Reposted by Rachel Lee, PhDChad Hobson @cmhobson.bsky.social · 18/09/2026I spy vFLIM!! www.biorxiv.org/content/10.6... 051
Reposted by Rachel Lee, PhDChad Hobson @cmhobson.bsky.social · 27/08/2026A 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.orgvFLIM: Machine Learning-enabled Light Sheet Fluorescence Lifetime ImagingThe lifetime of fluorescent molecules provides an orthogonal readout to fluorescence intensity, opening experimental possibilities of measuring changes in local molecular environments, mechanical tens... 13513
Reposted by Rachel Lee, PhDJesse Aaron @jesseaic.bsky.social · 31/07/2026Always great fun doing the #IALSJanelia boot camp. Absolutely phenomenal group of participants! 0103
Rachel Lee, PhD @scientistrachel.bsky.social · 30/07/2026As #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! 🔬 072
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 30/07/2026We 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! 093
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 30/07/2026During 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. 0207
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 29/07/2026We'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. 1185
Reposted by Rachel Lee, PhDTeng-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.comAdapting upright light sheet fluorescence microscopy for imaging at air-liquid interface - npj Imagingnpj Imaging - Adapting upright light sheet fluorescence microscopy for imaging at air-liquid interface 0205
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 28/07/2026Continuing 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. 0113
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 27/07/2026Today is super-resolution day at #IALSJanelia! We're spending the afternoon at the microscope exploring these beautiful tubulin networks🔬 Images by @harikrushnan.bsky.social 0103
Rachel Lee, PhD @scientistrachel.bsky.social · 27/07/2026Today 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 0116
Rachel Lee, PhD @scientistrachel.bsky.social · 25/07/2026Lattice light sheet data taken by the participants of #IALSJanelia 2026, with guidance from @cmhobson.bsky.social. I rendered the actin dynamics using #AGAVE 🔬 0255
Reposted by Rachel Lee, PhDAafke Gros @aafkegros.bsky.social · 24/07/2026Microscopy 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... 26827
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 24/07/2026How does resolution impact colocalization? This afternoon at #IALSJanelia participants are exploring the impact of imaging modality on measurements of co-occurrence and correlation. 092
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 24/07/2026We 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! 0122
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 23/07/2026This 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 05218
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 22/07/2026During 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? 0164
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 21/07/2026We'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! 0167
Rachel Lee, PhD @scientistrachel.bsky.social · 21/07/2026You have to love the diversity of shapes that these HL60 cells make! #IALSJanelia 2026 091
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 21/07/2026This morning at #IALSJanelia, we're jumping into image analysis with #FIJI / #ImageJ! Our practical exercises on image filtering include comparisons of denoising approaches. 063
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 20/07/2026This morning at #IALSJanelia we're getting started with some microscopy fundamentals in a lecture by @cmhobson.bsky.social 🔬 0133
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 19/07/2026We'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! 🔬 0126
Rachel Lee, PhD @scientistrachel.bsky.social · 17/07/2026Microscopy 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)journals.biologists.comOpticalFlow3D – a tool for measuring amorphous motion in three-dimensional fluorescence microscopy imagesSummary: 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... 13412
Reposted by Rachel Lee, PhDTeng-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 03717
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 07/07/2026Despite 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! 0115
Reposted by Rachel Lee, PhDPhil Abitua @ohnolog.bsky.social · 30/06/2026Annual 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 720357
Reposted by Rachel Lee, PhDHanadi @hanadi-h.bsky.social · 01/07/2026Blebbing 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 231
Reposted by Rachel Lee, PhDChad Hobson @cmhobson.bsky.social · 20/04/2026My 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... 33113
