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scientistrachel.bsky.social
Rachel Lee, PhD
@scientistrachel.bsky.social
200 followers 160 following 16 posts
BioImage Analysis Lead at AIC Janelia
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Reposted by Rachel Lee, PhD
aicjanelia.bsky.social
And, 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...
You can appreciate a lot by looking – using the best microscope in the world – A day in the life of an AIC visitor - FocalPlane
You 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
focalplane.biologists.com
November 24, 2025 at 5:25 PM
Reposted by Rachel Lee, PhD
aicjanelia.bsky.social
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...
AIC at HHMI Janelia
Introduction to the AIC at HHMI Janelia blog on FocalPlane
focalplane.biologists.com
November 24, 2025 at 5:25 PM
Reposted by Rachel Lee, PhD
janfunkey.bsky.social
We 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/...
November 17, 2025 at 7:44 PM
Reposted by Rachel Lee, PhD
stevenssostre.bsky.social
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! 🔬
November 8, 2025 at 4:31 PM
Reposted by Rachel Lee, PhD
aicjanelia.bsky.social
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.
November 7, 2025 at 9:37 PM
Reposted by Rachel Lee, PhD
aicjanelia.bsky.social
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.
November 6, 2025 at 10:20 PM
Reposted by Rachel Lee, PhD
aicjanelia.bsky.social
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.
November 6, 2025 at 2:53 PM
scientistrachel.bsky.social
Working with #TrackMate, participants at #InsightFromImaging were able to explore tracking parameters and the tradeoffs inherent in analysis. It was another fun discussion! 🤓
aicjanelia.bsky.social AIC at Janelia @aicjanelia.bsky.social · 21d
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.
November 5, 2025 at 8:10 PM
scientistrachel.bsky.social
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
November 4, 2025 at 10:36 PM
Reposted by Rachel Lee, PhD
aicjanelia.bsky.social
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.
November 4, 2025 at 10:33 PM
Reposted by Rachel Lee, PhD
aicjanelia.bsky.social
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.
November 4, 2025 at 4:33 PM
Reposted by Rachel Lee, PhD
aicjanelia.bsky.social
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.
November 3, 2025 at 10:31 PM
scientistrachel.bsky.social
I had a wonderful time discussing image analysis with HHMI #HannaGrayFellows this morning. I look forward to continuing the chat throughout #InsightFromImaging this week.
aicjanelia.bsky.social AIC at Janelia @aicjanelia.bsky.social · 23d
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.
November 3, 2025 at 6:05 PM
Reposted by Rachel Lee, PhD
aicjanelia.bsky.social
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.
November 2, 2025 at 10:28 PM
Reposted by Rachel Lee, PhD
oozguc.bsky.social
When #halloween meets #FluorescenceFriday 🎃
October 31, 2025 at 4:21 PM
Reposted by Rachel Lee, PhD
aicjanelia.bsky.social
Wishing 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.
October 31, 2025 at 3:35 PM
Reposted by Rachel Lee, PhD
martinowk.bsky.social
Hippocampus masquerading as a 🦇 for Halloween 🎃
#FluorescenceFriday

Image credit to the @lieberinstitute.bsky.social Microscopy and Spatial Biology Core 🧠🔬🧪
Immunolabeling outlining structures in purple color in a tissue section of human brain at the level of the hippocampus
October 31, 2025 at 12:31 PM
scientistrachel.bsky.social
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.
October 31, 2025 at 3:29 PM
Reposted by Rachel Lee, PhD
tomgauld.bsky.social
A halloween cartoon for @newscientist.com
Image: three figures in protective suits watch from behind a screen as a child approaches a door-like mechanical structure in which stands a man. Between them is an amorphous glowing shape. Caption: Scientists at the institute of halloween studies have succeeded in creating "The treak": a quantum state that is simultaneously trick and treat. It is stable for a millionth of a second before decaying into a half-hearted prank and a mediocre candy bar.
October 31, 2025 at 11:27 AM
scientistrachel.bsky.social
I'm excited to be co-organizing #InsightFromImaging 2025! We have many interactive activities planned, including hands-on image analysis labs 🤓
aicjanelia.bsky.social AIC at Janelia @aicjanelia.bsky.social · Oct 27
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 🔬
A microscopy image of a cell stained for actin (magneta color) and focal adhesions (green color).
October 27, 2025 at 5:28 PM
scientistrachel.bsky.social
Today marks 4 years of enjoying the beautiful @hhmijanelia.bsky.social campus 🌳
October 12, 2025 at 12:17 AM
Reposted by Rachel Lee, PhD
aicjanelia.bsky.social
Today we're wrapping up a flatworm imaging project on our SiMView microscope. We've enjoyed having @kinglhung.bsky.social and team from the lab of @ardemp.bskyverified.social here and look forward to working with them on analyzing their images!
A photo of two rows of people. The first row of people is sitting on bench while the second row stands behind them, in front of floor to ceiling windows. Outside the windows is a fall scene with trees.
October 10, 2025 at 4:16 PM
Reposted by Rachel Lee, PhD
tom-bssnnt.bsky.social
Who does microscopy and has never heard of Bio-Formats? You probably used it anyway
June 4, 2025 at 9:13 PM
Reposted by Rachel Lee, PhD
aicjanelia.bsky.social
We've enjoyed having Marise and Samara from the lab of @melaniedwhite.bsky.social here to image quail embryos on our MOSAIC system. We wish them safe travels home and happy data analyzing!
A photo of a group of five people standing in a room filled with scientific equipment.
August 8, 2025 at 8:47 PM
Reposted by Rachel Lee, PhD
joshgondelman.bsky.social
Google search's AI summary is like the loud confident idiot in the room who doesn't always know the answer to your question but HAS TO be the first one to reply to it.
July 28, 2025 at 12:17 PM