Rachel Lee, PhD
@scientistrachel.bsky.social
BioImage Analysis Lead at AIC Janelia
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...
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...
biorxiv.org
Always great fun doing the #IALSJanelia boot camp. Absolutely phenomenal group of participants!
AIC at Janelia@aicjanelia.bsky.social · 2mo agoWe 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.
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
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
Lattice light sheet data taken by the participants of #IALSJanelia 2026, with guidance from @cmhobson.bsky.social. I rendered the actin dynamics using #AGAVE 🔬
Microscopy Nodes 3.1 is out for Blender 5.2! 🎉 This has cool new features for conditional masking, working with even larger data (regional upscaling), and data manipulation! Watch the new youtube tutorials that explain the features: www.youtube.com/playlist?lis...
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?
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!
You have to love the diversity of shapes that these HL60 cells make! #IALSJanelia 2026
AIC at Janelia@aicjanelia.bsky.social · 2mo agoFor 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 🔬
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!
Annual killifish continue to surprise us: they make neutrophils before almost every other cell type, even before gastrulation. Neutrophils usually arise from the lateral plate mesoderm (forming in cyan), but in killifish they are already patrolling around the embryo in gold. tinyurl.com/killiphil
Blebbing cells are so fun. Pink~positive curvature regions, Cyan~negative curvature regions. Thanks for the curvature mapping tip @scientistrachel.bsky.social. Acquired with lattice-lightsheet wizard @niallgeoghegan.bsky.social
My first post here, we have a new preprint out from @aicjanelia.bsky.social! Upright LSFM is fantastic for live imaging, but not amenable to all samples - especially those requiring an air-liquid interface. We worked with Tokai Hit to try to fix that. www.biorxiv.org/content/10.6...
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 · 8mo 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!
🧪 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!