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 28/01/2026Check 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/... 0114
Reposted by Rachel Lee, PhDTeng-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! 24621
Reposted by Rachel Lee, PhDMaggie Utgaard @maggieutgaard.bsky.social · 23/01/2026Looking 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. 193
Rachel Lee, PhD @scientistrachel.bsky.social · 15/12/2025Starting with your biological question can help focus your #bioimageAnalysis goals. Learn more in the latest @aicjanelia.bsky.social post on @focalplane.bsky.social 👇 010
Reposted by Rachel Lee, PhDFocalPlane @focalplane.bsky.social · 27/11/2025In a new post from @aicjanelia.bsky.social and @anjanja1024.bsky.social, Kevin Hamill shares ‘a day in the life’ of an AIC visitor. Kevin’s team went to the AIC to image components of the basal membrane using iPALM. focalplane.biologists.com/2025/11/24/y...focalplane.biologists.comYou can appreciate a lot by looking – using the best microscope in the world – A day in the life of an AIC visitor - FocalPlaneYou can appreciate a lot by looking – using the best microscope in the world – A day in the life of an AIC visitor - AIC at HHMI Janelia 0102
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 24/11/2025And, if you've ever wondered what it is like to be a visitor to the AIC, check out this post by @anjanja1024.bsky.social and Kevin Hamill about visiting to use our iPALM system: focalplane.biologists.com/2025/11/24/y...focalplane.biologists.comYou can appreciate a lot by looking – using the best microscope in the world – A day in the life of an AIC visitor - FocalPlaneYou can appreciate a lot by looking – using the best microscope in the world – A day in the life of an AIC visitor - AIC at HHMI Janelia 062
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 24/11/2025We 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.comAIC at HHMI JaneliaIntroduction to the AIC at HHMI Janelia blog on FocalPlane 1114
Reposted by Rachel Lee, PhDJan Funke @janfunkey.bsky.social · 17/11/2025We moved the AI@MBL course "Deep Learning for Microscopy Image Analysis" to HHMI Janelia (@hhmijanelia.bsky.social). Join us for two weeks of intense lectures, exercise, and hands-on project work! Course dates: June 4-18 2026 Application by: January 15 2026 www.janelia.org/you-janelia/...janelia.orgDeep Learning for Microscopy Image AnalysisTopics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g., 1189
Reposted by Rachel Lee, PhDWhitney Stevens-Sostre, PhD Boricua @stevenssostre.bsky.social · 08/11/2025I 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! 🔬 072
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 07/11/2025One 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 🔬 072
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 06/11/2025We 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 0102
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 06/11/2025Today 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. 052
Rachel Lee, PhD @scientistrachel.bsky.social · 05/11/2025Working with #TrackMate, participants at #InsightFromImaging were able to explore tracking parameters and the tradeoffs inherent in analysis. It was another fun discussion! 🤓 020
Rachel Lee, PhD @scientistrachel.bsky.social · 04/11/2025HL60 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 47117
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 04/11/2025Continuing 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. 0103
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 04/11/2025Today's theme at #InsightFromImaging 2025 is imaging speed. We're kicking things off with a lecture by Chad Hobson. 162
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 03/11/2025For 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? 0165
Rachel Lee, PhD @scientistrachel.bsky.social · 03/11/2025I had a wonderful time discussing image analysis with HHMI #HannaGrayFellows this morning. I look forward to continuing the chat throughout #InsightFromImaging this week. 061
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 02/11/2025We'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 🔬 052
Reposted by Rachel Lee, PhDÖzge Özgüç @oozguc.bsky.social · 31/10/2025When #halloween meets #FluorescenceFriday 🎃 07913
Reposted by Rachel Lee, PhDAIC at Janelia @aicjanelia.bsky.social · 31/10/2025Wishing everyone a happy #FluorescenceFriday and a #HappyHalloween! This expansion microscopy visualization of blood vessels in a zebrafish is the result of a collaboration between Ellen, Jenny, @nicolasdenans.bsky.social, and @scientistrachel.bsky.social. 0176
Reposted by Rachel Lee, PhDKeri Martinowich @martinowk.bsky.social · 31/10/2025Hippocampus masquerading as a 🦇 for Halloween 🎃 #FluorescenceFriday Image credit to the @lieberinstitute.bsky.social Microscopy and Spatial Biology Core 🧠🔬🧪 0548
