjanelia.bsky.social. Thanks a ton for helping us with this and the amazing #LightSheet imaging! Take a look at our work: www.biorxiv.org/content/10.6...

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Reposted by AIC at Janelia

Chad Hobson @cmhobson.bsky.social · 01/05/2026

Happy #FluorescenceFriday, here is a macrophage engulfing a deformable particle imaged on our LLSM. This project from Mira Krendel's lab and the @aicjanelia.bsky.social just came out as a preprint today! www.biorxiv.org/content/10.6...

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Reposted by AIC at Janelia

New England Society for Microscopy @nesmicroscopy.bsky.social · 23/02/2026

GORGEOUS data from Laura Smithson for #MicroscopyMonday! 🏆 Our #NESM Fall Symposium Poster Winner (Brown Univ., de Graffenried Lab) used customized #FIB-SEM to reconstruct the T. brucei cytoskeleton at 4 nm res — 9,000+ images & 660 GB. @brown.edu @aicjanelia.bsky.social #Microscopy #VolumeEM #EM

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Reposted by AIC at Janelia

Leonel Malacrida @malacridalab.bsky.social · 29/01/2026

It’s great to see this document supporting colocalization via Phasor analysis of HSI data, now available on confocal microscopes. Thanks to @scopeshifu.bsky.social and @aicjanelia.bsky.social teams for their collaboration starting in 2022 during the Imaging Latinoamérica workshop.

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AIC at Janelia @aicjanelia.bsky.social · 28/01/2026

Check out this new approach to colocalization analysis from @owfpuls.bsky.social along with members of the AIC and Advanced Bioimaging Unit teams, now out in @jcellsci.bsky.social! journals.biologists.com/jcs/article/...

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Reposted by AIC at Janelia

Maggie Utgaard @maggieutgaard.bsky.social · 23/01/2026

Looking a little closer with the help of the @aicjanelia.bsky.social we used iPALM to see where septins were in relation to the actin. While they colocalize in the X-Y plane, septins are actually consistently below the actin stress fibers, closer to the membrane.

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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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AIC at Janelia @aicjanelia.bsky.social · 24/11/2025

We are kicking off a blog series with @focalplane.bsky.social to provide insight into life at the AIC, microscopy careers, image analysis, and more! Read our intro post here: 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 AIC at Janelia

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 AIC at Janelia

Whitney Stevens-Sostre, PhD Boricua @stevenssostre.bsky.social · 08/11/2025

I learned so much from the @aicjanelia.bsky.social team at the #InsightFromImaging 2025 workshop this past week. Thank you so much! It was so fun and informative. I enjoyed the discussions between #HannaGrayFellows and the AIC team at @hhmijanelia.bsky.social. I’m off to do bioimaging experiments! 🔬

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AIC at Janelia @aicjanelia.bsky.social · 07/11/2025

One last Bob's coffee break at @hhmijanelia.bsky.social before our final #InsightFromImaging activity: Participants are working in groups to formulate a hypothesis and design an imaging experiment to test it 🔬

A photo of a coffee mug. The mug is labeled with writing that says "hhmi | janelia Research Campus." The drink in the mug has the words "Insight From Imaging 2025" printed on the foam.

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AIC at Janelia @aicjanelia.bsky.social · 07/11/2025

For our final lecture at #InsightFromImaging 2025, @jesseaic.bsky.social is discussing electron microscopy and correlative approaches, including results from our FIB-SEM system, which can achieve 4 nm resolution in 3D!

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AIC at Janelia @aicjanelia.bsky.social · 06/11/2025

We spent the afternoon at #InsightFromImaging in the lab exploring 5 different microscopes (& 5 different samples!) to understand approaches for imaging depth. Kidney slice prep by Ellen, imaged by Jenny using 2P (green tubulin) + SHG (magenta), viz by @scientistrachel.bsky.social in #AGAVE

A 3D rendering of microscopy data. Fluorescently labeled tubulin is shown in green, while second harmonic generation is shown in magenta.

