Dr. Leafbeaver, DS @calico. You can't spell imaging without "im aging" and boy am I. Organelle enthusiast. Creator of Nellie and Mitometer.
San Francisco, CA
Joined September 2012
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Do you LOVE organelles??
Well I am THRILLED to announce that Nellie has been published in @naturemethods!
Nellie a fully automated pipeline for organelle segmentation, tracking, and hierarchical feature extraction in 2D, 3D, timelapse, multichannel live-cell microscopy
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Austin E. Y. T. Lefebvre retweeted
Finally a more intuitive way to learn pLDDT/pAE? 😎
sokrypton.github.io/protein_…
(Character idea from @HannesStaerk & Alex Waldherr)
Austin E. Y. T. Lefebvre retweeted
Do you LOVE organelles??
Well I am THRILLED to announce that Nellie has been published in @naturemethods!
Nellie a fully automated pipeline for organelle segmentation, tracking, and hierarchical feature extraction in 2D, 3D, timelapse, multichannel live-cell microscopy
🧵1/N
Austin E. Y. T. Lefebvre retweeted
Genomics has scaled massively, but phenotyping is still painstakingly manual. What if we stopped throwing away the rich, subtle signals in medical images? We propose Vector2Variant (V2V), a framework that discovers genetic associations without subjective phenotype engineering.1/7
Austin E. Y. T. Lefebvre retweeted
The Landoni Lab opens this summer @unil !🔬 Quantitative #imaging + systems biology to decipher how #metabolic architecture & #mtDNA dynamically shape tissue development, #aging and #mitodisease. Beyond excited to fire up the lasers, open positions soon! 🧪 #mitochondria #newPI
Austin E. Y. T. Lefebvre retweeted
We’re excited to announce FDA Orphan Drug Designation for ABBV-CLS-628, an investigational therapy to treat ADPKD, the most common inherited kidney disease.
Last month, it received Fast Track Designation and is now in a Phase 2 clinical trial.
calicolabs.com/press/calico-…
Austin E. Y. T. Lefebvre retweeted
An iPSC-derived heart muscle cell assembling sarcomeres videoed through a spinning disk confocal microscope by Burnette Lab graduate student, @EmmaKoory. Alpha-actinin-2 is shown. Colors denote Z slices (red-bottom; green-middle; blue-top). Movie length- 40 hours.
Austin E. Y. T. Lefebvre retweeted
An iPSC heart muscle cell forming sarcomeres videoed through a microscope by @EmmaKoory for 20 h before it dies most dramatically. This was our first try on a new microscope, and Emma now has the imaging parameters dialed in so her cells do not go POP! #CellBiology
Austin E. Y. T. Lefebvre retweeted
Mitochondrial pearling isn’t random—it’s physics.
Researchers identified two mechanisms:
Internal pressure from ionic flux
External pulling via motors
Both cause membrane tension to exceed bending energy—a Rayleigh-Plateau instability.
Full paper: biorxiv.org/content/10.1101/…
Austin E. Y. T. Lefebvre retweeted
My lab’s 5-year NIH R01 grant, awarded to study gene therapy for hearing loss, was abruptly terminated. I want to share how this action has been incredibly harmful and disruptive, not just to my lab, but to the scientific process itself. 1/15
I’m hiring for a microscopy image analysis role at Calico!
calicolabs.com/careers/?gh_j…
We’re looking for someone at ~recent PhD lvl who has previous experience with biological samples and analyzing microscopy datasets.
Feel free to reach out with any questions!
Austin E. Y. T. Lefebvre retweeted
Analyzing organelles is HARD. They're complex, but critical to understanding biology. Current tools are manual, organelle-specific, or can't handle large 3D datasets.
With an easy install and a click of a button, Nellie solves ALL these problems!
nature.com/articles/s41592-0…
🧵2/N
Austin E. Y. T. Lefebvre retweeted
In the physical world, almost all information is transmitted through traveling waves -- why should it be any different in your neural network?
Super excited to share recent work with the brilliant @mozesjacobs: "Traveling Waves Integrate Spatial Information Through Time"
1/14
Already some cool applications for Nellie: If you're used to MitoGraph data and want some of the same outputs from Nellie, check out Gav's Python code.
Austin E. Y. T. Lefebvre retweeted
New from Lefebvre and colleagues! Nellie is a comprehensive automated pipeline for studying the structure and intracellular dynamics of diverse organelles that offers accurate segmentation, tracking and feature extraction on both 2D and 3D data. nature.com/articles/s41592-0…
We also compare Nellie to existing state of the art methods for both segmentation and tracking across imaging resolution, structure widths, and structure lengths, as well as the pipeline's speed on different sized images
🧵14/N
Try and share Nellie today!
We've included some sample data if you want to explore what Nellie can do.
Code: github.com/aelefebv/nellie
Paper: nature.com/articles/s41592-0…
And please share your results with us! We're excited to see how you'll use it in your research.
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