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

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!

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! 🔬

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!

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.

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.

🧪 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...

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

nature.com

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.

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/...

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

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

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

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

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!

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

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?

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 🔬

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!

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

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

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! 🔬

Microscopy beautifully reveals the dynamic nature of biology but quantifying that motion can be tricky! In the latest paper from @aicjanelia.bsky.social, out now in @jcellsci.bsky.social, we present a tool for measuring amorphous motion: OpticalFlow3D journals.biologists.com/jcs/article/... (1/7)

OpticalFlow3D – a tool for measuring amorphous motion in three-dimensional fluorescence microscopy images

Summary: Biological motion can be difficult to define and measure. Optical flow is uniquely suited to this challenge. We provide tools for 3D optical flow and illustrate its use in extracting biologic...

journals.biologists.com

🧪 @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

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!

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!

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...

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...

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

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.

Teng-Leong Chew@scopeshifu.bsky.social · 6mo ago

🧪 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!

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/...

Teng-Leong Chew@scopeshifu.bsky.social · 6mo ago

🧪 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!

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.