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AIC at Janelia @aicjanelia.bsky.social · 06/11/2025

Today at #InsightFromImaging we're focusing on imaging depth, starting with a lecture by @cmhobson.bsky.social. Adaptive optics (available on our MOSAIC system!) can improve deep imaging, as shown by these mitochondria in a zebrafish embryo.

A microscopy image with text annotation. The left side of the image is labeled "System Correction Only" and shows blurry and aberrated mitochondria. The right side of the image is labeled "Adaptive Optics + Deconvolution" and shows a clearer image of mitochondria.

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AIC at Janelia @aicjanelia.bsky.social · 05/11/2025

This morning at #InsightFromImaging we focused on particle tracking. After a lecture by @jesseaic.bsky.social, participants split into groups to use #TrackMate to track our HL60 migration data from yesterday, followed by presentations on their results 📈

A collage of photos, which show people analyzing images and giving presentations.

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Reposted by AIC at Janelia

Rachel Lee, PhD @scientistrachel.bsky.social · 05/11/2025

Yes, they are the same field of view 😄 Bonus additional #InsightFromImaging cell from a different FOV here:

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Reposted by AIC at Janelia

Rachel Lee, PhD @scientistrachel.bsky.social · 04/11/2025

HL60 cells take on so many fun shapes as they migrate! This #InsightFromImaging data features cells prepared by Leanna and imaged on the @aicjanelia.bsky.social LLSM by @cmhobson.bsky.social

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AIC at Janelia @aicjanelia.bsky.social · 04/11/2025

Continuing our speed theme at #InsightFromImaging, we spent the afternoon at the microscope exploring imaging speed, as well as tradeoffs in imaging scale. Video featuring imaging of neutrophil-like HL60 cells on a widefield vs the AIC's LLSM.

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AIC at Janelia @aicjanelia.bsky.social · 04/11/2025

Today's theme at #InsightFromImaging 2025 is imaging speed. We're kicking things off with a lecture by Chad Hobson.

A photo of a classroom. A man stands at the podium next to a projector screen. The audience sits at tables in front of the screen.

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AIC at Janelia @aicjanelia.bsky.social · 03/11/2025

For our first #InsightFromImaging lab, we're exploring imaging resolution across a variety of microscopy systems. When is increased resolution really necessary? What trade-offs does it require?

A microscopy image of a cell labeled for actin (magenta) and paxillin (green). The left half of the image is taken in widefield mode, while the right half is taken in confocal mode. The scale bar is 10 um.

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Reposted by AIC at Janelia

Rachel Lee, PhD @scientistrachel.bsky.social · 03/11/2025

I had a wonderful time discussing image analysis with HHMI #HannaGrayFellows this morning. I look forward to continuing the chat throughout #InsightFromImaging this week.

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AIC at Janelia @aicjanelia.bsky.social · 03/11/2025

This morning at #InsightFromImaging we jumped into hands on image analysis activities, including comparing the pros and cons of imaging denoising approaches

A photo of a classroom. There is a projector screen at the front of the room, and participants sit at tables with laptops performing image analysis tasks.

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AIC at Janelia @aicjanelia.bsky.social · 02/11/2025

We're kicking off #InsightFromImaging 2025 with a keynote lecture by @scopeshifu.bsky.social on advanced microscopy and the resources available through the Advanced Imaging Center's visitor program 🔬

A photo of a man giving a presentation. He is standing in front of a projector screen. In the front of the photo, the audience sits at long tables.

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Reposted by AIC at Janelia

Rachel Lee, PhD @scientistrachel.bsky.social · 31/10/2025

When #FluorescenceFriday falls on Halloween, we break out the spooky data 👻 Here we are looking at the blood vessels of a zebrafish through its eye 🎃

A 3D rendering of microscopy data. The structure of a fish is visible in gray while green blood vessels are visible through the eye.

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